| Chain sequence(s) |
A: QIVLTQSPAIMSASPGEKVTITCSASSSVSYMHWFQQKSGTSPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQRRSFPPTFGGGTKLEIKVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
B: EVQLQQSGPELVKPGASVKISCKASGYTFTDFYMNWVKQSHGKSLEWIGDINPNNGDTSYNQKFKGKATLTVDKSSSTAYMELRSLTSEDSAVYYCARIYYYGSSDYWGQGTTLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS input PDB |
| Selected Chain(s) | A,B |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage | No |
| Dynamic mode | No |
| Automated mutations | No |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:05:24)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/6474dcf9f3f8067/tmp/folded.pdb (00:05:24)
[INFO] Main: Simulation completed successfully. (00:07:37)
|
The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan4D score | mutation |
|---|---|---|---|---|
| 1 | Q | A | -0.4272 | |
| 2 | I | A | 0.3862 | |
| 3 | V | A | 1.4039 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | 0.1509 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.0739 | |
| 8 | P | A | 0.2701 | |
| 9 | A | A | 0.5171 | |
| 10 | I | A | 1.3427 | |
| 11 | M | A | 0.6010 | |
| 12 | S | A | -0.3831 | |
| 13 | A | A | 0.0000 | |
| 14 | S | A | -1.8440 | |
| 15 | P | A | -2.2690 | |
| 16 | G | A | -2.7143 | |
| 17 | E | A | -3.3592 | |
| 18 | K | A | -3.2488 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.6113 | |
| 21 | I | A | 0.0000 | |
| 22 | T | A | -0.2431 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.1199 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | 0.0493 | |
| 27 | S | A | -0.2872 | |
| 28 | S | A | -0.7158 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.7234 | |
| 31 | Y | A | -0.2774 | |
| 32 | M | A | 0.0000 | |
| 33 | H | A | 0.0000 | |
| 34 | W | A | 0.0000 | |
| 35 | F | A | 0.0000 | |
| 36 | Q | A | 0.0000 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -1.3437 | |
| 39 | S | A | -1.1691 | |
| 40 | G | A | -1.0639 | |
| 41 | T | A | -0.8667 | |
| 42 | S | A | -0.7240 | |
| 43 | P | A | 0.0000 | |
| 44 | K | A | -0.7784 | |
| 45 | L | A | 0.0000 | |
| 46 | W | A | -0.1341 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | 0.4954 | |
| 49 | S | A | 0.0000 | |
| 50 | T | A | -0.2223 | |
| 51 | S | A | -0.4574 | |
| 52 | N | A | -0.5533 | |
| 53 | L | A | 0.0353 | |
| 54 | A | A | 0.0000 | |
| 55 | S | A | -0.3695 | |
| 56 | G | A | -0.4004 | |
| 57 | V | A | -0.1219 | |
| 58 | P | A | -0.1444 | |
| 59 | A | A | -0.3091 | |
| 60 | R | A | -1.1911 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.3722 | |
| 63 | G | A | -0.3827 | |
| 64 | S | A | -0.5632 | |
| 65 | G | A | -0.5496 | |
| 66 | S | A | -0.5442 | |
| 67 | G | A | -0.5664 | |
| 68 | T | A | -0.5297 | |
