| Chain sequence(s) |
A: DVVVTQIPLSLPVSLGDQASISCRSSQSLVHSFGITYLHWYLQKPGQSPKLLIYRVSNRFSGVPDRFSGSGSGTDFTLKISRVAAEDLGVYFCSQTTHVPYTFGGGTKLEIKASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS
B: QVQLQQSGAELARPGASVKLSCKASGYTFTSYGISWVSQRTGQGLEWIGEIYPRTANTYYNEKFKGKATLTADKSSNTAYMELRSLTSEDSAIYFCARKSTDGVDYWGQGTSVTVSSVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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] (00:00:01)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:01)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:01)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:01)
[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 (00:06:03)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/57e5a6f5c14c14e/tmp/folded.pdb (00:06:03)
[INFO] Main: Simulation completed successfully. (00:08:26)
|
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 | D | A | -1.4167 | |
| 2 | V | A | 0.0000 | |
| 3 | V | A | 0.6955 | |
| 4 | V | A | 0.0000 | |
| 5 | T | A | -0.0517 | |
| 6 | Q | A | 0.0000 | |
| 7 | I | A | 1.3329 | |
| 8 | P | A | 1.2522 | |
| 9 | L | A | 1.6372 | |
| 10 | S | A | 0.5536 | |
| 11 | L | A | 0.2587 | |
| 12 | P | A | -0.3565 | |
| 13 | V | A | 0.0000 | |
| 14 | S | A | -0.6882 | |
| 15 | L | A | -0.0038 | |
| 16 | G | A | -1.2427 | |
| 17 | D | A | -2.2774 | |
| 18 | Q | A | -2.6287 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.6815 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.3623 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.1355 | |
| 25 | S | A | -1.1535 | |
| 26 | S | A | -1.0023 | |
| 27 | Q | A | -1.5431 | |
| 28 | S | A | -0.9441 | |
| 29 | L | A | 0.0000 | |
| 30 | V | A | 1.0025 | |
| 31 | H | A | 0.8363 | |
| 32 | S | A | 0.8257 | |
| 33 | F | A | 1.8980 | |
| 34 | G | A | 0.9466 | |
| 35 | I | A | 1.0900 | |
| 36 | T | A | 0.6537 | |
| 37 | Y | A | 0.2166 | |
| 38 | L | A | 0.0000 | |
| 39 | H | A | 0.0000 | |
| 40 | W | A | 0.0000 | |
| 41 | Y | A | 0.0000 | |
| 42 | L | A | 0.0000 | |
| 43 | Q | A | -1.0287 | |
| 44 | K | A | -1.4750 | |
| 45 | P | A | -0.9551 | |
| 46 | G | A | -1.4374 | |
| 47 | Q | A | -2.1015 | |
| 48 | S | A | -1.3728 | |
| 49 | P | A | 0.0000 | |
| 50 | K | A | -1.2309 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | -0.4035 | |
| 55 | R | A | -0.5171 | |
| 56 | V | A | 0.0000 | |
| 57 | S | A | -0.7921 | |
| 58 | N | A | -0.9704 | |
| 59 | R | A | -1.3023 | |
| 60 | F | A | -0.5071 | |
| 61 | S | A | -0.4600 | |
| 62 | G | A | -0.7454 | |
| 63 | V | A | -0.8919 | |
| 64 | P | A | -1.2374 | |
| 65 | D | A | -2.3768 | |
| 66 | R | A | -2.1381 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.2527 | |
| 69 | G | A | -0.8130 | |
| 70 | S | A | -0.8877 | |
| 71 | G | A | -1.0392 | |
| 72 | S | A | -0.7571 | |
| 73 | G | A | -0.8134 | |
| 74 | T | A | -1.5515 | |
| 75 | D | A | -2.2192 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -0.8713 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -1.5879 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.4650 | |
