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Evolutionary Scale Modeling (esm): Pretrained language models for proteins
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The shape of contact map is not consistent with residue length #251

Closed zhenyuhe00 closed 2 years ago

zhenyuhe00 commented 2 years ago

Bug description Hi, I use your "contacts_from_pdb()" in contact_prediction.ipynb to get the contact map of residue sequences but find the length of contact map is shorter than the length of residues.

Reproduction steps The dataset I use is CASP14.

Expected behavior The length of the contact map should be equal to the length of residues.

Logs

id: T1042  contact_map shape: (276, 276)  residue length: 289
id: T1058  contact_map shape: (365, 365)  residue length: 382
id: T1084  contact_map shape: (71, 71)  residue length: 73
id: T1039  contact_map shape: (161, 161)  residue length: 161
id: T1050  contact_map shape: (765, 765)  residue length: 779
zhenyuhe00 commented 2 years ago

For example, the suquence of T1084 is: "MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH", which has length of 73 the pdb file of T1084 is: REMARK T1084 REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 R VALUE (WORKING + TEST SET) : 0.20965 REMARK 3 FREE R VALUE : 0.24349 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.390 CRYST1 105.450 105.450 141.340 90.00 90.00 120.00 H 3 2
ATOM 1 N ALA 3 16.145 17.538 15.729 1.00 52.74 N ATOM 2 CA ALA 3 15.168 17.334 16.837 1.00 52.61 C ATOM 3 CB ALA 3 13.738 17.364 16.307 1.00 54.78 C ATOM 4 C ALA 3 15.448 15.979 17.535 1.00 47.50 C ATOM 5 O ALA 3 15.668 14.972 16.873 1.00 53.66 O ATOM 6 N HIS 4 15.498 15.974 18.858 1.00 39.08 N ATOM 7 CA HIS 4 15.710 14.750 19.579 1.00 32.73 C ATOM 8 CB HIS 4 16.414 15.093 20.886 1.00 30.54 C ATOM 9 CG HIS 4 16.851 13.911 21.672 1.00 26.68 C ATOM 10 ND1 HIS 4 16.013 13.254 22.542 1.00 24.67 N ATOM 11 CE1 HIS 4 16.644 12.220 23.066 1.00 25.17 C ATOM 12 NE2 HIS 4 17.899 12.251 22.647 1.00 25.52 N ATOM 13 CD2 HIS 4 18.041 13.270 21.735 1.00 26.39 C ATOM 14 C HIS 4 14.340 14.061 19.794 1.00 30.16 C ATOM 15 O HIS 4 13.436 14.659 20.354 1.00 27.65 O ATOM 16 N LYS 5 14.173 12.828 19.318 1.00 29.87 N ATOM 17 CA LYS 5 12.836 12.139 19.398 1.00 31.78 C ATOM 18 CB LYS 5 12.819 10.848 18.592 1.00 35.96 C ATOM 19 CG LYS 5 12.902 11.090 17.107 1.00 45.63 C ATOM 20 CD LYS 5 12.609 9.809 16.326 1.00 52.00 C ATOM 21 CE LYS 5 13.579 9.622 15.195 1.00 56.62 C ATOM 22 NZ LYS 5 13.707 10.821 14.303 1.00 61.76 N ATOM 23 C LYS 5 12.402 11.814 20.824 1.00 27.51 C ATOM 24 O LYS 5 11.221 11.813 21.172 1.00 27.48 O ATOM 25 N GLY 6 13.376 11.533 21.661 1.00 23.90 N ATOM 26 CA GLY 6 13.148 11.372 23.076 1.00 21.87 C ATOM 27 C GLY 6 12.596 12.630 23.731 1.00 21.38 C ATOM 28 O GLY 6 11.581 12.565 24.449 1.00 19.15 O ATOM 29 N ALA 7 13.300 13.748 23.536 1.00 21.79 N ATOM 30 CA ALA 7 12.911 15.058 24.073 1.00 22.19 C ATOM 31 CB ALA 7 13.836 16.153 23.525 1.00 22.86 C ATOM 32 C ALA 7 11.495 15.350 23.630 1.00 21.00 C ATOM 33 O ALA 7 10.709 15.860 24.394 1.00 21.18 O ATOM 34 N GLU 8 11.180 15.075 22.363 1.00 22.88 N ATOM 35 CA GLU 8 9.816 15.355 21.846 1.00 25.65 C ATOM 36 CB GLU 8 9.646 14.937 20.369 1.00 30.52 C ATOM 37 CG GLU 8 10.442 15.713 19.391 1.00 37.99 C ATOM 38 CD GLU 8 10.376 15.140 17.977 1.00 45.58 C ATOM 39 OE1 GLU 8 9.860 14.008 17.767 1.00 48.02 O ATOM 40 OE2 GLU 8 10.839 15.841 17.072 1.00 50.11 O ATOM 41 C GLU 8 8.760 14.612 22.680 1.00 23.46 C ATOM 42 O GLU 8 7.717 15.175 23.039 1.00 22.13 O ATOM 43 N HIS 9 9.030 13.338 22.956 1.00 21.79 N ATOM 44 CA HIS 9 8.157 12.538 23.824 1.00 20.52 C ATOM 45 CB HIS 9 8.568 11.071 23.847 1.00 21.26 C ATOM 46 CG HIS 9 8.129 10.301 22.652 1.00 24.31 C ATOM 47 ND1 HIS 9 6.813 10.095 22.351 1.00 26.31 N ATOM 48 CE1 HIS 9 6.717 9.410 21.230 1.00 29.82 C ATOM 49 NE2 HIS 9 7.934 9.125 20.815 1.00 27.91 N ATOM 50 CD2 HIS 9 8.836 9.663 21.690 1.00 27.84 C ATOM 51 C HIS 9 8.066 13.093 25.251 