MODELLER 9.16, 2016/01/07, r10745 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2016 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux sunflower.rnet.missouri.edu 2.6.32-431.23.3.el6.x86_64 x86_64 Date and time of compilation : 2016/01/07 10:19:44 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2016/04/05 22:42:01 Multiple dynamic programming alignment (MALIGN): Residue-residue metric : $(LIB)/as1.sim.mat ALIGN_BLOCK : 1 Gap introduction penalty: -600.0000 Gap extension penalty : -400.0000 Length of alignment : 75 # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 2ctx 2abx 2nbt 1fas # ============================================= 1 1.361 0.654 C 3 C 3 C 3 Y 4 # ============================================= 2 2.010 0.968 T 10 S 12 T 10 S 10 # ============================================= 3 1.613 0.784 C 14 C 16 C 14 T 15 # ============================================= 4 1.796 0.263 G 17 G 19 Q 18 C 17 # ============================================= 5 1.488 0.579 V 19 L 22 I 20 S 21 6 0.967 0.270 * C 20 C 23 C 21 C 22 7 0.722 0.206 Y 21 Y 24 F 22 Y 23 8 0.972 0.158 T 22 R 25 L 23 R 24 9 0.942 0.316 * K 23 K 26 K 24 K 25 10 1.026 0.469 T 24 M 27 A 25 S 26 # ============================================= 11 1.842 0.471 R 36 V 39 V 37 M 33 12 1.203 0.469 V 37 V 40 I 38 V 34 13 1.186 0.369 D 38 E 41 E 39 L 35 14 1.577 0.694 L 39 L 42 Q 40 G 36 15 0.781 0.195 G 40 G 43 G 41 R 37 16 0.993 0.576 C 41 C 44 C 42 G 38 17 2.133 0.254 A 42 A 45 V 43 C 39 # ============================================= 18 1.516 0.159 T 44 T 47 T 45 G 40 19 1.143 0.278 * C 45 C 48 C 46 C 41 # ============================================= 20 1.873 0.466 P 46 S 50 P 47 P 42 # ============================================= 21 1.936 0.501 D 53 E 56 S 55 E 49 22 1.358 0.287 I 54 V 57 L 56 V 50 23 1.312 0.833 Q 55 T 58 L 57 K 51 24 0.806 0.271 * C 56 C 59 C 58 C 52 25 0.846 0.115 * C 57 C 60 C 59 C 53 # ============================================= 26 1.490 0.576 S 58 S 61 T 61 T 54 # ============================================= 27 1.217 0.161 D 60 D 63 C 64 D 57 28 1.389 0.452 N 61 K 64 N 65 K 58 # ============================================= # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 2ctx 2abx 2nbt 1fas # ============================================= 1 2.068 0.642 R 2 V 2 T 2 C 3 2 1.563 0.575 C 3 C 3 C 3 Y 4 # ============================================= 3 1.339 0.396 C 14 C 16 C 14 T 15 # ============================================= 4 2.027 0.711 H 18 N 21 D 19 N 20 5 1.468 0.531 V 19 L 22 I 20 S 21 6 0.879 0.382 * C 20 C 23 C 21 C 22 7 0.684 0.172 Y 21 Y 24 F 22 Y 23 8 0.829 0.087 T 22 R 25 L 23 R 24 9 0.758 0.214 * K 23 K 26 K 24 K 25 10 0.658 0.282 T 24 M 27 A 25 S 26 # ============================================= 11 1.622 0.551 R 36 V 39 V 37 M 33 12 0.840 0.356 V 37 V 40 I 38 V 34 13 0.860 0.358 D 38 E 41 E 39 L 35 14 1.325 0.773 L 39 L 42 Q 40 G 36 15 0.694 0.331 G 40 G 43 G 41 R 37 16 0.708 0.331 C 41 C 44 C 42 G 38 17 1.895 0.428 A 42 A 45 V 43 C 39 # ============================================= 18 1.198 0.248 T 44 T 47 T 45 G 40 19 0.916 0.318 * C 45 C 48 C 46 C 41 # ============================================= 20 1.601 0.362 P 46 S 50 P 47 P 42 # ============================================= 21 1.648 0.765 T 50 P 53 N 52 D 45 22 1.774 0.585 G 51 Y 54 Y 53 D 46 # ============================================= 23 1.630 0.413 D 53 E 56 S 55 E 49 24 1.119 0.215 I 54 V 57 L 56 V 50 25 1.057 0.885 Q 55 T 58 L 57 K 51 26 0.582 0.319 * C 56 C 59 C 58 C 52 27 0.809 0.329 * C 57 C 60 C 59 C 53 # ============================================= 28 1.381 0.687 S 58 S 61 T 61 T 54 # ============================================= 29 1.315 0.185 D 60 D 63 C 64 D 57 # ============================================= 30 1.393 0.689 C 62 C 65 N 65 C 59 # ============================================= # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 2ctx 2abx 2nbt 1fas # ============================================= 1 1.583 0.406 R 2 V 2 T 2 M 2 2 1.297 0.553 * C 3 C 3 C 3 C 3 # ============================================= 3 1.426 0.697 F 4 T 5 Q 12 Y 4 # ============================================= 4 1.207 0.275 C 14 C 16 C 14 T 15 # ============================================= 5 2.340 0.323 G 17 G 19 G 17 C 17 # ============================================= 6 1.587 0.432 H 18 N 21 D 19 N 20 7 1.160 0.403 V 19 L 22 I 20 S 21 8 0.756 0.357 * C 20 C 23 C 21 C 22 9 0.647 0.212 Y 21 Y 24 F 22 Y 23 10 0.793 0.075 T 22 R 25 L 23 R 24 11 0.831 0.230 * K 23 K 26 K 24 K 25 12 0.742 0.217 T 24 M 27 A 25 S 26 # ============================================= 13 1.568 0.368 R 36 V 39 V 37 M 33 14 0.800 0.172 V 37 V 40 I 38 V 34 15 0.949 0.383 D 38 E 41 E 39 L 35 16 1.340 0.731 L 39 L 42 Q 40 G 36 17 0.622 0.325 G 40 G 43 G 41 R 37 18 0.722 0.289 C 41 C 44 C 42 G 38 19 1.881 0.536 A 42 A 45 V 43 C 39 # ============================================= 20 1.329 0.349 T 44 T 47 T 45 G 40 21 0.918 0.236 * C 45 C 48 C 46 C 41 # ============================================= 22 1.775 0.515 V 48 K 52 R 50 G 44 # ============================================= 23 