| 82 | R | A | -2.8626 | |
| 83 | V | A | 0.0000 | |
| 84 | A | A | -0.9063 | |
| 85 | A | A | -0.4561 | |
| 86 | E | A | -1.7288 | |
| 87 | D | A | 0.0000 | |
| 88 | L | A | -0.4132 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | 0.0179 | |
| 91 | Y | A | 0.0000 | |
| 92 | F | A | 0.0000 | |
| 93 | C | A | 0.0000 | |
| 94 | S | A | 0.0000 | |
| 95 | Q | A | 0.0000 | |
| 96 | T | A | -0.0151 | |
| 97 | T | A | 0.0688 | |
| 98 | H | A | -0.3355 | |
| 99 | V | A | 0.2230 | |
| 100 | P | A | -0.4717 | |
| 101 | Y | A | 0.0000 | |
| 102 | T | A | 0.0114 | |
| 103 | F | A | 0.2270 | |
| 104 | G | A | 0.0000 | |
| 105 | G | A | -0.2073 | |
| 106 | G | A | 0.0362 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.4613 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -0.2108 | |
| 111 | I | A | 0.0490 | |
| 112 | K | A | -0.7101 | |
| 113 | A | A | -0.5423 | |
| 114 | S | A | -0.7548 | |
| 115 | T | A | -1.1890 | |
| 116 | K | A | -1.7904 | |
| 117 | G | A | -1.6866 | |
| 118 | P | A | 0.0000 | |
| 119 | S | A | -0.5864 | |
| 120 | V | A | 0.0000 | |
| 121 | F | A | 0.0000 | |
| 122 | P | A | -1.1759 | |
| 123 | L | A | 0.0000 | |
| 124 | A | A | -1.2875 | |
| 125 | P | A | 0.0000 | |
| 126 | S | A | -0.9288 | |
| 127 | S | A | -0.6539 | |
| 128 | K | A | -0.5320 | |
| 129 | S | A | 0.0000 | |
| 130 | T | A | -0.4994 | |
| 131 | S | A | -0.5927 | |
| 132 | G | A | -0.7916 | |
| 133 | G | A | -0.8636 | |
| 134 | T | A | -0.5834 | |
| 135 | A | A | 0.0000 | |
| 136 | A | A | 0.0000 | |
| 137 | L | A | 0.0000 | |
| 138 | G | A | 0.0000 | |
| 139 | C | A | 0.0000 | |
| 140 | L | A | 0.0000 | |
| 141 | V | A | 0.0000 | |
| 142 | K | A | 0.0000 | |
| 143 | D | A | -0.6652 | |
| 144 | Y | A | 0.0000 | |
| 145 | F | A | 0.0000 | |
| 146 | P | A | 0.0000 | |
| 147 | E | A | -0.7400 | |
| 148 | P | A | -0.4724 | |
| 149 | V | A | -0.6058 | |
| 150 | T | A | -0.5430 | |
| 151 | V | A | -0.1314 | |
| 152 | S | A | -0.3318 | |
| 153 | W | A | 0.0000 | |
| 154 | N | A | -0.6855 | |
| 155 | S | A | -0.6134 | |
| 156 | G | A | -0.5263 | |
| 157 | A | A | -0.2499 | |
| 158 | L | A | -0.0166 | |
| 159 | T | A | -0.2043 | |
| 160 | S | A | -0.2380 | |
| 161 | G | A | -0.3294 | |
| 162 | V | A | 0.1141 | |
| 163 | H | A | -0.3187 | |
| 164 | T | A | 0.0146 | |
| 165 | F | A | 0.0000 | |
| 166 | P | A | -0.2752 | |
| 167 | A | A | 0.2073 | |
| 168 | V | A | 0.3698 | |
| 169 | L | A | 0.8158 | |
| 170 | Q | A | 0.1003 | |
| 171 | S | A | -0.1429 | |
| 172 | S | A | -0.2888 | |
| 173 | G | A | -0.0811 | |
| 174 | L | A | -0.1287 | |
| 175 | Y | A | 0.1799 | |
| 176 | S | A | 0.0000 | |
| 177 | L | A | 0.0000 | |
| 178 | S | A | 0.0000 | |
| 179 | S | A | 0.0000 | |
| 180 | V | A | 0.0000 | |
| 181 | V | A | 0.0000 | |
| 182 | T | A | -0.1687 | |
| 183 | V | A | 0.0000 | |
| 184 | P | A | -0.6008 | |
| 185 | S | A | -0.5524 | |
| 186 | S | A | -0.5570 | |
| 187 | S | A | -0.5289 | |
| 188 | L | A | -0.7468 | |
| 189 | G | A | -0.9328 | |
| 190 | T | A | -0.6502 | |
| 191 | Q | A | -1.0709 | |
| 192 | T | A | -0.9911 | |