1.00 19.50 C ATOM 52 O HIS 9 6.980 13.120 25.846 1.00 17.88 O ATOM 53 N HIS 10 9.203 13.514 25.812 1.00 18.95 N ATOM 54 CA HIS 10 9.227 14.145 27.118 1.00 20.08 C ATOM 55 CB HIS 10 10.615 14.562 27.549 1.00 20.61 C ATOM 56 CG HIS 10 11.460 13.433 28.064 1.00 20.45 C ATOM 57 ND1 HIS 10 11.247 12.866 29.285 1.00 20.26 N ATOM 58 CE1 HIS 10 12.180 11.960 29.528 1.00 22.25 C ATOM 59 NE2 HIS 10 12.970 11.909 28.481 1.00 21.84 N ATOM 60 CD2 HIS 10 12.575 12.861 27.578 1.00 20.54 C ATOM 61 C HIS 10 8.339 15.393 27.133 1.00 21.72 C ATOM 62 O HIS 10 7.562 15.552 28.086 1.00 22.56 O ATOM 63 N HIS 11 8.461 16.251 26.120 1.00 21.70 N ATOM 64 CA HIS 11 7.615 17.471 26.090 1.00 24.57 C ATOM 65 CB HIS 11 7.961 18.350 24.920 1.00 27.98 C ATOM 66 CG HIS 11 9.168 19.217 25.144 1.00 32.36 C ATOM 67 ND1 HIS 11 9.288 20.055 26.234 1.00 32.88 N ATOM 68 CE1 HIS 11 10.406 20.753 26.136 1.00 35.04 C ATOM 69 NE2 HIS 11 11.031 20.377 25.035 1.00 35.08 N ATOM 70 CD2 HIS 11 10.269 19.443 24.377 1.00 33.25 C ATOM 71 C HIS 11 6.110 17.105 26.042 1.00 23.31 C ATOM 72 O HIS 11 5.262 17.736 26.693 1.00 21.59 O ATOM 73 N LYS 12 5.784 16.078 25.284 1.00 24.32 N ATOM 74 CA LYS 12 4.357 15.668 25.149 1.00 25.18 C ATOM 75 CB LYS 12 4.176 14.727 23.934 1.00 27.44 C ATOM 76 CG LYS 12 4.289 15.465 22.624 1.00 32.24 C ATOM 77 CD LYS 12 4.051 14.540 21.452 1.00 35.70 C ATOM 78 CE LYS 12 4.087 15.282 20.095 1.00 39.96 C ATOM 79 NZ LYS 12 2.790 16.010 19.870 1.00 43.38 N ATOM 80 C LYS 12 3.850 15.044 26.403 1.00 21.94 C ATOM 81 O LYS 12 2.680 15.282 26.783 1.00 21.04 O ATOM 82 N ALA 13 4.688 14.254 27.078 1.00 19.87 N ATOM 83 CA ALA 13 4.363 13.785 28.454 1.00 18.60 C ATOM 84 CB ALA 13 5.443 12.908 29.047 1.00 17.74 C ATOM 85 C ALA 13 4.064 14.936 29.380 1.00 19.17 C ATOM 86 O ALA 13 3.017 14.931 30.044 1.00 18.99 O ATOM 87 N ALA 14 4.930 15.951 29.383 1.00 18.97 N ATOM 88 CA ALA 14 4.731 17.123 30.196 1.00 18.91 C ATOM 89 CB ALA 14 5.881 18.091 29.951 1.00 19.37 C ATOM 90 C ALA 14 3.364 17.840 29.924 1.00 19.36 C ATOM 91 O ALA 14 2.671 18.242 30.828 1.00 19.72 O ATOM 92 N GLU 15 3.030 18.042 28.671 1.00 19.69 N ATOM 93 CA GLU 15 1.774 18.674 28.279 1.00 21.96 C ATOM 94 CB GLU 15 1.692 18.843 26.748 1.00 25.92 C ATOM 95 CG GLU 15 2.758 19.786 26.245 1.00 28.94 C ATOM 96 CD GLU 15 2.933 19.796 24.705 1.00 34.99 C ATOM 97 OE1 GLU 15 2.409 18.927 23.992 1.00 36.30 O ATOM 98 OE2 GLU 15 3.607 20.723 24.214 1.00 37.22 O ATOM 99 C GLU 15 0.583 17.888 28.749 1.00 20.33 C ATOM 100 O GLU 15 -0.370 18.470 29.189 1.00 22.80 O ATOM 101 N HIS 16 0.633 16.558 28.663 1.00 19.07 N ATOM 102 CA HIS 16 -0.448 15.741 29.150 1.00 18.63 C ATOM 103 CB HIS 16 -0.379 14.319 28.584 1.00 18.29 C ATOM 104 CG HIS 16 -0.812 14.237 27.139 1.00 19.91 C ATOM 105 ND1 HIS 16 -2.132 14.334 26.759 1.00 20.14 N ATOM 106 CE1 HIS 16 -2.224 14.260 25.434 1.00 23.92 C ATOM 107 NE2 HIS 16 -1.003 14.091 24.941 1.00 22.15 N ATOM 108 CD2 HIS 16 -0.104 14.057 25.991 1.00 21.47 C ATOM 109 C HIS 16 -0.521 15.734 30.639 1.00 19.87 C ATOM 110 O HIS 16 -1.627 15.788 31.222 1.00 18.50 O ATOM 111 N HIS 17 0.634 15.745 31.320 1.00 20.10 N ATOM 112 CA HIS 17 0.623 15.912 32.787 1.00 20.75 C ATOM 113 CB HIS 17 2.054 15.863 33.351 1.00 20.34 C ATOM 114 CG HIS 17 2.554 14.492 33.539 1.00 19.31 C ATOM 115 ND1 HIS 17 1.940 13.593 34.379 1.00 20.12 N ATOM 116 CE1 HIS 17 2.620 12.458 34.384 1.00 20.89 C ATOM 117 NE2 HIS 17 3.648 12.600 33.571 1.00 20.97 N ATOM 118 CD2 HIS 17 3.621 13.846 33.010 1.00 22.06 C ATOM 119 C HIS 17 -0.005 17.247 33.196 1.00 20.96 C ATOM 120 O HIS 17 -0.720 17.300 34.172 1.00 18.85 O ATOM 121 N GLU 18 0.301 18.310 32.449 1.00 20.48 N ATOM 122 CA GLU 18 -0.237 19.643 32.719 1.00 22.90 C ATOM 123 CB GLU 18 0.341 20.715 31.777 1.00 23.78 C ATOM 124 CG GLU 18 1.780 21.047 32.108 1.00 24.77 C ATOM 125 CD GLU 18 2.538 21.711 30.966 1.00 27.47 C ATOM 126 OE1 GLU 18 1.945 21.935 29.862 1.00 28.82 O ATOM 127 OE2 GLU 18 3.727 22.025 31.198 1.00 28.68 O ATOM 128 C GLU 18 -1.766 