1.331 0.364 T 50 P 53 N 52 D 45 # ============================================= 24 1.319 0.726 G 51 Y 54 Y 53 Y 47 # ============================================= 25 1.450 0.097 D 53 E 56 S 55 E 49 26 0.945 0.241 I 54 V 57 L 56 V 50 27 0.849 0.691 Q 55 T 58 L 57 K 51 28 0.459 0.166 * C 56 C 59 C 58 C 52 29 0.616 0.195 * C 57 C 60 C 59 C 53 # ============================================= 30 1.074 0.402 S 58 S 61 T 61 T 54 # ============================================= 31 0.785 0.361 D 60 D 63 N 63 D 57 # ============================================= 32 1.310 0.712 C 62 C 65 N 65 C 59 # ============================================= # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 2ctx 2abx 2nbt 1fas # ============================================= 1 1.361 0.423 R 2 V 2 T 2 M 2 2 1.409 0.679 * C 3 C 3 C 3 C 3 # ============================================= 3 1.203 0.700 F 4 T 5 Q 12 Y 4 # ============================================= 4 1.248 0.372 C 14 C 16 C 14 T 15 # ============================================= 5 2.333 0.288 G 17 G 19 G 17 C 17 # ============================================= 6 1.490 0.388 H 18 N 21 D 19 N 20 7 1.019 0.398 V 19 L 22 I 20 S 21 8 0.745 0.226 * C 20 C 23 C 21 C 22 9 0.581 0.225 Y 21 Y 24 F 22 Y 23 10 0.724 0.149 T 22 R 25 L 23 R 24 11 0.779 0.347 * K 23 K 26 K 24 K 25 12 0.657 0.144 T 24 M 27 A 25 S 26 # ============================================= 13 1.505 0.412 R 36 V 39 V 37 M 33 14 0.684 0.117 V 37 V 40 I 38 V 34 15 1.138 0.442 D 38 E 41 E 39 L 35 16 1.477 0.757 L 39 L 42 Q 40 G 36 17 0.776 0.371 G 40 G 43 G 41 R 37 18 0.810 0.355 C 41 C 44 C 42 G 38 19 1.766 0.495 A 42 A 45 V 43 C 39 # ============================================= 20 1.309 0.397 T 44 T 47 T 45 G 40 21 0.864 0.168 * C 45 C 48 C 46 C 41 # ============================================= 22 1.577 0.453 V 48 K 52 R 50 G 44 # ============================================= 23 1.438 0.748 T 50 P 53 N 52 D 46 24 1.158 0.569 G 51 Y 54 Y 53 Y 47 # ============================================= 25 1.411 0.100 D 53 E 56 S 55 E 49 26 0.928 0.261 I 54 V 57 L 56 V 50 27 0.787 0.591 Q 55 T 58 L 57 K 51 28 0.454 0.138 * C 56 C 59 C 58 C 52 29 0.649 0.198 * C 57 C 60 C 59 C 53 # ============================================= 30 0.939 0.366 S 58 S 61 T 61 T 54 31 1.698 0.917 T 59 T 62 D 62 S 55 # ============================================= 32 0.990 0.092 D 60 D 63 N 63 D 57 # ============================================= 33 1.409 0.765 C 62 C 65 N 65 C 59 # ============================================= # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 2ctx 2abx 2nbt 1fas # ============================================= 1 1.309 0.430 R 2 V 2 T 2 M 2 2 1.445 0.723 * C 3 C 3 C 3 C 3 # ============================================= 3 1.161 0.675 F 4 T 5 Q 12 Y 4 # ============================================= 4 1.335 0.330 C 14 C 16 C 14 T 15 # ============================================= 5 1.433 0.303 H 18 N 21 D 19 N 20 6 0.959 0.386 V 19 L 22 I 20 S 21 7 0.793 0.208 * C 20 C 23 C 21 C 22 8 0.589 0.249 Y 21 Y 24 F 22 Y 23 9 0.738 0.122 T 22 R 25 L 23 R 24 10 0.816 0.317 * K 23 K 26 K 24 K 25 11 0.687 0.136 T 24 M 27 A 25 S 26 # ============================================= 12 1.495 0.417 R 36 V 39 V 37 M 33 13 0.670 0.128 V 37 V 40 I 38 V 34 14 1.153 0.444 D 38 E 41 E 39 L 35 15 1.498 0.759 L 39 L 42 Q 40 G 36 16 0.769 0.349 G 40 G 43 G 41 R 37 17 0.816 0.358 C 41 C 44 C 42 G 38 18 1.774 0.557 A 42 A 45 V 43 C 39 # ============================================= 19 1.306 0.395 T 44 T 47 T 45 G 40 20 0.826 0.222 * C 45 C 48 C 46 C 41 # ============================================= 21 1.531 0.472 V 48 K 52 R 50 G 44 # ============================================= 22 1.378 0.667 T 50 P 53 N 52 D 46 23 1.144 0.489 G 51 Y 54 Y 53 Y 47 # ============================================= 24 1.481 0.105 D 53 E 56 S 55 E 49 25 0.982 0.319 I 54 V 57 L 56 V 50 26 0.824 0.563 Q 55 T 58 L 57 K 51 27 0.504 0.144 * C 56 C 59 C 58 C 52 28 0.635 0.167 * C 57 C 60 C 59 C 53 # ============================================= 29 0.849 0.340 S 58 S 61 T 61 T 54 30 1.562 0.854 T 59 T 62 D 62 S 55 # ============================================= 31 1.029 0.095 D 60 D 63 N 63 D 57 # ============================================= 32 1.441 0.791 C 62 C 65 N 65 C 59 # ============================================= # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 2ctx 2abx 2nbt 1fas # ============================================= 1 1.297 0.476 R 2 V 2 T 2 M 2 2 1.413 0.711 * C 3 C 3 C 3 C 3 # ============================================= 3 1.104 0.569 F 4 T 5 Q 12 Y 4 # ============================================= 4 1.809 0.553 C 14 C 16 C 14 N 16 # ============================================= 5 1.376 0.206 H 18 N 21 D 19 N 20 6 0.942 0.313 V 19 L 22 I 20 S 21 7 0.754 0.212 * C 20 C 23 C 21 C 22 8 0.597 0.266 Y 21 Y 24 F 22 Y 23 9 0.747 0.153 T 22 R 25 L 23 R 24 10 0.827 0.306 * K 23 K 26 K 24 K 25 11 0.685 0.158 T 24 M 27 A 25 S 26 # ============================================= 12 1.539 0.406 R 36 V 39 V 37 M 33 13 0.682 0.127 V 37 V 40 I 38 V 34 14 1.163 0.455 D 38 E 41 E 