| 69 | S | A | -0.5787 | |
| 70 | Y | A | 0.0000 | |
| 71 | S | A | -0.3447 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.7922 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.3220 | |
| 76 | R | A | -3.5848 | |
| 77 | V | A | 0.0000 | |
| 78 | E | A | -3.0216 | |
| 79 | A | A | -2.3105 | |
| 80 | E | A | -2.6655 | |
| 81 | D | A | 0.0000 | |
| 82 | A | A | 0.0000 | |
| 83 | A | A | 0.0000 | |
| 84 | T | A | 0.0000 | |
| 85 | Y | A | 0.0000 | |
| 86 | Y | A | 0.0000 | |
| 87 | C | A | 0.0000 | |
| 88 | Q | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | R | A | -0.6764 | |
| 91 | R | A | -1.5071 | |
| 92 | S | A | -0.3629 | |
| 93 | F | A | 1.0251 | |
| 94 | P | A | 0.3350 | |
| 95 | P | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.1937 | |
| 98 | G | A | 0.0000 | |
| 99 | G | A | -0.5965 | |
| 100 | G | A | -0.3232 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -0.1138 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.0068 | |
| 105 | I | A | 0.0000 | |
| 106 | K | A | -1.6946 | |
| 107 | V | A | -0.1752 | |
| 108 | A | A | -0.4002 | |
| 109 | A | A | -0.2731 | |
| 110 | P | A | 0.0000 | |
| 111 | S | A | -0.1769 | |
| 112 | V | A | 0.0000 | |
| 113 | F | A | 0.0000 | |
| 114 | I | A | 0.0000 | |
| 115 | F | A | 0.0000 | |
| 116 | P | A | -0.7347 | |
| 117 | P | A | -0.8607 | |
| 118 | S | A | -1.9637 | |
| 119 | D | A | -3.2925 | |
| 120 | E | A | -3.3014 | |
| 121 | Q | A | 0.0000 | |
| 122 | L | A | -2.3196 | |
| 123 | K | A | -2.9784 | |
| 124 | S | A | -1.8611 | |
| 125 | G | A | -1.3062 | |
| 126 | T | A | -1.1429 | |
| 127 | A | A | 0.0000 | |
| 128 | S | A | 0.0000 | |
| 129 | V | A | 0.0000 | |
| 130 | V | A | 0.0000 | |
| 131 | C | A | 0.0000 | |
| 132 | L | A | 0.0000 | |
| 133 | L | A | 0.0000 | |
| 134 | N | A | 0.0000 | |
| 135 | N | A | -0.7527 | |
| 136 | F | A | 0.0000 | |
| 137 | Y | A | -1.2846 | |
| 138 | P | A | -1.9138 | |
| 139 | R | A | -3.2941 | |
| 140 | E | A | -3.2361 | |
| 141 | A | A | -2.3723 | |
| 142 | K | A | -2.4393 | |
| 143 | V | A | -1.1716 | |
| 144 | Q | A | -0.5988 | |
| 145 | W | A | 0.0000 | |
| 146 | K | A | -0.4587 | |
| 147 | V | A | 0.0000 | |
| 148 | D | A | -1.8950 | |
| 149 | N | A | -1.4984 | |
| 150 | A | A | -0.2458 | |
| 151 | L | A | 0.7376 | |
| 152 | Q | A | -0.3138 | |
| 153 | S | A | -0.6717 | |
| 154 | G | A | -1.3130 | |
| 155 | N | A | -1.6624 | |
| 156 | S | A | -1.5862 | |
| 157 | Q | A | -1.6063 | |
| 158 | E | A | -2.0067 | |
| 159 | S | A | -1.0386 | |
| 160 | V | A | -1.0361 | |
| 161 | T | A | -1.0685 | |
| 162 | E | A | -2.0466 | |
| 163 | Q | A | -2.1554 | |
| 164 | D | A | -2.1147 | |
| 165 | S | A | -2.3923 | |
| 166 | K | A | -2.8126 | |
| 167 | D | A | -2.0747 | |