19.650 32.635 1.00 22.48 C ATOM 129 O GLU 18 -2.444 20.206 33.501 1.00 19.98 O ATOM 130 N GLN 19 -2.281 18.980 31.621 1.00 23.07 N ATOM 131 CA GLN 19 -3.740 18.854 31.437 1.00 24.91 C ATOM 132 CB GLN 19 -4.060 18.383 30.027 1.00 27.09 C ATOM 133 CG GLN 19 -3.656 19.428 29.006 1.00 31.55 C ATOM 134 CD GLN 19 -3.684 18.897 27.604 1.00 38.26 C ATOM 135 OE1 GLN 19 -2.701 18.337 27.104 1.00 44.12 O ATOM 136 NE2 GLN 19 -4.800 19.073 26.957 1.00 42.48 N ATOM 137 C GLN 19 -4.414 17.987 32.503 1.00 21.71 C ATOM 138 O GLN 19 -5.493 18.329 32.959 1.00 19.58 O ATOM 139 N ALA 20 -3.781 16.857 32.872 1.00 16.61 N ATOM 140 CA ALA 20 -4.250 16.014 33.947 1.00 16.57 C ATOM 141 CB ALA 20 -3.350 14.795 34.111 1.00 14.57 C ATOM 142 C ALA 20 -4.362 16.841 35.261 1.00 17.26 C ATOM 143 O ALA 20 -5.348 16.735 35.976 1.00 17.09 O ATOM 144 N ALA 21 -3.328 17.609 35.587 1.00 18.14 N ATOM 145 CA ALA 21 -3.362 18.509 36.710 1.00 18.46 C ATOM 146 CB ALA 21 -2.088 19.322 36.838 1.00 19.14 C ATOM 147 C ALA 21 -4.569 19.444 36.708 1.00 21.57 C ATOM 148 O ALA 21 -5.215 19.564 37.765 1.00 21.38 O ATOM 149 N LYS 22 -4.840 20.129 35.578 1.00 19.65 N ATOM 150 CA LYS 22 -5.935 21.071 35.503 1.00 23.24 C ATOM 151 CB LYS 22 -5.996 21.818 34.114 1.00 25.10 C ATOM 152 CG LYS 22 -4.934 22.900 33.891 1.00 29.94 C ATOM 153 CD LYS 22 -4.785 23.770 35.145 1.00 35.68 C ATOM 154 CE LYS 22 -4.670 25.280 34.933 1.00 44.46 C ATOM 155 NZ LYS 22 -6.003 25.989 34.881 1.00 49.37 N ATOM 156 C LYS 22 -7.255 20.373 35.803 1.00 21.45 C ATOM 157 O LYS 22 -8.091 20.897 36.556 1.00 19.89 O ATOM 158 N HIS 23 -7.442 19.194 35.249 1.00 19.21 N ATOM 159 CA HIS 23 -8.697 18.482 35.441 1.00 17.40 C ATOM 160 CB HIS 23 -8.903 17.503 34.309 1.00 17.53 C ATOM 161 CG HIS 23 -9.259 18.168 33.019 1.00 17.90 C ATOM 162 ND1 HIS 23 -10.474 18.770 32.824 1.00 18.15 N ATOM 163 CE1 HIS 23 -10.521 19.302 31.623 1.00 20.51 C ATOM 164 NE2 HIS 23 -9.358 19.078 31.032 1.00 21.07 N ATOM 165 CD2 HIS 23 -8.551 18.382 31.890 1.00 19.80 C ATOM 166 C HIS 23 -8.849 17.860 36.811 1.00 17.46 C ATOM 167 O HIS 23 -9.972 17.822 37.353 1.00 18.23 O ATOM 168 N HIS 24 -7.744 17.428 37.432 1.00 17.74 N ATOM 169 CA HIS 24 -7.798 17.043 38.838 1.00 16.94 C ATOM 170 CB HIS 24 -6.557 16.309 39.312 1.00 16.43 C ATOM 171 CG HIS 24 -6.541 14.869 38.945 1.00 15.97 C ATOM 172 ND1 HIS 24 -7.443 13.960 39.440 1.00 17.68 N ATOM 173 CE1 HIS 24 -7.185 12.764 38.963 1.00 18.97 C ATOM 174 NE2 HIS 24 -6.164 12.865 38.129 1.00 19.15 N ATOM 175 CD2 HIS 24 -5.735 14.173 38.109 1.00 17.91 C ATOM 176 C HIS 24 -8.125 18.162 39.793 1.00 18.52 C ATOM 177 O HIS 24 -8.989 17.996 40.679 1.00 18.97 O ATOM 178 N HIS 25 -7.490 19.327 39.643 1.00 18.66 N ATOM 179 CA HIS 25 -7.878 20.512 40.408 1.00 19.70 C ATOM 180 CB HIS 25 -7.056 21.735 40.034 1.00 23.76 C ATOM 181 CG HIS 25 -5.655 21.759 40.593 1.00 24.91 C ATOM 182 ND1 HIS 25 -5.389 21.673 41.941 1.00 26.46 N ATOM 183 CE1 HIS 25 -4.080 21.757 42.141 1.00 30.42 C ATOM 184 NE2 HIS 25 -3.493 21.962 40.972 1.00 30.06 N ATOM 185 CD2 HIS 25 -4.452 21.968 39.986 1.00 27.30 C ATOM 186 C HIS 25 -9.379 20.855 40.218 1.00 21.31 C ATOM 187 O HIS 25 -10.096 21.163 41.188 1.00 21.39 O ATOM 188 N ALA 26 -9.867 20.828 38.981 1.00 20.38 N ATOM 189 CA ALA 26 -11.287 21.098 38.747 1.00 21.30 C ATOM 190 CB ALA 26 -11.621 21.204 37.287 1.00 20.57 C ATOM 191 C ALA 26 -12.200 20.064 39.415 1.00 21.17 C ATOM 192 O ALA 26 -13.224 20.435 40.014 1.00 21.09 O ATOM 193 N ALA 27 -11.839 18.799 39.336 1.00 19.02 N ATOM 194 CA ALA 27 -12.605 17.730 40.018 1.00 19.15 C ATOM 195 CB ALA 27 -11.940 16.395 39.815 1.00 19.68 C ATOM 196 C ALA 27 -12.722 17.995 41.504 1.00 18.38 C ATOM 197 O ALA 27 -13.796 17.934 42.088 1.00 20.47 O ATOM 198 N ALA 28 -11.633 18.404 42.090 1.00 19.20 N ATOM 199 CA ALA 28 -11.593 18.785 43.508 1.00 19.84 C ATOM 200 CB ALA 28 -10.180 19.126 43.886 1.00 21.01 C ATOM 201 C ALA 28 -12.530 19.954 43.826 1.00 20.19 C ATOM 202 O ALA 28 -13.294 19.919 44.817 1.00 20.06 O ATOM 203 