39 L 35 15 1.481 0.750 L 39 L 42 Q 40 G 36 16 0.796 0.364 G 40 G 43 G 41 R 37 17 0.853 0.344 C 41 C 44 C 42 G 38 18 1.786 0.579 A 42 A 45 V 43 C 39 # ============================================= 19 1.349 0.455 T 44 T 47 T 45 G 40 20 0.834 0.174 * C 45 C 48 C 46 C 41 # ============================================= 21 1.507 0.473 V 48 K 52 R 50 G 44 # ============================================= 22 1.325 0.660 T 50 P 53 N 52 D 46 23 1.183 0.494 G 51 Y 54 Y 53 Y 47 # ============================================= 24 1.477 0.130 D 53 E 56 S 55 E 49 25 0.960 0.348 I 54 V 57 L 56 V 50 26 0.809 0.561 Q 55 T 58 L 57 K 51 27 0.489 0.134 * C 56 C 59 C 58 C 52 28 0.615 0.169 * C 57 C 60 C 59 C 53 # ============================================= 29 0.855 0.336 S 58 S 61 T 61 T 54 30 1.583 0.880 T 59 T 62 D 62 S 55 # ============================================= 31 1.044 0.103 D 60 D 63 N 63 D 57 # ============================================= 32 1.387 0.821 C 62 C 65 N 65 C 59 # ============================================= Least-squares dynamic programming alignment: FIT_ATOMS atoms for alignment : CA Max dist from frw for equivalence : 4.0000 Gap introduction penalty : 0.0000 Gap extension penalty : 2.0000 Numb of residues in framework : 32 COMPARISON OF SEVERAL 3D STRUCTURES: # ALGNMT CODE ATOM FILE 1 2ctx 2ctx_fit.pdb 2 2abx 2abx_fit.pdb 3 2nbt 2nbt_fit.pdb 4 1fas 1fas_fit.pdb Variability at a given position is calculated as: VAR = 1/Nij * sum_ij (feat_i - feat_j) sum runs over all pairs of proteins with residues present. >> Least-squares superposition (FIT) : T Atom types for superposition/RMS (FIT_ATOMS): CA Atom type for position average/variability (VARATOM): CA Position comparison (FIT_ATOMS): Cutoff for RMS calculation: 999.0000 Upper = RMS, Lower = numb equiv positions 2ctx 2abx 2nbt 1fas 2ctx 0.000 2.034 1.952 1.809 2abx 57 0.000 2.110 2.511 2nbt 36 41 0.000 2.416 1fas 50 47 36 0.000 Distance comparison (FIT_ATOMS): Cutoff for rms calculation: 999.0000 Upper = Distance RMS, Lower = numb equiv distances 2ctx 2abx 2nbt 1fas 2ctx 0.000 1.502 1.410 1.424 2abx 1596 0.000 1.459 2.017 2nbt 630 820 0.000 1.778 1fas 1225 1081 630 0.000 >> Sequence comparison: Diag=numb res, Upper=numb equiv res, Lower = % seq ID 2ctx 2abx 2nbt 1fas 2ctx 71 25 12 13 2abx 35 74 17 19 2nbt 18 26 66 8 1fas 21 31 13 61 >> Dihedral angle comparison: Alph Cutoff for rms comparison: 999.0000 Upper = RMS Alph, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 72.428 65.158 71.841 2abx 56 0.000 82.187 87.561 2nbt 35 40 0.000 93.925 1fas 47 44 35 0.000 >> Dihedral angle comparison: Phi Cutoff for rms comparison: 999.0000 Upper = RMS Phi , Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 98.679 47.226 50.674 2abx 56 0.000 84.109 99.729 2nbt 36 41 0.000 60.062 1fas 49 46 36 0.000 >> Dihedral angle comparison: Psi Cutoff for rms comparison: 999.0000 Upper = RMS Psi , Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 94.113 73.691 58.213 2abx 57 0.000 92.691 87.718 2nbt 36 41 0.000 90.580 1fas 49 46 36 0.000 >> Dihedral angle comparison: Omeg Cutoff for rms comparison: 999.0000 Upper = RMS Omeg, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 7.526 2.485 42.399 2abx 57 0.000 7.196 36.656 2nbt 36 41 0.000 28.086 1fas 49 46 36 0.000 >> Dihedral angle comparison: chi1 Cutoff for rms comparison: 999.0000 Upper = RMS chi1, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 100.959 74.715 91.387 2abx 48 0.000 99.481 106.798 2nbt 31 36 0.000 95.121 1fas 40 37 30 0.000 >> Dihedral angle comparison: chi2 Cutoff for rms comparison: 999.0000 Upper = RMS chi2, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 98.056 100.703 82.829 2abx 25 0.000 69.505 97.949 2nbt 20 26 0.000 111.059 1fas 25 23 20 0.000 >> Dihedral angle comparison: chi3 Cutoff for rms comparison: 999.0000 Upper = RMS chi3, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 130.264 83.779 47.880 2abx 11 0.000 117.207 118.449 2nbt 9 14 0.000 86.883 1fas 13 14 9 0.000 >> Dihedral angle comparison: chi4 Cutoff for rms comparison: 999.0000 Upper = RMS chi4, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 94.661 102.912 26.887 2abx 11 0.000 72.327 110.748 2nbt 8 9 0.000 93.473 1fas 8 9 6 0.000 >> Dihedral angle comparison: chi5 Cutoff for rms comparison: 999.0000 Upper = RMS chi5, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 116.326 61.086 8.019 2abx 9 0.000 104.303 114.872 2nbt 7 7 0.000 61.611 1fas 6 6 5 0.000 >> Ramachandran mainchain class substitution prot 1 --> prot 2; class on vert --> class on horiz A P B L E U A 14 7 12 2 5 0 P 10 13 16 8 1 2 B 17 25 78 7 8 0 L 5 8 12 2 0 0 E 2 3 6 1 0 0 U 0 0 0 0 0 3 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT A 14 26 40 5.3 9.8 15.2 P 13 37 50 4.9 14.0 18.9 B 78 57 135 29.5 21.6 51.1 L 2 25 27 0.8 9.5 10.2 E 0 12 12 0.0 4.5 4.5 -------------------------------------------- SUMS 107 157 264 40.5 59.5 100.0 -------------------------------------------- U 3 0 3 1.1 0.0 1.1 >> Dihedral class substitution: Alph prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 2 10 18 1 2 9 23 20 2 3 19 25 131 3 4 0 1 0 3 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 