| 168 | S | A | 0.0000 | |
| 169 | T | A | 0.0000 | |
| 170 | Y | A | 0.0000 | |
| 171 | S | A | 0.0000 | |
| 172 | L | A | 0.0000 | |
| 173 | S | A | 0.0000 | |
| 174 | S | A | 0.0000 | |
| 175 | T | A | -0.8618 | |
| 176 | L | A | 0.0000 | |
| 177 | T | A | -0.7151 | |
| 178 | L | A | -0.9129 | |
| 179 | S | A | -1.1462 | |
| 180 | K | A | -2.1009 | |
| 181 | A | A | -1.9365 | |
| 182 | D | A | -2.8198 | |
| 183 | Y | A | 0.0000 | |
| 184 | E | A | -3.1080 | |
| 185 | K | A | -3.4998 | |
| 186 | H | A | -2.8348 | |
| 187 | K | A | -2.9313 | |
| 188 | V | A | -1.2634 | |
| 189 | Y | A | 0.0000 | |
| 190 | A | A | 0.0000 | |
| 191 | C | A | 0.0000 | |
| 192 | E | A | -0.7950 | |
| 193 | V | A | 0.0000 | |
| 194 | T | A | -1.2653 | |
| 195 | H | A | 0.0000 | |
| 196 | Q | A | -2.0531 | |
| 197 | G | A | -0.9006 | |
| 198 | L | A | -0.4414 | |
| 199 | S | A | -0.4957 | |
| 200 | S | A | -0.4832 | |
| 201 | P | A | -0.6253 | |
| 202 | V | A | -0.0696 | |
| 203 | T | A | -0.4133 | |
| 204 | K | A | -0.7667 | |
| 205 | S | A | -0.5983 | |
| 206 | F | A | 0.0000 | |
| 207 | N | A | -1.6523 | |
| 208 | R | A | -2.1504 | |
| 209 | G | A | -1.8090 | |
| 210 | E | A | -2.3086 | |
| 211 | C | A | -1.0374 | |
| 1 | E | B | -2.2823 | |
| 2 | V | B | 0.0000 | |
| 3 | Q | B | -2.2647 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -2.1180 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.9121 | |
| 8 | G | B | -0.8657 | |
| 9 | P | B | -0.6874 | |
| 10 | E | B | -1.0942 | |
| 11 | L | B | -0.5432 | |
| 12 | V | B | -0.8657 | |
| 13 | K | B | -1.9837 | |
| 14 | P | B | -1.6287 | |
| 15 | G | B | -1.3169 | |
| 16 | A | B | -1.1128 | |
| 17 | S | B | -1.4090 | |
| 18 | V | B | 0.0000 | |
| 19 | K | B | -1.8384 | |
| 20 | I | B | 0.0000 | |
| 21 | S | B | -0.7486 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -1.5314 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.4292 | |
| 26 | G | B | -1.4561 | |
| 27 | Y | B | -0.8454 | |
| 28 | T | B | -0.5721 | |
| 29 | F | B | 0.0000 | |
| 30 | T | B | -1.6851 | |
| 31 | D | B | -1.6832 | |
| 32 | F | B | -0.0937 | |
| 33 | Y | B | 0.0471 | |
| 34 | M | B | 0.0000 | |
| 35 | N | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | K | B | 0.0000 | |
| 39 | Q | B | 0.0000 | |
| 40 | S | B | -1.2695 | |
| 41 | H | B | -1.6834 | |
| 42 | G | B | -1.4426 | |
| 43 | K | B | -1.5205 | |
| 44 | S | B | -1.1071 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -0.8309 | |
| 47 | W | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | G | B | 0.0000 | |
| 50 | D | B | 0.0000 | |
| 51 | I | B | 0.0000 | |
| 52 | N | B | -1.5696 | |
| 53 | P | B | 0.0000 | |
| 54 | N | B | -2.8688 | |
| 55 | N | B | -2.7636 | |
| 56 | G | B | -2.2996 | |