N GLU 29 -12.497 20.975 42.988 1.00 20.72 N ATOM 204 CA GLU 29 -13.352 22.160 43.200 1.00 22.23 C ATOM 205 CB GLU 29 -13.066 23.223 42.160 1.00 24.22 C ATOM 206 CG GLU 29 -11.696 23.808 42.339 1.00 27.78 C ATOM 207 CD GLU 29 -11.302 24.816 41.261 1.00 36.17 C ATOM 208 OE1 GLU 29 -12.173 25.305 40.470 1.00 38.27 O ATOM 209 OE2 GLU 29 -10.099 25.127 41.232 1.00 32.13 O ATOM 210 C GLU 29 -14.825 21.748 43.137 1.00 21.34 C ATOM 211 O GLU 29 -15.621 22.161 43.975 1.00 22.15 O ATOM 212 N HIS 30 -15.192 20.970 42.141 1.00 19.09 N ATOM 213 CA HIS 30 -16.518 20.421 42.066 1.00 20.44 C ATOM 214 CB HIS 30 -16.758 19.617 40.805 1.00 20.07 C ATOM 215 CG HIS 30 -16.907 20.448 39.568 1.00 20.50 C ATOM 216 ND1 HIS 30 -17.964 21.285 39.350 1.00 22.28 N ATOM 217 CE1 HIS 30 -17.804 21.906 38.194 1.00 24.64 C ATOM 218 NE2 HIS 30 -16.657 21.490 37.662 1.00 22.98 N ATOM 219 CD2 HIS 30 -16.088 20.582 38.502 1.00 21.95 C ATOM 220 C HIS 30 -16.919 19.583 43.281 1.00 20.38 C ATOM 221 O HIS 30 -18.032 19.766 43.793 1.00 21.12 O ATOM 222 N HIS 31 -16.076 18.634 43.679 1.00 19.93 N ATOM 223 CA HIS 31 -16.376 17.801 44.833 1.00 20.72 C ATOM 224 CB HIS 31 -15.206 16.891 45.142 1.00 21.99 C ATOM 225 CG HIS 31 -15.163 15.634 44.323 1.00 21.91 C ATOM 226 ND1 HIS 31 -16.253 14.806 44.196 1.00 23.51 N ATOM 227 CE1 HIS 31 -15.910 13.725 43.512 1.00 22.62 C ATOM 228 NE2 HIS 31 -14.630 13.818 43.196 1.00 20.90 N ATOM 229 CD2 HIS 31 -14.136 14.998 43.701 1.00 22.64 C ATOM 230 C HIS 31 -16.657 18.672 46.059 1.00 23.13 C ATOM 231 O HIS 31 -17.601 18.389 46.834 1.00 22.98 O ATOM 232 N GLU 32 -15.847 19.725 46.248 1.00 22.92 N ATOM 233 CA GLU 32 -16.012 20.605 47.387 1.00 27.08 C ATOM 234 CB GLU 32 -14.877 21.663 47.451 1.00 32.44 C ATOM 235 CG GLU 32 -13.478 21.110 47.795 1.00 35.84 C ATOM 236 CD GLU 32 -12.265 22.047 47.390 1.00 47.55 C ATOM 237 OE1 GLU 32 -11.073 21.588 47.343 1.00 42.73 O ATOM 238 OE2 GLU 32 -12.468 23.274 47.112 1.00 54.67 O ATOM 239 C GLU 32 -17.383 21.293 47.371 1.00 27.78 C ATOM 240 O GLU 32 -17.829 21.746 48.409 1.00 27.70 O ATOM 241 N LYS 33 -18.001 21.444 46.193 1.00 24.80 N ATOM 242 CA LYS 33 -19.353 22.005 46.088 1.00 26.88 C ATOM 243 CB LYS 33 -19.450 22.843 44.824 1.00 29.06 C ATOM 244 CG LYS 33 -18.557 24.091 44.832 1.00 34.34 C ATOM 245 CD LYS 33 -18.601 24.787 43.478 1.00 36.20 C ATOM 246 CE LYS 33 -19.993 25.291 43.179 1.00 40.00 C ATOM 247 NZ LYS 33 -20.029 26.266 42.059 1.00 39.91 N ATOM 248 C LYS 33 -20.459 20.947 46.030 1.00 24.15 C ATOM 249 O LYS 33 -21.629 21.280 45.843 1.00 25.06 O ATOM 250 N GLY 34 -20.113 19.694 46.204 1.00 23.96 N ATOM 251 CA GLY 34 -21.100 18.594 46.176 1.00 23.88 C ATOM 252 C GLY 34 -21.452 18.211 44.744 1.00 23.62 C ATOM 253 O GLY 34 -22.460 17.570 44.538 1.00 23.82 O ATOM 254 N GLU 35 -20.663 18.648 43.751 1.00 22.00 N ATOM 255 CA GLU 35 -20.998 18.433 42.336 1.00 20.96 C ATOM 256 CB GLU 35 -20.689 19.695 41.501 1.00 22.05 C ATOM 257 CG GLU 35 -21.614 20.875 41.788 1.00 23.65 C ATOM 258 CD GLU 35 -21.154 22.199 41.180 1.00 27.65 C ATOM 259 OE1 GLU 35 -20.010 22.319 40.695 1.00 26.26 O ATOM 260 OE2 GLU 35 -21.983 23.118 41.155 1.00 33.09 O ATOM 261 C GLU 35 -20.242 17.230 41.804 1.00 21.06 C ATOM 262 O GLU 35 -19.294 17.389 41.034 1.00 17.84 O ATOM 263 N HIS 36 -20.647 16.052 42.240 1.00 20.37 N ATOM 264 CA HIS 36 -19.859 14.840 42.037 1.00 21.78 C ATOM 265 CB HIS 36 -20.300 13.768 43.026 1.00 23.15 C ATOM 266 CG HIS 36 -20.242 14.245 44.442 1.00 24.67 C ATOM 267 ND1 HIS 36 -19.092 14.769 44.985 1.00 24.27 N ATOM 268 CE1 HIS 36 -19.323 15.150 46.231 1.00 26.03 C ATOM 269 NE2 HIS 36 -20.589 14.895 46.508 1.00 25.09 N ATOM 270 CD2 HIS 36 -21.190 14.325 45.412 1.00 25.19 C ATOM 271 C HIS 36 -19.892 14.308 40.595 1.00 22.93 C ATOM 272 O HIS 36 -18.917 13.731 40.137 1.00 21.39 O ATOM 273 N GLU 37 -20.999 14.541 39.885 1.00 22.26 N ATOM 274 CA GLU 37 -21.092 14.168 38.459 1.00 24.17 C ATOM 275 CB GLU 37 -22.455 14.432 37.835 1.00 28.48 C ATOM 276 CG GLU 37 -23.492 13.483 