2 29 31 0.8 11.0 11.8 2 23 31 54 8.7 11.8 20.5 3 131 47 178 49.8 17.9 67.7 -------------------------------------------- SUMS 156 107 263 59.3 40.7 100.0 -------------------------------------------- 4 3 1 4 1.1 0.4 1.5 >> Dihedral class substitution: Phi prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 25 8 29 0 2 9 1 14 0 3 39 14 125 0 4 0 0 0 3 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 25 37 62 9.5 14.0 23.5 2 1 23 24 0.4 8.7 9.1 3 125 53 178 47.3 20.1 67.4 -------------------------------------------- SUMS 151 113 264 57.2 42.8 100.0 -------------------------------------------- 4 3 0 3 1.1 0.0 1.1 >> Dihedral class substitution: Psi prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 5 9 14 0 2 13 10 22 1 3 18 33 141 1 4 0 0 0 0 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 5 23 28 1.9 8.6 10.5 2 10 36 46 3.7 13.5 17.2 3 141 52 193 52.8 19.5 72.3 -------------------------------------------- SUMS 156 111 267 58.4 41.6 100.0 -------------------------------------------- 4 0 0 0 0.0 0.0 0.0 >> Dihedral class substitution: Omeg prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 259 5 0 2 2 1 0 0 0 3 0 0 0 0 4 0 0 0 0 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 259 7 266 97.0 2.6 99.6 2 0 1 1 0.0 0.4 0.4 3 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 259 8 267 97.0 3.0 100.0 -------------------------------------------- 4 0 0 0 0.0 0.0 0.0 >> Dihedral class substitution: chi1 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 30 42 18 5 2 39 29 16 7 3 18 17 13 7 4 10 4 3 9 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 30 65 95 12.4 27.0 39.4 2 29 62 91 12.0 25.7 37.8 3 13 42 55 5.4 17.4 22.8 -------------------------------------------- SUMS 72 169 241 29.9 70.1 100.0 -------------------------------------------- 4 9 17 26 3.4 6.4 9.7 >> Dihedral class substitution: chi2 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 51 12 6 26 2 17 12 7 3 3 10 13 11 7 4 34 10 3 45 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 51 44 95 29.1 25.1 54.3 2 12 27 39 6.9 15.4 22.3 3 11 30 41 6.3 17.1 23.4 -------------------------------------------- SUMS 74 101 175 42.3 57.7 100.0 -------------------------------------------- 4 45 47 92 16.9 17.6 34.5 >> Dihedral class substitution: chi3 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 20 15 2 14 2 16 13 1 13 3 1 2 0 7 4 24 15 4 120 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 20 31 51 19.2 29.8 49.0 2 13 30 43 12.5 28.8 41.3 3 0 10 10 0.0 9.6 9.6 -------------------------------------------- SUMS 33 71 104 31.7 68.3 100.0 -------------------------------------------- 4 120 43 163 44.9 16.1 61.0 >> Dihedral class substitution: chi4 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 11 2 3 9 2 3 5 6 4 3 5 9 7 11 4 10 4 9 169 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 11 14 25 14.7 18.7 33.3 2 5 13 18 6.7 17.3 24.0 3 7 25 32 9.3 33.3 42.7 -------------------------------------------- SUMS 23 52 75 30.7 69.3 100.0 -------------------------------------------- 4 169 23 192 63.3 8.6 71.9 >> Dihedral class substitution: chi5 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 7 5 6 3 2 3 7 1 4 3 4 1 6 5 4 5 0 1 209 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 7 14 21 13.5 26.9 40.4 2 7 8 15 13.5 15.4 28.8 3 6 10 16 11.5 19.2 30.8 -------------------------------------------- SUMS 20 32 52 38.5 61.5 100.0 -------------------------------------------- 4 209 6 215 78.3 2.2 80.5 >> Detailed comparison: Structure : 2 2abx_fit.pdb Structure : 3 2nbt_fit.pdb Structure : 4 1fas_fit.pdb ALN ... alignment position RESID... ... residue numbers 1/2/3 AAA ... amino acid types 1/2/3 MNC ... mainchain classes 1/2/3 ALP... ... dihedral angle classes (alpha,phi,psi,...) ALN RESIDUE_NUMBERS AAA MNC ALP PHI PSI OMG CH1 CH2 CH3 CH4 CH5 --------------------------------------------------------------- 1 ---- 1 ---- -R- -U- -4- -4- -2- -1- -1- -2- -1- -1- -4- 2 1 ---- 1 I-T U-U 4-4 4-4 3-3 1-1 3-1 1-4 4-4 4-4 4-4 3 2 2 2 VTM ABP 233 333 133 111 221 442 441 444 444 4 3 3 3 CCC BAB 323 333 323 111 311 331 121 321 121 5 ---- 4 ---- -L- -B- -3- -3- -3- -1- -1- -1- -4- -4- -4- 6 ---- 5 ---- -I- -B- -2- -3- -2- -1- -1- -1- -4- -4- -4- 7 ---- 6 ---- -S- -L- -2- -3- -1- -1- -3- -4- -4- -4- -4- 8 ---- 7 ---- -P- -A- -1- -1- -1- -1- -2- -1- -2- -4- -4- 9 ---- 8 ---- -S- -A- -3- -3- -1- -1- -1- -4- -4- -4- -4- 10 ---- 9 ---- -S- -L- -3- -2- -2- -1- -2- -4- -4- -4- -4- 11 ---- 10 ---- -T- -A- -3- -3- -2- -1- -2- -4- -4- -4- -4- 12 4 11 ---- HP- BP- 23- 31- 32- 11- 12- 21- 42- 44- 44- 13 5 12 4 TQY BAP 123 331 323 111 221 411 414 444 444 14 ---- 13 ---- -T- -P- -3- -3- -3- -1- -1- -4- -4- -4- -4- 15 6 ---- ---- T-- P-- 3-- 1-- 3-- 1-- 1-- 4-- 4-- 4-- 4-- 16 7 ---- 5 A-S L-A 2-2 2-3 3-2 1-1 4-1 4-4 4-4 4-4 4-4 17 8 ---- ---- T-- L-- 1-- 2-- 3-- 1-- 1-- 4-- 4-- 4-- 4-- 18 ---- ---- 6 --H --B --3 --3 --3 --1 --1 --2 --4 --4 --4 19 ---- ---- 7 --T --A --2 --1 --1 --1 --2 --4 --4 --4 --4 20 ---- ---- 8 --T --B --3 --3 --3 --1 --2 --4 --4 --4 --4 21 ---- ---- 9 --T --A --2 --3 --2 --1 --2 --4 --4 --4 --4 22 9 ---- ---- I-- E-- 