| 57 | D | B | -2.4951 | |
| 58 | T | B | -1.1055 | |
| 59 | S | B | -0.5935 | |
| 60 | Y | B | -0.8802 | |
| 61 | N | B | 0.0000 | |
| 62 | Q | B | -2.6256 | |
| 63 | K | B | -2.9224 | |
| 64 | F | B | 0.0000 | |
| 65 | K | B | -2.9099 | |
| 66 | G | B | -2.0118 | |
| 67 | K | B | -1.9174 | |
| 68 | A | B | 0.0000 | |
| 69 | T | B | -0.9639 | |
| 70 | L | B | 0.0000 | |
| 71 | T | B | -0.5559 | |
| 72 | V | B | -1.1855 | |
| 73 | D | B | -1.7046 | |
| 74 | K | B | -2.4359 | |
| 75 | S | B | -1.2364 | |
| 76 | S | B | -1.0532 | |
| 77 | S | B | -1.1436 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.4279 | |
| 81 | M | B | 0.0000 | |
| 82 | E | B | -1.4463 | |
| 83 | L | B | 0.0000 | |
| 84 | R | B | -1.6797 | |
| 85 | S | B | -1.2225 | |
| 86 | L | B | 0.0000 | |
| 87 | T | B | -1.3700 | |
| 88 | S | B | -1.4559 | |
| 89 | E | B | -2.0931 | |
| 90 | D | B | 0.0000 | |
| 91 | S | B | -0.8193 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | -0.0357 | |
| 94 | Y | B | 0.0000 | |
| 95 | Y | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | R | B | 0.0000 | |
| 99 | I | B | 0.0000 | |
| 100 | Y | B | 1.4747 | |
| 101 | Y | B | 1.9387 | |
| 102 | Y | B | 1.0221 | |
| 103 | G | B | 0.5521 | |
| 104 | S | B | 0.0000 | |
| 105 | S | B | 0.0000 | |
| 106 | D | B | 0.2663 | |
| 107 | Y | B | -0.0714 | |
| 108 | W | B | -0.5759 | |
| 109 | G | B | 0.0000 | |
| 110 | Q | B | -1.6199 | |
| 111 | G | B | -0.7857 | |
| 112 | T | B | 0.0000 | |
| 113 | T | B | -0.2718 | |
| 114 | L | B | 0.0000 | |
| 115 | T | B | 0.0000 | |
| 116 | V | B | 0.0000 | |
| 117 | S | B | -0.8034 | |
| 118 | S | B | -0.9014 | |
| 119 | A | B | -0.5212 | |
| 120 | S | B | -0.6365 | |
| 121 | T | B | -0.7694 | |
| 122 | K | B | -1.2866 | |
| 123 | G | B | -1.4430 | |
| 124 | P | B | -0.7041 | |
| 125 | S | B | -0.4459 | |
| 126 | V | B | 0.0000 | |
| 127 | F | B | 0.0000 | |
| 128 | P | B | -1.3782 | |
| 129 | L | B | 0.0000 | |
| 130 | A | B | -1.4094 | |
| 131 | P | B | 0.0000 | |
| 132 | S | B | -0.9985 | |
| 133 | S | B | -0.6806 | |
| 134 | K | B | -1.1325 | |
| 135 | S | B | 0.0000 | |
| 136 | T | B | -0.7251 | |
| 137 | S | B | -0.7018 | |
| 138 | G | B | -0.8240 | |
| 139 | G | B | -0.8785 | |
| 140 | T | B | -0.6092 | |
| 141 | A | B | 0.0000 | |
| 142 | A | B | 0.0000 | |
| 143 | L | B | 0.0000 | |
| 144 | G | B | 0.0000 | |
| 145 | C | B | 0.0000 | |
| 146 | L | B | 0.0000 | |
| 147 | V | B | 0.0000 | |
| 148 | K | B | 0.0000 | |
| 149 | D | B | -0.3919 | |
| 150 | Y | B | 0.0000 | |
| 151 | F | B | 0.0000 | |
| 152 | P | B | 0.0000 | |
| 153 | E | B | -0.6665 | |
| 154 | P | B | -0.8466 | |
| 155 | V | B | -0.8260 | |
| 156 | T | B | -0.7685 | |
| 157 | V | B | -0.5094 | |