38.042 1.00 36.15 C ATOM 277 CD GLU 37 -24.643 13.586 36.969 1.00 40.69 C ATOM 278 OE1 GLU 37 -24.617 14.373 35.925 1.00 39.54 O ATOM 279 OE2 GLU 37 -25.597 12.857 37.206 1.00 43.28 O ATOM 280 C GLU 37 -20.189 15.001 37.630 1.00 21.49 C ATOM 281 O GLU 37 -19.411 14.460 36.862 1.00 23.21 O ATOM 282 N GLN 38 -20.223 16.322 37.825 1.00 20.99 N ATOM 283 CA GLN 38 -19.235 17.205 37.173 1.00 21.90 C ATOM 284 CB GLN 38 -19.502 18.667 37.452 1.00 22.34 C ATOM 285 CG GLN 38 -20.766 19.152 36.712 1.00 25.80 C ATOM 286 CD GLN 38 -20.965 20.641 36.916 1.00 29.36 C ATOM 287 OE1 GLN 38 -21.794 21.094 37.687 1.00 31.01 O ATOM 288 NE2 GLN 38 -20.151 21.395 36.230 1.00 28.88 N ATOM 289 C GLN 38 -17.798 16.882 37.515 1.00 20.66 C ATOM 290 O GLN 38 -16.915 16.881 36.621 1.00 21.08 O ATOM 291 N ALA 39 -17.528 16.590 38.791 1.00 18.06 N ATOM 292 CA ALA 39 -16.185 16.215 39.210 1.00 18.07 C ATOM 293 CB ALA 39 -16.172 15.872 40.688 1.00 19.27 C ATOM 294 C ALA 39 -15.707 14.991 38.444 1.00 18.16 C ATOM 295 O ALA 39 -14.561 14.919 38.018 1.00 18.47 O ATOM 296 N ALA 40 -16.574 14.006 38.306 1.00 18.41 N ATOM 297 CA ALA 40 -16.217 12.771 37.615 1.00 19.56 C ATOM 298 CB ALA 40 -17.330 11.751 37.778 1.00 21.48 C ATOM 299 C ALA 40 -15.915 12.997 36.113 1.00 19.26 C ATOM 300 O ALA 40 -15.060 12.317 35.544 1.00 18.71 O ATOM 301 N HIS 41 -16.603 13.926 35.483 1.00 19.59 N ATOM 302 CA HIS 41 -16.352 14.272 34.065 1.00 20.53 C ATOM 303 CB HIS 41 -17.407 15.269 33.570 1.00 22.85 C ATOM 304 CG HIS 41 -17.490 15.370 32.073 1.00 25.24 C ATOM 305 ND1 HIS 41 -18.164 16.391 31.436 1.00 28.24 N ATOM 306 CE1 HIS 41 -18.113 16.206 30.130 1.00 30.27 C ATOM 307 NE2 HIS 41 -17.338 15.151 29.894 1.00 27.86 N ATOM 308 CD2 HIS 41 -16.935 14.617 31.089 1.00 25.45 C ATOM 309 C HIS 41 -14.930 14.842 33.917 1.00 19.75 C ATOM 310 O HIS 41 -14.156 14.417 33.043 1.00 20.03 O ATOM 311 N HIS 42 -14.537 15.686 34.857 1.00 18.53 N ATOM 312 CA HIS 42 -13.179 16.132 34.946 1.00 18.49 C ATOM 313 CB HIS 42 -12.998 17.251 35.975 1.00 18.57 C ATOM 314 CG HIS 42 -13.527 18.570 35.548 1.00 19.73 C ATOM 315 ND1 HIS 42 -12.868 19.388 34.651 1.00 20.99 N ATOM 316 CE1 HIS 42 -13.537 20.517 34.509 1.00 22.04 C ATOM 317 NE2 HIS 42 -14.623 20.442 35.255 1.00 20.99 N ATOM 318 CD2 HIS 42 -14.655 19.220 35.882 1.00 21.94 C ATOM 319 C HIS 42 -12.181 14.994 35.259 1.00 20.05 C ATOM 320 O HIS 42 -11.104 14.978 34.671 1.00 19.75 O ATOM 321 N ALA 43 -12.553 14.083 36.145 1.00 20.07 N ATOM 322 CA ALA 43 -11.686 12.946 36.534 1.00 19.92 C ATOM 323 CB ALA 43 -12.365 12.143 37.659 1.00 21.82 C ATOM 324 C ALA 43 -11.376 12.018 35.341 1.00 19.13 C ATOM 325 O ALA 43 -10.246 11.584 35.165 1.00 17.92 O ATOM 326 N ASP 44 -12.401 11.654 34.586 1.00 18.43 N ATOM 327 CA ASP 44 -12.274 10.766 33.401 1.00 20.01 C ATOM 328 CB ASP 44 -13.667 10.405 32.848 1.00 22.18 C ATOM 329 CG ASP 44 -13.653 9.296 31.834 1.00 23.75 C ATOM 330 OD1 ASP 44 -12.877 8.312 31.982 1.00 24.33 O ATOM 331 OD2 ASP 44 -14.478 9.360 30.880 1.00 27.91 O ATOM 332 C ASP 44 -11.381 11.446 32.333 1.00 20.33 C ATOM 333 O ASP 44 -10.551 10.812 31.704 1.00 18.23 O ATOM 334 N THR 45 -11.473 12.766 32.241 1.00 20.06 N ATOM 335 CA THR 45 -10.607 13.524 31.349 1.00 20.30 C ATOM 336 CB THR 45 -11.100 15.002 31.241 1.00 19.99 C ATOM 337 OG1 THR 45 -12.489 14.976 30.940 1.00 20.29 O ATOM 338 CG2 THR 45 -10.370 15.732 30.139 1.00 21.20 C ATOM 339 C THR 45 -9.165 13.476 31.818 1.00 20.29 C ATOM 340 O THR 45 -8.274 13.269 31.020 1.00 18.14 O ATOM 341 N ALA 46 -8.942 13.705 33.118 1.00 18.66 N ATOM 342 CA ALA 46 -7.611 13.549 33.666 1.00 17.45 C ATOM 343 CB ALA 46 -7.591 13.933 35.142 1.00 17.98 C ATOM 344 C ALA 46 -7.027 12.151 33.486 1.00 16.43 C ATOM 345 O ALA 46 -5.818 12.024 33.256 1.00 15.39 O ATOM 346 N TYR 47 -7.850 11.118 33.608 1.00 16.08 N ATOM 347 CA TYR 47 -7.385 9.751 33.366 1.00 18.35 C ATOM 348 CB TYR 47 -8.528 8.785 33.696 1.00 21.00 C ATOM 349 CG TYR 47 -8.306 7.341 33.292 1.00 26.17 C ATOM 350 CD1 TYR 47 -7.389 