2-- 2-- 3-- 1-- 1-- 3-- 4-- 4-- 4-- 23 10 ---- ---- P-- A-- 3-- 1-- 1-- 1-- 1-- 2-- 1-- 4-- 4-- 24 11 ---- ---- S-- E-- 3-- 2-- 3-- 1-- 2-- 4-- 4-- 4-- 4-- 25 ---- ---- 10 --S --A --2 --1 --1 --1 --2 --4 --4 --4 --4 26 ---- ---- 11 --R --P --3 --1 --3 --1 --1 --1 --1 --1 --4 27 12 ---- 12 S-A A-A 3-2 3-1 2-2 1-1 2-4 4-4 4-4 4-4 4-4 28 13 ---- 13 A-I L-B 3-3 2-3 1-3 1-1 4-3 4-1 4-4 4-4 4-4 29 14 ---- 14 V-L E-B 3-3 2-3 1-3 1-1 1-1 4-1 4-4 4-4 4-4 30 15 ---- 15 T-T L-B 3-3 2-3 2-3 1-1 2-3 4-4 4-4 4-4 4-4 31 16 14 16 CCN ELB 133 233 323 111 332 321 214 314 234 32 17 15 17 PPC PPA 133 111 221 111 321 111 221 441 441 33 ---- ---- 18 --G --E --1 --2 --3 --1 --4 --4 --4 --4 --4 34 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 35 18 16 ---- PN- PA- 21- 11- 21- 11- 21- 11- 24- 44- 44- 36 19 17 ---- GG- EA- 32- 23- 31- 11- 44- 44- 44- 44- 44- 37 20 18 19 EQE LBA 232 331 332 111 111 332 111 444 444 38 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 39 21 19 20 NDN EBP 233 213 333 111 312 211 444 444 444 40 22 20 21 LIS EBP 333 231 333 111 211 114 444 444 444 41 23 21 22 CCC BPB 333 313 333 111 121 321 121 331 311 42 24 22 23 YFY BBB 333 133 333 111 323 212 444 444 444 43 25 23 24 RLR PBB 333 133 333 111 222 121 141 142 444 44 26 24 25 KKK BBB 233 333 333 111 223 111 111 111 444 45 27 25 26 MAS EBB 321 233 333 111 241 144 344 444 444 46 28 ---- ---- W-- L-- 2-- 3-- 1-- 1-- 2-- 1-- 4-- 4-- 4-- 47 29 ---- ---- C-- A-- 3-- 3-- 2-- 1-- 2-- 1-- 1-- 1-- 1-- 48 ---- 26 27 -QR -BP -13 -31 -33 -11 -31 -11 -13 -43 -44 49 ---- ---- 28 --R --A --2 --1 --1 --1 --2 --1 --2 --2 --4 50 ---- ---- 29 --H --B --1 --3 --3 --1 --1 --1 --4 --4 --4 51 ---- 27 ---- -C- -P- -3- -1- -3- -1- -3- -2- -2- -1- -1- 52 ---- 28 ---- -D- -B- -1- -3- -3- -1- -2- -1- -4- -4- -4- 53 ---- 29 ---- -K- -E- -2- -2- -3- -1- -1- -3- -1- -1- -4- 54 ---- 30 ---- -F- -L- -3- -2- -1- -1- -1- -1- -4- -4- -4- 55 ---- 31 ---- -C- -L- -2- -2- -2- -1- -1- -1- -2- -2- -3- 56 ---- 32 ---- -S- -A- -2- -3- -2- -1- -2- -4- -4- -4- -4- 57 ---- 33 ---- -I- -A- -2- -3- -1- -1- -1- -1- -4- -4- -4- 58 ---- 34 ---- -R- -A- -3- -3- -1- -1- -3- -2- -2- -1- -4- 59 ---- 35 ---- -G- -E- -1- -2- -3- -1- -4- -4- -4- -4- -4- 60 30 36 ---- DP- EP- 33- 21- 12- 11- 12- 11- 42- 44- 44- 61 31 ---- ---- A-- L-- 2-- 3-- 2-- 1-- 4-- 4-- 4-- 4-- 4-- 62 32 ---- ---- F-- B-- 3-- 3-- 3-- 1-- 3-- 1-- 4-- 4-- 4-- 63 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 64 33 ---- 30 C-P A-P 3-2 1-1 2-2 1-2 1-1 1-2 1-1 1-4 2-4 65 34 ---- ---- S-- A-- 1-- 3-- 2-- 1-- 1-- 4-- 4-- 4-- 4-- 66 35 ---- ---- S-- E-- 2-- 2-- 3-- 1-- 2-- 4-- 4-- 4-- 4-- 67 36 ---- ---- R-- E-- 3-- 2-- 3-- 1-- 1-- 1-- 3-- 1-- 4-- 68 37 ---- 31 G-P L-P 3-3 3-1 2-2 1-1 4-2 4-1 4-2 4-4 4-4 69 38 ---- ---- K-- A-- 2-- 3-- 2-- 1-- 2-- 1-- 3-- 1-- 4-- 70 ---- ---- 32 --K --B --3 --1 --2 --1 --1 --1 --1 --1 --4 71 39 37 33 VVM BBP 333 331 333 111 213 441 442 444 444 72 40 38 34 VIV PBP 333 331 333 111 231 414 444 444 444 73 41 39 35 EEL BBA 331 333 331 111 221 321 114 444 444 74 42 40 36 LQG LBB 223 333 233 111 334 114 414 444 444 75 43 41 37 GGR ABB 312 333 333 111 441 441 441 443 444 76 44 42 38 CCG BBB 331 333 333 111 234 314 214 324 334 77 45 43 39 AVC LBB 112 333 233 111 411 441 441 441 441 78 46 44 ---- AA- EA- 21- 21- 11- 11- 44- 44- 44- 44- 44- 79 47 45 40 TTG BBE 333 332 233 111 314 444 444 444 444 80 48 46 41 CCC LPB 333 213 232 111 222 332 122 233 221 81 49 47 ---- PP- AP- 31- 11- 12- 11- 32- 11- 22- 44- 44- 82 ---- 48 ---- -Q- -A- -3- -1- -2- -1- -3- -1- -2- -4- -4- 83 ---- 49 ---- -F- -E- -3- -2- -3- -1- -1- -2- -4- -4- -4- 84 50 ---- 42 S-P L-P 3-3 2-1 1-2 1-1 1-2 4-1 4-2 4-4 4-4 85 51 ---- 43 K-P B-P 1-3 3-1 3-2 1-1 1-2 1-1 1-2 3-4 4-4 86 52 50 44 KRG PBP 133 331 333 111 124 334 134 114 444 87 ---- 51 45 -SD -AB -21 -13 -23 -11 -13 -41 -44 -44 -44 88 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 89 53 52 46 PND AAA 222 131 121 111 223 121 244 444 444 90 54 53 47 YYY PPA 132 131 331 111 312 222 444 444 444 91 55 54 ---- ER- PA- 21- 13- 31- 11- 12- 13- 11- 41- 44- 92 ---- ---- 48 --L --B --3 --3 --3 --1 --2 --2 --4 --4 --4 93 56 55 49 ESE PLB 333 133 333 111 132 141 241 444 444 94 57 56 50 VLV BBB 333 333 333 111 121 434 444 444 444 95 58 57 51 TLK BBB 333 333 333 111 321 412 441 443 444 96 59 58 52 CCC BBB 333 333 333 111 221 233 122 332 222 97 60 59 53 CCC PAB 333 133 313 111 123 332 122 322 133 98 ---- 60 ---- -T- -L- -2- -2- -2- -1- -2- -4- -4- -4- -4- 99 61 61 54 STT LBA 332 333 231 111 322 444 444 444 444 100 62 62 55 TDS ABB 122 333 233 112 221 414 444 444 444 101 ---- ---- 56 --P --P --3 --1 --2 --1 --2 --1 --2 --4 --4 102 63 63 57 DND LLP 132 321 123 111 211 221 444 444 444 103 ---- 64 ---- -C- -A- -2- -3- -2- -1- -3- -2- -2- -3- -2- 104 64 ---- 58 K-K P-L 3-3 3-2 3-2 1-1 3-1 1-1 3-2 2-1 4-4 105 65 65 59 CNC LBA 242 331 131 111 123 312 142 342 143 106 ---- 66 ---- -H- -U- -4- -3- -4- -4- -2- -1- -4- -4- -4- 107 66 ---- 60 N-N A-A 3-4 3-3 1-2 1-1 3-3 1-1 4-4 4-4 4-4 108 67 ---- 61 H-Y P-U 3-4 1-1 3-4 1-4 1-2 2-1 4-4 4-4 4-4 109 68 ---- ---- P-- P-- 3-- 1-- 2-- 1-- 2-- 1-- 2-- 4-- 4-- 110 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 