| 158 | S | B | -0.4696 | |
| 159 | W | B | 0.0000 | |
| 160 | N | B | -0.7200 | |
| 161 | S | B | -0.6474 | |
| 162 | G | B | -0.5211 | |
| 163 | A | B | -0.2344 | |
| 164 | L | B | 0.0182 | |
| 165 | T | B | -0.1572 | |
| 166 | S | B | -0.1633 | |
| 167 | G | B | -0.1747 | |
| 168 | V | B | 0.1858 | |
| 169 | H | B | -0.2632 | |
| 170 | T | B | 0.0157 | |
| 171 | F | B | 0.0000 | |
| 172 | P | B | -0.3732 | |
| 173 | A | B | 0.2119 | |
| 174 | V | B | 0.5780 | |
| 175 | L | B | 1.3538 | |
| 176 | Q | B | 0.3724 | |
| 177 | S | B | -0.1486 | |
| 178 | S | B | -0.1991 | |
| 179 | G | B | 0.0544 | |
| 180 | L | B | 0.1758 | |
| 181 | Y | B | 0.4594 | |
| 182 | S | B | 0.0000 | |
| 183 | L | B | 0.0000 | |
| 184 | S | B | 0.0000 | |
| 185 | S | B | 0.0000 | |
| 186 | V | B | 0.0000 | |
| 187 | V | B | 0.0000 | |
| 188 | T | B | -0.1226 | |
| 189 | V | B | 0.0000 | |
| 190 | P | B | -0.5340 | |
| 191 | S | B | -0.5751 | |
| 192 | S | B | -0.5816 | |
| 193 | S | B | -0.6058 | |
| 194 | L | B | -0.7585 | |
| 195 | G | B | -0.9379 | |
| 196 | T | B | -0.6910 | |
| 197 | Q | B | -1.1424 | |
| 198 | T | B | -1.1167 | |
| 199 | Y | B | 0.0000 | |
| 200 | I | B | -1.2597 | |
| 201 | C | B | 0.0000 | |
| 202 | N | B | -1.5275 | |
| 203 | V | B | 0.0000 | |
| 204 | N | B | -2.4278 | |
| 205 | H | B | 0.0000 | |
| 206 | K | B | -2.6501 | |
| 207 | P | B | -1.6162 | |
| 208 | S | B | -1.8242 | |
| 209 | N | B | -2.5592 | |
| 210 | T | B | -2.1573 | |
| 211 | K | B | -2.7955 | |
| 212 | V | B | -1.5569 | |
| 213 | D | B | -2.2773 | |
| 214 | K | B | -1.9846 | |
| 215 | K | B | -2.4519 | |
| 216 | V | B | 0.0000 | |
| 217 | E | B | -2.8892 | |
| 218 | P | B | -1.8979 | |
| 219 | K | B | -2.5813 | |
| 220 | S | B | -1.3473 |
Calculations for various pH values
This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is globular. Max score is recommended for pH analysis.
pH |
Average A4D Score |
Max A4D Score |
|||
| 4.0 | -0.7722 | 2.6947 | View | CSV | PDB |
| 4.5 | -0.8135 | 2.6947 | View | CSV | PDB |
| 5.0 | -0.8621 | 2.6947 | View | CSV | PDB |
| 5.5 | -0.9072 | 2.6947 | View | CSV | PDB |
| 6.0 | -0.936 | 2.6947 | View | CSV | PDB |
| 6.5 | -0.9381 | 2.6947 | View | CSV | PDB |
| 7.0 | -0.9136 | 2.6947 | View | CSV | PDB |
| 7.5 | -0.8719 | 2.6947 | View | CSV | PDB |
| 8.0 | -0.8211 | 2.6947 | View | CSV | PDB |
| 8.5 | -0.7647 | 2.6946 | View | CSV | PDB |
| 9.0 | -0.7037 | 2.6946 | View | CSV | PDB |
ALA alanine
ARG arginine
ASN asparagine
ASP aspartic acid
CYS cysteine
GLN glutamine
GLU glutamic acid
GLY glycine
HIS histidine
ILE isoleucine
LEU leucine
LYS lysine
MET methionine
PHE phenylalanine
PRO proline
SER serine
THR threonine
TRP tryptophan
TYR tyrosine
VAL valine