6.533 33.948 1.00 29.78 C ATOM 351 CE1 TYR 47 -7.201 5.220 33.554 1.00 33.21 C ATOM 352 CZ TYR 47 -7.995 4.699 32.549 1.00 36.49 C ATOM 353 OH TYR 47 -7.899 3.359 32.105 1.00 50.76 O ATOM 354 CE2 TYR 47 -8.909 5.489 31.920 1.00 34.37 C ATOM 355 CD2 TYR 47 -9.046 6.791 32.269 1.00 29.11 C ATOM 356 C TYR 47 -6.863 9.577 31.930 1.00 18.98 C ATOM 357 O TYR 47 -5.813 8.960 31.727 1.00 19.12 O ATOM 358 N ALA 48 -7.646 10.047 30.936 1.00 18.23 N ATOM 359 CA ALA 48 -7.150 10.051 29.550 1.00 19.52 C ATOM 360 CB ALA 48 -8.158 10.734 28.606 1.00 20.43 C ATOM 361 C ALA 48 -5.785 10.698 29.439 1.00 18.15 C ATOM 362 O ALA 48 -4.868 10.134 28.824 1.00 19.55 O ATOM 363 N HIS 49 -5.640 11.910 29.962 1.00 18.92 N ATOM 364 CA HIS 49 -4.348 12.580 29.888 1.00 19.26 C ATOM 365 CB HIS 49 -4.451 14.052 30.325 1.00 19.74 C ATOM 366 CG HIS 49 -5.206 14.890 29.342 1.00 22.70 C ATOM 367 ND1 HIS 49 -4.709 15.188 28.094 1.00 25.38 N ATOM 368 CE1 HIS 49 -5.614 15.875 27.405 1.00 26.82 C ATOM 369 NE2 HIS 49 -6.677 16.043 28.172 1.00 26.24 N ATOM 370 CD2 HIS 49 -6.454 15.426 29.384 1.00 24.79 C ATOM 371 C HIS 49 -3.214 11.837 30.647 1.00 19.53 C ATOM 372 O HIS 49 -2.075 11.823 30.191 1.00 19.13 O ATOM 373 N HIS 50 -3.531 11.220 31.774 1.00 17.07 N ATOM 374 CA HIS 50 -2.552 10.415 32.517 0.50 18.52 C ATOM 376 CB HIS 50 -3.093 9.899 33.891 0.50 18.85 C ATOM 378 CG HIS 50 -2.006 9.665 34.905 0.50 20.26 C ATOM 380 ND1 HIS 50 -2.241 9.569 36.258 0.50 22.18 N ATOM 382 CE1 HIS 50 -1.102 9.390 36.897 0.50 21.49 C ATOM 384 NE2 HIS 50 -0.131 9.390 36.010 0.50 22.61 N ATOM 386 CD2 HIS 50 -0.665 9.569 34.759 0.50 20.30 C ATOM 388 C HIS 50 -2.083 9.252 31.650 1.00 19.48 C ATOM 389 O HIS 50 -0.862 8.953 31.644 1.00 18.46 O ATOM 390 N LYS 51 -3.004 8.625 30.889 1.00 18.64 N ATOM 391 CA LYS 51 -2.647 7.504 30.030 1.00 22.17 C ATOM 392 CB LYS 51 -3.865 6.732 29.509 1.00 23.92 C ATOM 393 CG LYS 51 -4.671 6.098 30.626 1.00 28.61 C ATOM 394 CD LYS 51 -3.918 5.019 31.424 1.00 32.09 C ATOM 395 CE LYS 51 -3.552 3.831 30.578 1.00 37.92 C ATOM 396 NZ LYS 51 -3.301 2.628 31.446 1.00 46.69 N ATOM 397 C LYS 51 -1.761 7.978 28.893 1.00 21.90 C ATOM 398 O LYS 51 -0.732 7.336 28.565 1.00 20.42 O ATOM 399 N HIS 52 -2.113 9.114 28.337 1.00 19.59 N ATOM 400 CA HIS 52 -1.272 9.728 27.261 1.00 21.61 C ATOM 401 CB HIS 52 -1.947 11.025 26.691 1.00 20.00 C ATOM 402 CG HIS 52 -3.051 10.804 25.704 1.00 22.59 C ATOM 403 ND1 HIS 52 -2.899 10.092 24.544 1.00 26.21 N ATOM 404 CE1 HIS 52 -4.024 10.117 23.845 1.00 27.82 C ATOM 405 NE2 HIS 52 -4.905 10.842 24.519 1.00 26.57 N ATOM 406 CD2 HIS 52 -4.307 11.308 25.662 1.00 23.82 C ATOM 407 C HIS 52 0.147 10.043 27.797 1.00 19.38 C ATOM 408 O HIS 52 1.147 9.769 27.119 1.00 20.42 O ATOM 409 N ALA 53 0.227 10.639 28.990 1.00 18.32 N ATOM 410 CA ALA 53 1.452 11.020 29.611 1.00 19.27 C ATOM 411 CB ALA 53 1.218 11.825 30.854 1.00 20.07 C ATOM 412 C ALA 53 2.335 9.808 29.913 1.00 20.76 C ATOM 413 O ALA 53 3.516 9.832 29.602 1.00 19.72 O ATOM 414 N GLU 54 1.736 8.729 30.368 1.00 18.52 N ATOM 415 CA GLU 54 2.457 7.480 30.668 1.00 23.06 C ATOM 416 CB GLU 54 1.539 6.492 31.411 1.00 23.70 C ATOM 417 CG GLU 54 2.178 5.192 31.830 1.00 30.03 C ATOM 418 CD GLU 54 1.188 4.256 32.584 1.00 38.61 C ATOM 419 OE1 GLU 54 -0.048 4.263 32.302 1.00 41.95 O ATOM 420 OE2 GLU 54 1.676 3.470 33.421 1.00 46.28 O ATOM 421 C GLU 54 3.017 6.835 29.380 1.00 23.32 C ATOM 422 O GLU 54 4.179 6.420 29.368 1.00 21.12 O ATOM 423 N GLU 55 2.231 6.864 28.306 1.00 22.13 N ATOM 424 CA GLU 55 2.673 6.352 27.029 1.00 24.48 C ATOM 425 CB GLU 55 1.522 6.288 26.044 1.00 29.89 C ATOM 426 CG GLU 55 0.630 5.078 26.379 1.00 37.14 C ATOM 427 CD GLU 55 -0.750 5.103 25.718 1.00 46.45 C ATOM 428 OE1 GLU 55 -1.383 6.165 25.613 1.00 47.41 O ATOM 429 OE2 GLU 55 -1.231 4.029 25.326 1.00 51.55 O ATOM 430 C GLU 55 3.852 7.154 26.459 1.00 23.82 C ATOM 431 O GLU 55 4.838 6.567 26.015 1.00 19.95 O ATOM 432 N HIS 56 3.752 8.484 26.505 1.00 19.79 N ATOM 433 CA HIS 56 4.831 9.311 