111 69 ---- ---- P-- P-- 2-- 1-- 2-- 1-- 3-- 1-- 2-- 4-- 4-- 112 70 ---- ---- K-- E-- 2-- 2-- 1-- 1-- 1-- 1-- 3-- 2-- 4-- 113 71 ---- ---- R-- E-- 1-- 2-- 3-- 1-- 1-- 1-- 3-- 3-- 4-- 114 72 ---- ---- Q-- B-- 1-- 3-- 3-- 1-- 1-- 2-- 1-- 4-- 4-- 115 73 ---- ---- P-- L-- 4-- 1-- 1-- 1-- 1-- 2-- 1-- 4-- 4-- 116 74 ---- ---- G-- U-- 4-- 3-- 4-- 4-- 4-- 4-- 4-- 4-- 4-- 117 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 118 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 119 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 120 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- COMPARISON OF SEVERAL 3D STRUCTURES: # ALGNMT CODE ATOM FILE 1 2ctx 2ctx_fit.pdb 2 2abx 2abx_fit.pdb 3 2nbt 2nbt_fit.pdb 4 1fas 1fas_fit.pdb Variability at a given position is calculated as: VAR = 1/Nij * sum_ij (feat_i - feat_j) sum runs over all pairs of proteins with residues present. >> Least-squares superposition (FIT) : T Atom types for superposition/RMS (FIT_ATOMS): CA Atom type for position average/variability (VARATOM): CA Position comparison (FIT_ATOMS): Cutoff for RMS calculation: 3.5000 Upper = RMS, Lower = numb equiv positions 2ctx 2abx 2nbt 1fas 2ctx 0.000 1.989 1.755 1.722 2abx 56 0.000 1.678 2.265 2nbt 34 36 0.000 2.108 1fas 49 43 31 0.000 Distance comparison (FIT_ATOMS): Cutoff for rms calculation: 3.5000 Upper = Distance RMS, Lower = numb equiv distances 2ctx 2abx 2nbt 1fas 2ctx 0.000 1.418 1.314 1.291 2abx 1566 0.000 1.247 1.653 2nbt 618 793 0.000 1.523 1fas 1194 988 599 0.000 >> Sequence comparison: Diag=numb res, Upper=numb equiv res, Lower = % seq ID 2ctx 2abx 2nbt 1fas 2ctx 71 25 12 13 2abx 35 74 17 19 2nbt 18 26 66 8 1fas 21 31 13 61 >> Dihedral angle comparison: Alph Cutoff for rms comparison: 60.0000 Upper = RMS Alph, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 29.319 25.141 22.274 2abx 35 0.000 36.274 32.793 2nbt 25 23 0.000 23.319 1fas 34 20 19 0.000 >> Dihedral angle comparison: Phi Cutoff for rms comparison: 60.0000 Upper = RMS Phi , Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 34.964 24.517 25.847 2abx 24 0.000 31.664 35.845 2nbt 29 19 0.000 34.273 1fas 41 19 24 0.000 >> Dihedral angle comparison: Psi Cutoff for rms comparison: 60.0000 Upper = RMS Psi , Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 35.058 21.676 26.209 2abx 22 0.000 35.459 36.924 2nbt 25 17 0.000 34.652 1fas 42 24 21 0.000 >> Dihedral angle comparison: Omeg Cutoff for rms comparison: 60.0000 Upper = RMS Omeg, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 7.526 2.485 5.053 2abx 57 0.000 7.196 9.714 2nbt 36 41 0.000 5.220 1fas 46 44 35 0.000 >> Dihedral angle comparison: chi1 Cutoff for rms comparison: 60.0000 Upper = RMS chi1, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 37.569 18.625 18.635 2abx 19 0.000 33.618 30.353 2nbt 12 19 0.000 27.417 1fas 21 12 11 0.000 >> Dihedral angle comparison: chi2 Cutoff for rms comparison: 60.0000 Upper = RMS chi2, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 20.511 34.909 19.918 2abx 9 0.000 30.619 36.747 2nbt 8 13 0.000 35.119 1fas 13 7 7 0.000 >> Dihedral angle comparison: chi3 Cutoff for rms comparison: 60.0000 Upper = RMS chi3, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 30.525 34.394 24.465 2abx 3 0.000 27.691 17.183 2nbt 4 4 0.000 21.989 1fas 11 4 3 0.000 >> Dihedral angle comparison: chi4 Cutoff for rms comparison: 60.0000 Upper = RMS chi4, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 46.829 27.026 26.887 2abx 3 0.000 30.808 0.969 2nbt 3 3 0.000 34.834 1fas 8 1 3 0.000 >> Dihedral angle comparison: chi5 Cutoff for rms comparison: 60.0000 Upper = RMS chi5, Lower = numb of equiv angles 2ctx 2abx 2nbt 1fas 2ctx 0.000 29.293 12.713 8.019 2abx 2 0.000 34.805 21.491 2nbt 4 3 0.000 18.823 1fas 6 2 3 0.000 >> Ramachandran mainchain class substitution prot 1 --> prot 2; class on vert --> class on horiz A P B L E U A 14 7 12 2 5 0 P 10 13 16 8 1 2 B 17 25 78 7 8 0 L 5 8 12 2 0 0 E 2 3 6 1 0 0 U 0 0 0 0 0 3 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT A 14 26 40 5.3 9.8 15.2 P 13 37 50 4.9 14.0 18.9 B 78 57 135 29.5 21.6 51.1 L 2 25 27 0.8 9.5 10.2 E 0 12 12 0.0 4.5 4.5 -------------------------------------------- SUMS 107 157 264 40.5 59.5 100.0 -------------------------------------------- U 3 0 3 1.1 0.0 1.1 >> Dihedral class substitution: Alph prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 2 10 18 1 2 9 23 20 2 3 19 25 131 3 4 0 1 0 3 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 2 29 31 0.8 11.0 11.8 2 23 31 54 8.7 11.8 20.5 3 131 47 178 49.8 17.9 67.7 -------------------------------------------- SUMS 156 107 263 59.3 40.7 100.0 -------------------------------------------- 4 3 1 4 1.1 0.4 1.5 >> Dihedral class substitution: Phi prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 25 8 29 0 2 9 1 14 0 3 39 14 125 0 4 0 0 0 3 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 25 37 62 9.5 14.0 23.5 2 1 23 24 0.4 8.7 9.1 3 125 53 178 47.3 20.1 67.4 -------------------------------------------- SUMS 151 113 264 57.2 42.8 100.0 -------------------------------------------- 4 3 0 3 1.1 0.0 1.1 >> Dihedral class substitution: Psi prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 5 9 14 0 2 13 10 22 1 3 18 33 141 1 4 0 0 0 0 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 5 23 28 1.9 8.6 10.5 2 10 36 46 3.7 13.5 17.2 3 141 52 193 52.8 19.5 72.3 -------------------------------------------- SUMS 156 111 267 58.4 41.6 100.0 -------------------------------------------- 4 0 0 0 0.0 0.0 0.0 >> Dihedral class substitution: Omeg prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 259 5 0 2 2 1 0 0 0 3 0 0 0 0 4 0 0 0 0 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 259 7 266 97.0 2.6 99.6 2 0 1 1 0.0 0.4 0.4 3 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 259 8 267 97.0 3.0 100.0 -------------------------------------------- 4 0 0 0 0.0 0.0 0.0 >> Dihedral class substitution: chi1 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 30 42 18 5 2 39 29 16 7 3 18 17 13 7 4 10 4 3 9 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 30 65 95 12.4 27.0 39.4 2 29 62 91 12.0 25.7 37.8 3 13 42 55 5.4 17.4 22.8 -------------------------------------------- SUMS 72 169 241 29.9 70.1 100.0 -------------------------------------------- 4 9 17 26 3.4 6.4 9.7 >> Dihedral class substitution: chi2 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 51 12 6 26 2 17 12 7 3 3 10 13 11 7 4 34 10 3 45 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 51 44 95 29.1 25.1 54.3 2 12 27 39 6.9 15.4 22.3 3 11 30 41 6.3 17.1 23.4 -------------------------------------------- SUMS 74 101 175 42.3 57.7 100.0 -------------------------------------------- 4 45 47 92 16.9 17.6 34.5 >> Dihedral class substitution: chi3 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 20 15 2 14 2 16 13 1 13 3 1 2 0 7 4 24 15 4 120 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 20 31 51 19.2 29.8 49.0 2 13 30 43 12.5 28.8 41.3 3 0 10 10 0.0 9.6 9.6 -------------------------------------------- SUMS 33 71 104 31.7 68.3 100.0 -------------------------------------------- 4 120 43 163 44.9 16.1 61.0 >> Dihedral class substitution: chi4 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 11 2 3 9 2 3 5 6 4 3 5 9 7 11 4 10 4 9 169 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 11 14 25 14.7 18.7 33.3 2 5 13 18 6.7 17.3 24.0 3 7 25 32 9.3 33.3 42.7 -------------------------------------------- SUMS 23 52 75 30.7 69.3 100.0 -------------------------------------------- 4 169 23 192 63.3 8.6 71.9 >> Dihedral class substitution: chi5 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 7 5 6 3 2 3 7 1 4 3 4 1 6 5 4 5 0 1 209 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 7 14 21 13.5 26.9 40.4 2 7 8 15 13.5 15.4 28.8 3 6 10 16 11.5 19.2 30.8 -------------------------------------------- SUMS 20 32 52 38.5 61.5 100.0 -------------------------------------------- 4 209 6 215 78.3 2.2 80.5 >> Detailed comparison: Structure : 2 2abx_fit.pdb Structure : 3 2nbt_fit.pdb Structure : 4 1fas_fit.pdb ALN ... alignment position RESID... ... residue numbers 1/2/3 AAA ... amino acid types 1/2/3 MNC ... mainchain classes 1/2/3 ALP... ... dihedral angle classes (alpha,phi,psi,...) ALN RESIDUE_NUMBERS AAA MNC ALP PHI PSI OMG CH1 CH2 CH3 CH4 CH5 --------------------------------------------------------------- 1 ---- 1 ---- -R- -U- -4- -4- -2- -1- -1- -2- -1- -1- -4- 2 1 ---- 1 I-T U-U 4-4 4-4 3-3 1-1 3-1 1-4 4-4 4-4 4-4 3 2 2 2 VTM ABP 233 333 133 111 221 442 441 444 444 4 3 3 3 CCC BAB 323 333 323 111 311 331 121 321 121 5 ---- 4 ---- -L- -B- -3- -3- -3- -1- -1- -1- -4- -4- -4- 6 ---- 5 ---- -I- -B- -2- -3- -2- -1- -1- -1- -4- -4- -4- 7 ---- 6 ---- -S- -L- -2- -3- -1- -1- -3- -4- -4- -4- -4- 8 ---- 7 ---- -P- -A- -1- -1- -1- -1- -2- -1- -2- -4- -4- 9 ---- 8 ---- -S- -A- -3- -3- -1- -1- -1- -4- -4- -4- -4- 10 ---- 9 ---- -S- -L- -3- -2- -2- -1- -2- -4- -4- -4- -4- 11 ---- 10 ---- -T- -A- -3- -3- -2- -1- -2- -4- -4- -4- -4- 12 4 11 ---- HP- BP- 23- 31- 32- 11- 12- 21- 42- 44- 44- 13 5 12 4 TQY BAP 123 331 323 111 221 411 414 444 444 14 ---- 13 ---- -T- -P- -3- -3- -3- -1- -1- -4- -4- -4- -4- 15 6 ---- ---- T-- P-- 3-- 1-- 3-- 1-- 1-- 4-- 4-- 4-- 4-- 16 7 ---- 5 A-S L-A 2-2 2-3 3-2 1-1 4-1 4-4 4-4 4-4 4-4 17 8 ---- ---- T-- L-- 1-- 2-- 3-- 1-- 1-- 4-- 4-- 4-- 4-- 18 ---- ---- 6 --H --B --3 --3 --3 --1 --1 --2 --4 --4 --4 19 ---- ---- 7 --T --A --2 --1 --1 --1 --2 --4 --4 --4 --4 20 ---- ---- 8 --T --B --3 --3 --3 --1 --2 --4 --4 --4 --4 21 ---- ---- 9 --T --A --2 --3 --2 --1 --2 --4 --4 --4 --4 22 9 ---- ---- I-- E-- 2-- 2-- 3-- 1-- 1-- 3-- 4-- 4-- 4-- 23 10 ---- ---- P-- A-- 3-- 1-- 1-- 1-- 1-- 2-- 1-- 4-- 4-- 24 11 ---- ---- S-- E-- 3-- 2-- 3-- 1-- 2-- 4-- 4-- 4-- 4-- 25 ---- ---- 10 --S --A --2 --1 --1 --1 --2 --4 --4 --4 --4 26 ---- ---- 11 --R --P --3 --1 --3 --1 --1 --1 --1 --1 --4 27 12 ---- 12 S-A A-A 3-2 3-1 2-2 1-1 2-4 4-4 4-4 4-4 4-4 28 13 ---- 13 A-I L-B 3-3 2-3 1-3 1-1 4-3 4-1 4-4 4-4 4-4 29 14 ---- 14 V-L E-B 3-3 2-3 1-3 1-1 1-1 4-1 4-4 4-4 4-4 30 15 ---- 15 T-T L-B 3-3 2-3 2-3 1-1 2-3 4-4 4-4 4-4 4-4 31 16 14 16 CCN ELB 133 233 323 111 332 321 214 314 234 32 17 15 17 PPC PPA 133 111 221 111 321 111 221 441 441 33 ---- ---- 18 --G --E --1 --2 --3 --1 --4 --4 --4 --4 --4 34 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 35 18 16 ---- PN- PA- 21- 11- 21- 11- 21- 11- 24- 44- 44- 36 19 17 ---- GG- EA- 32- 23- 31- 11- 44- 44- 44- 44- 44- 37 20 18 19 EQE LBA 232 331 332 111 111 332 111 444 444 38 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 39 21 19 20 NDN EBP 233 213 333 111 312 211 444 444 444 40 22 20 21 LIS EBP 333 231 333 111 211 114 444 444 444 41 23 21 22 CCC BPB 333 313 333 111 121 321 121 331 311 42 24 22 23 YFY BBB 333 133 333 111 323 212 444 444 444 43 25 23 24 RLR PBB 333 133 333 111 222 121 141 142 444 44 26 24 25 KKK BBB 233 333 333 111 223 111 111 111 444 45 27 25 26 MAS EBB 321 233 333 111 241 144 344 444 444 46 28 ---- ---- W-- L-- 2-- 3-- 1-- 1-- 2-- 1-- 4-- 4-- 4-- 47 29 ---- ---- C-- A-- 3-- 3-- 2-- 1-- 2-- 1-- 1-- 1-- 1-- 48 ---- 26 27 -QR -BP -13 -31 -33 -11 -31 -11 -13 -43 -44 49 ---- ---- 28 --R --A --2 --1 --1 --1 --2 --1 --2 --2 --4 50 ---- ---- 29 --H --B --1 --3 --3 --1 --1 --1 --4 --4 --4 51 ---- 27 ---- -C- -P- -3- -1- -3- -1- -3- -2- -2- -1- -1- 52 ---- 28 ---- -D- -B- -1- -3- -3- -1- -2- -1- -4- -4- -4- 53 ---- 29 ---- -K- -E- -2- -2- -3- -1- -1- -3- -1- -1- -4- 54 ---- 30 ---- -F- -L- -3- -2- -1- -1- -1- -1- -4- -4- -4- 55 ---- 31 ---- -C- -L- -2- -2- -2- -1- -1- -1- -2- -2- -3- 56 ---- 32 ---- -S- -A- -2- -3- -2- -1- -2- -4- -4- -4- -4- 57 ---- 33 ---- -I- -A- -2- -3- -1- -1- -1- -1- -4- -4- -4- 58 ---- 34 ---- -R- -A- -3- -3- -1- -1- -3- -2- -2- -1- -4- 59 ---- 35 ---- -G- -E- -1- -2- -3- -1- -4- -4- -4- -4- -4- 60 30 36 ---- DP- EP- 33- 21- 12- 11- 12- 11- 42- 44- 44- 61 31 ---- ---- A-- L-- 2-- 3-- 2-- 1-- 4-- 4-- 4-- 4-- 4-- 62 32 ---- ---- F-- B-- 3-- 3-- 3-- 1-- 3-- 1-- 4-- 4-- 4-- 63 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 64 33 ---- 30 C-P A-P 3-2 1-1 2-2 1-2 1-1 1-2 1-1 1-4 2-4 65 34 ---- ---- S-- A-- 1-- 3-- 2-- 1-- 1-- 4-- 4-- 4-- 4-- 66 35 ---- ---- S-- E-- 2-- 2-- 3-- 1-- 2-- 4-- 4-- 4-- 4-- 67 36 ---- ---- R-- E-- 3-- 2-- 3-- 1-- 1-- 1-- 3-- 1-- 4-- 68 37 ---- 31 G-P L-P 3-3 3-1 2-2 1-1 4-2 4-1 4-2 4-4 4-4 69 38 ---- ---- K-- A-- 2-- 3-- 2-- 1-- 2-- 1-- 3-- 1-- 4-- 70 ---- ---- 32 --K --B --3 --1 --2 --1 --1 --1 --1 --1 --4 71 39 37 33 VVM BBP 333 331 333 111 213 441 442 444 444 72 40 38 34 VIV PBP 333 331 333 111 231 414 444 444 444 73 41 39 35 EEL BBA 331 333 331 111 221 321 114 444 444 74 42 40 36 LQG LBB 223 333 233 111 334 114 414 444 444 75 43 41 37 GGR ABB 312 333 333 111 441 441 441 443 444 76 44 42 38 CCG BBB 331 333 333 111 234 314 214 324 334 77 45 43 39 AVC LBB 112 333 233 111 411 441 441 441 441 78 46 44 ---- AA- EA- 21- 21- 11- 11- 44- 44- 44- 44- 44- 79 47 45 40 TTG BBE 333 332 233 111 314 444 444 444 444 80 48 46 41 CCC LPB 333 213 232 111 222 332 122 233 221 81 49 47 ---- PP- AP- 31- 11- 12- 11- 32- 11- 22- 44- 44- 82 ---- 48 ---- -Q- -A- -3- -1- -2- -1- -3- -1- -2- -4- -4- 83 ---- 49 ---- -F- -E- -3- -2- -3- -1- -1- -2- -4- -4- -4- 84 50 ---- 42 S-P L-P 3-3 2-1 1-2 1-1 1-2 4-1 4-2 4-4 4-4 85 51 ---- 43 K-P B-P 1-3 3-1 3-2 1-1 1-2 1-1 1-2 3-4 4-4 86 52 50 44 KRG PBP 133 331 333 111 124 334 134 114 444 87 ---- 51 45 -SD -AB -21 -13 -23 -11 -13 -41 -44 -44 -44 88 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 89 53 52 46 PND AAA 222 131 121 111 223 121 244 444 444 90 54 53 47 YYY PPA 132 131 331 111 312 222 444 444 444 91 55 54 ---- ER- PA- 21- 13- 31- 11- 12- 13- 11- 41- 44- 92 ---- ---- 48 --L --B --3 --3 --3 --1 --2 --2 --4 --4 --4 93 56 55 49 ESE PLB 333 133 333 111 132 141 241 444 444 94 57 56 50 VLV BBB 333 333 333 111 121 434 444 444 444 95 58 57 51 TLK BBB 333 333 333 111 321 412 441 443 444 96 59 58 52 CCC BBB 333 333 333 111 221 233 122 332 222 97 60 59 53 CCC PAB 333 133 313 111 123 332 122 322 133 98 ---- 60 ---- -T- -L- -2- -2- -2- -1- -2- -4- -4- -4- -4- 99 61 61 54 STT LBA 332 333 231 111 322 444 444 444 444 100 62 62 55 TDS ABB 122 333 233 112 221 414 444 444 444 101 ---- ---- 56 --P --P --3 --1 --2 --1 --2 --1 --2 --4 --4 102 63 63 57 DND LLP 132 321 123 111 211 221 444 444 444 103 ---- 64 ---- -C- -A- -2- -3- -2- -1- -3- -2- -2- -3- -2- 104 64 ---- 58 K-K P-L 3-3 3-2 3-2 1-1 3-1 1-1 3-2 2-1 4-4 105 65 65 59 CNC LBA 242 331 131 111 123 312 142 342 143 106 ---- 66 ---- -H- -U- -4- -3- -4- -4- -2- -1- -4- -4- -4- 107 66 ---- 60 N-N A-A 3-4 3-3 1-2 1-1 3-3 1-1 4-4 4-4 4-4 108 67 ---- 61 H-Y P-U 3-4 1-1 3-4 1-4 1-2 2-1 4-4 4-4 4-4 109 68 ---- ---- P-- P-- 3-- 1-- 2-- 1-- 2-- 1-- 2-- 4-- 4-- 110 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 111 69 ---- ---- P-- P-- 2-- 1-- 2-- 1-- 3-- 1-- 2-- 4-- 4-- 112 70 ---- ---- K-- E-- 2-- 2-- 1-- 1-- 1-- 1-- 3-- 2-- 4-- 113 71 ---- ---- R-- E-- 1-- 2-- 3-- 1-- 1-- 1-- 3-- 3-- 4-- 114 72 ---- ---- Q-- B-- 1-- 3-- 3-- 1-- 1-- 2-- 1-- 4-- 4-- 115 73 ---- ---- P-- L-- 4-- 1-- 1-- 1-- 1-- 2-- 1-- 4-- 4-- 116 74 ---- ---- G-- U-- 4-- 3-- 4-- 4-- 4-- 4-- 4-- 4-- 4-- 117 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 118 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 119 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- 120 ---- ---- ---- --- --- --- --- --- --- --- --- --- --- --- Total CPU time [seconds] : 0.22