26.029 1.00 20.59 C ATOM 434 CB HIS 56 4.409 10.778 25.915 1.00 19.48 C ATOM 435 CG HIS 56 3.616 11.055 24.675 1.00 21.48 C ATOM 436 ND1 HIS 56 4.169 11.035 23.426 1.00 24.65 N ATOM 437 CE1 HIS 56 3.224 11.248 22.506 1.00 25.36 C ATOM 438 NE2 HIS 56 2.096 11.519 23.149 1.00 25.90 N ATOM 439 CD2 HIS 56 2.310 11.392 24.499 1.00 22.64 C ATOM 440 C HIS 56 6.115 9.153 26.905 1.00 21.52 C ATOM 441 O HIS 56 7.215 9.137 26.385 1.00 20.92 O ATOM 442 N ALA 57 5.960 9.080 28.225 1.00 20.20 N ATOM 443 CA ALA 57 7.129 8.899 29.080 1.00 20.68 C ATOM 444 CB ALA 57 6.706 8.979 30.557 1.00 21.73 C ATOM 445 C ALA 57 7.799 7.542 28.783 1.00 20.46 C ATOM 446 O ALA 57 9.010 7.449 28.770 1.00 20.21 O ATOM 447 N ALA 58 7.018 6.505 28.560 1.00 19.12 N ATOM 448 CA ALA 58 7.540 5.183 28.148 1.00 20.76 C ATOM 449 CB ALA 58 6.421 4.153 28.141 1.00 21.70 C ATOM 450 C ALA 58 8.274 5.235 26.802 1.00 24.26 C ATOM 451 O ALA 58 9.392 4.692 26.684 1.00 22.39 O ATOM 452 N GLN 59 7.685 5.919 25.810 1.00 22.10 N ATOM 453 CA GLN 59 8.345 6.097 24.546 1.00 24.83 C ATOM 454 CB GLN 59 7.408 6.770 23.509 1.00 27.47 C ATOM 455 CG GLN 59 6.183 5.944 23.083 1.00 32.57 C ATOM 456 CD GLN 59 6.494 4.629 22.413 1.00 39.30 C ATOM 457 OE1 GLN 59 5.649 3.716 22.415 1.00 51.33 O ATOM 458 NE2 GLN 59 7.674 4.495 21.838 1.00 43.12 N ATOM 459 C GLN 59 9.637 6.919 24.683 1.00 22.05 C ATOM 460 O GLN 59 10.619 6.595 24.046 1.00 20.52 O ATOM 461 N ALA 60 9.650 7.919 25.541 1.00 20.26 N ATOM 462 CA ALA 60 10.902 8.651 25.785 1.00 20.01 C ATOM 463 CB ALA 60 10.684 9.840 26.678 1.00 19.06 C ATOM 464 C ALA 60 12.022 7.738 26.369 1.00 20.16 C ATOM 465 O ALA 60 13.145 7.795 25.923 1.00 19.12 O ATOM 466 N ALA 61 11.663 6.908 27.360 1.00 20.28 N ATOM 467 CA ALA 61 12.590 6.000 27.954 1.00 18.96 C ATOM 468 CB ALA 61 11.959 5.398 29.246 1.00 18.33 C ATOM 469 C ALA 61 13.085 4.913 27.010 1.00 20.20 C ATOM 470 O ALA 61 14.266 4.583 27.036 1.00 18.84 O ATOM 471 N LYS 62 12.207 4.394 26.165 1.00 20.04 N ATOM 472 CA LYS 62 12.568 3.417 25.183 1.00 23.38 C ATOM 473 CB LYS 62 11.316 2.852 24.483 1.00 24.57 C ATOM 474 CG LYS 62 10.496 1.899 25.369 1.00 27.81 C ATOM 475 CD LYS 62 9.190 1.538 24.686 1.00 30.36 C ATOM 476 CE LYS 62 8.263 0.741 25.611 1.00 32.39 C ATOM 477 NZ LYS 62 7.017 0.386 24.910 1.00 35.67 N ATOM 478 C LYS 62 13.531 3.985 24.158 1.00 22.54 C ATOM 479 O LYS 62 14.513 3.321 23.786 1.00 20.93 O ATOM 480 N HIS 63 13.309 5.232 23.772 1.00 22.27 N ATOM 481 CA HIS 63 14.261 5.906 22.899 1.00 23.11 C ATOM 482 CB HIS 63 13.835 7.362 22.607 1.00 23.92 C ATOM 483 CG HIS 63 14.883 8.127 21.857 1.00 24.19 C ATOM 484 ND1 HIS 63 14.927 8.157 20.481 1.00 29.15 N ATOM 485 CE1 HIS 63 15.975 8.874 20.087 1.00 30.23 C ATOM 486 NE2 HIS 63 16.590 9.331 21.161 1.00 28.89 N ATOM 487 CD2 HIS 63 15.925 8.872 22.283 1.00 25.99 C ATOM 488 C HIS 63 15.664 5.968 23.523 1.00 22.57 C ATOM 489 O HIS 63 16.671 5.581 22.907 1.00 23.72 O ATOM 490 N ASP 64 15.725 6.506 24.725 1.00 22.15 N ATOM 491 CA ASP 64 17.016 6.582 25.424 1.00 23.23 C ATOM 492 CB ASP 64 16.874 7.246 26.783 1.00 22.79 C ATOM 493 CG ASP 64 16.321 8.643 26.691 1.00 22.75 C ATOM 494 OD1 ASP 64 16.288 9.259 25.567 1.00 21.10 O ATOM 495 OD2 ASP 64 15.907 9.128 27.778 1.00 22.28 O ATOM 496 C ASP 64 17.707 5.247 25.581 1.00 22.83 C ATOM 497 O ASP 64 18.949 5.190 25.493 1.00 23.24 O ATOM 498 N ALA 65 16.944 4.205 25.877 1.00 21.46 N ATOM 499 CA ALA 65 17.548 2.873 26.059 1.00 23.58 C ATOM 500 CB ALA 65 16.561 1.895 26.599 1.00 23.40 C ATOM 501 C ALA 65 18.181 2.341 24.793 1.00 26.06 C ATOM 502 O ALA 65 19.150 1.527 24.838 1.00 26.02 O ATOM 503 N GLU 66 17.647 2.754 23.654 1.00 26.14 N ATOM 504 CA GLU 66 18.204 2.318 22.389 1.00 30.23 C ATOM 505 CB GLU 66 17.096 2.173 21.301 1.00 35.26 C ATOM 506 CG GLU 66 16.112 1.075 21.595 1.00 43.72 C ATOM 507 CD GLU 66 16.754 -0.204 22.205 1.00 54.56 C ATOM 508 OE1 GLU 66 17.762 -0.694 21.631 1.00 54.52 O ATOM 509 OE2 GLU 66 16.249 -0.731 23.259 1.00 50.61 O ATOM 510 C GLU 66 19.330 3.216 21.923 1.00 27.48 C ATOM 511 O GLU 66 20.221 2.757 21.225 1.00 29.09 O ATOM 512 N HIS 67 19.319 4.488 22.293 1.00 25.20 N ATOM 513 CA HIS 67 20.338 5.450 21.808 1.00 26.76 C ATOM 514 CB HIS 67 19.646 6.697 21.234 1.00 27.50 C ATOM 515 CG HIS 67 18.847 6.402 19.997 1.00 28.52 C ATOM 516 ND1 HIS 67 19.400 6.419 18.741 1.00 30.73 N ATOM 517 CE1 HIS 67 18.477 6.081 17.845 1.00 33.17 C ATOM 518 NE2 HIS 67 17.349 5.826 18.490 1.00 29.69 N ATOM 519 CD2 HIS 67 17.551 6.033 19.839 1.00 27.50 C ATOM 520 C HIS 67 21.416 5.932 22.777 1.00 27.40 C ATOM 521 O HIS 67 22.508 6.313 22.340 1.00 27.82 O ATOM 522 N HIS 68 21.090 6.000 24.057 1.00 24.16 N ATOM 523 CA HIS 68 21.933 6.663 25.062 1.00 28.15 C ATOM 524 CB HIS 68 21.241 7.951 25.553 1.00 26.46 C ATOM 525 CG HIS 68 20.793 8.825 24.449 1.00 26.58 C ATOM 526 ND1 HIS 68 21.649 9.252 23.466 1.00 27.31 N ATOM 527 CE1 HIS 68 20.989 10.013 22.618 1.00 30.50 C ATOM 528 NE2 HIS 68 19.737 10.115 23.046 1.00 29.67 N ATOM 529 CD2 HIS 68 19.600 9.412 24.201 1.00 26.05 C ATOM 530 C HIS 68 22.197 5.823 26.324 1.00 26.66 C ATOM 531 O HIS 68 22.567 6.392 27.340 1.00 31.08 O ATOM 532 N ALA 69 21.960 4.528 26.282 1.00 24.14 N ATOM 533 CA ALA 69 21.966 3.753 27.495 1.00 24.05 C ATOM 534 CB ALA 69 21.471 2.352 27.213 1.00 26.83 C ATOM 535 C ALA 69 23.376 3.647 28.101 1.00 23.36 C ATOM 536 O ALA 69 24.356 3.460 27.388 1.00 23.22 O ATOM 537 N PRO 70 23.455 3.722 29.409 1.00 21.34 N ATOM 538 CA PRO 70 24.707 3.337 30.043 1.00 23.52 C ATOM 539 CB PRO 70 24.465 3.657 31.485 1.00 22.92 C ATOM 540 CG PRO 70 23.010 3.554 31.671 1.00 23.63 C ATOM 541 CD PRO 70 22.396 3.970 30.386 1.00 23.32 C ATOM 542 C PRO 70 24.979 1.844 29.891 1.00 24.57 C ATOM 543 O PRO 70 24.048 1.066 29.730 1.00 25.67 O ATOM 544 N LYS 71 26.226 1.450 30.000 1.00 28.10 N ATOM 545 CA LYS 71 26.567 0.030 30.004 1.00 31.51 C ATOM 546 CB LYS 71 28.036 -0.161 29.752 1.00 34.45 C ATOM 547 CG LYS 71 28.516 0.340 28.382 1.00 42.64 C ATOM 548 CD LYS 71 27.700 -0.273 27.240 1.00 48.70 C ATOM 549 CE LYS 71 28.466 -0.286 25.912 1.00 56.88 C ATOM 550 NZ LYS 71 28.797 1.100 25.471 1.00 58.35 N ATOM 551 C LYS 71 26.179 -0.640 31.339 1.00 31.82 C ATOM 552 O LYS 71 26.293 -0.039 32.394 1.00 29.17 O ATOM 553 N PRO 72 25.741 -1.901 31.283 1.00 30.89 N ATOM 554 CA PRO 72 25.583 -2.623 32.530 1.00 31.19 C ATOM 555 CB PRO 72 24.985 -3.984 32.090 1.00 34.88 C ATOM 556 CG PRO 72 25.441 -4.141 30.658 1.00 35.62 C ATOM 557 CD PRO 72 25.433 -2.732 30.099 1.00 33.42 C ATOM 558 C PRO 72 26.943 -2.802 33.210 1.00 30.02 C ATOM 559 O PRO 72 27.941 -2.617 32.584 1.00 28.88 O ATOM 560 N HIS 73 26.942 -3.154 34.495 1.00 31.37 N ATOM 561 CA HIS 73 28.167 -3.338 35.248 1.00 33.81 C ATOM 562 CB HIS 73 27.983 -2.842 36.691 1.00 33.03 C ATOM 563 CG HIS 73 27.748 -1.368 36.810 1.00 31.07 C ATOM 564 ND1 HIS 73 27.687 -0.715 38.029 1.00 31.82 N ATOM 565 CE1 HIS 73 27.428 0.567 37.822 1.00 30.10 C ATOM 566 NE2 HIS 73 27.343 0.773 36.514 1.00 28.84 N ATOM 567 CD2 HIS 73 27.550 -0.417 35.860 1.00 29.00 C ATOM 568 C HIS 73 28.581 -4.814 35.234 1.00 36.95 C ATOM 569 O HIS 73 27.823 -5.713 34.885 1.00 38.66 O ATOM 570 OXT HIS 73 29.668 -5.117 35.664 1.00 40.37 O TER

the code I use to get the contact map is:

filename='T1084.pdb'
structure = bsio.load_structure(file)
contact = contacts_from_pdb(structure, chain=None) # shape (71, 71), which is not consistent with the length of residues
tomsercu commented 2 years ago

From input examples provided, it probably has to do with biotite loading a mismatched sequence when there are gaps in residue index. But biotite should be able to give the "correct" sequence easily.

naailkhan28 commented 2 years ago

It looks like T1042 does indeed have a length of 73 residues, but from the PDB text you post @zhenyuhe00 the crystal structure only models residues 3-73. This would mean that when you load the coordinates you can only generate a contact map for 71 residues since two are missing from the crystal structure.