| 193 | Y | A | 0.0000 | |
| 194 | I | A | -1.1052 | |
| 195 | C | A | 0.0000 | |
| 196 | N | A | -1.3499 | |
| 197 | V | A | 0.0000 | |
| 198 | N | A | -1.8115 | |
| 199 | H | A | 0.0000 | |
| 200 | K | A | -2.7173 | |
| 201 | P | A | -1.7177 | |
| 202 | S | A | -2.0013 | |
| 203 | N | A | -2.6792 | |
| 204 | T | A | -2.1558 | |
| 205 | K | A | -2.6352 | |
| 206 | V | A | -1.4844 | |
| 207 | D | A | -2.1482 | |
| 208 | K | A | -2.1050 | |
| 209 | K | A | -2.3655 | |
| 210 | V | A | 0.0000 | |
| 211 | E | A | -2.8383 | |
| 212 | P | A | -1.9672 | |
| 213 | K | A | -2.2388 | |
| 214 | S | A | -1.3423 | |
| 1 | Q | B | -1.5760 | |
| 2 | V | B | -1.0734 | |
| 3 | Q | B | -2.0491 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -2.1561 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -1.1070 | |
| 8 | G | B | -0.9533 | |
| 9 | A | B | -0.1680 | |
| 10 | E | B | -0.3140 | |
| 11 | L | B | 0.7221 | |
| 12 | A | B | -0.5149 | |
| 13 | R | B | -1.8304 | |
| 14 | P | B | -1.6376 | |
| 15 | G | B | -1.4965 | |
| 16 | A | B | -1.3906 | |
| 17 | S | B | -1.8220 | |
| 18 | V | B | 0.0000 | |
| 19 | K | B | -2.0898 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -0.8612 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -1.7176 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.3714 | |
| 26 | G | B | -1.1246 | |
| 27 | Y | B | -0.4752 | |
| 28 | T | B | -0.1454 | |
| 29 | F | B | 0.0000 | |
| 30 | T | B | -1.1667 | |
| 31 | S | B | -0.4126 | |
| 32 | Y | B | -0.0201 | |
| 33 | G | B | 0.0000 | |
| 34 | I | B | 0.0000 | |
| 35 | S | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | S | B | 0.0000 | |
| 39 | Q | B | -0.5726 | |
| 40 | R | B | -1.4510 | |
| 41 | T | B | -1.8363 | |
| 42 | G | B | -1.6311 | |
| 43 | Q | B | -1.8339 | |
| 44 | G | B | -1.2306 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -0.7625 | |
| 47 | W | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | G | B | 0.0000 | |
| 50 | E | B | 0.0000 | |
| 51 | I | B | 0.0000 | |
| 52 | Y | B | -0.4588 | |
| 53 | P | B | 0.0000 | |
| 54 | R | B | -2.3076 | |
| 55 | T | B | -1.2665 | |
| 56 | A | B | -1.2864 | |
| 57 | N | B | -1.2165 | |
| 58 | T | B | 0.0936 | |
| 59 | Y | B | 0.8322 | |
| 60 | Y | B | -0.3103 | |
| 61 | N | B | 0.0000 | |
| 62 | E | B | -2.9785 | |
| 63 | K | B | -3.1471 | |
| 64 | F | B | 0.0000 | |
| 65 | K | B | -2.9024 | |
| 66 | G | B | -2.2439 | |
| 67 | K | B | -2.2762 | |
| 68 | A | B | 0.0000 | |
| 69 | T | B | -1.1040 | |
| 70 | L | B | 0.0000 | |
| 71 | T | B | -0.5171 | |
| 72 | A | B | -1.2884 | |
| 73 | D | B | -2.0396 | |
| 74 | K | B | -2.6279 | |
| 75 | S | B | -1.4341 | |
| 76 | S | B | -1.3301 | |
| 77 | N | B | -1.7064 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.5433 | |
| 81 | M | B | 0.0000 | |
| 82 | E | B | -1.7470 | |
| 83 | L | B | 0.0000 | |
| 84 | R | B | -2.5863 | |
| 85 | S | B | -1.6756 | |
| 86 | L | B | 0.0000 | |
| 87 | T | B | -1.8040 | |
| 88 | S | B | -2.1751 | |
| 89 | E | B | -2.6605 | |
| 90 | D | B | 0.0000 | |
| 91 | S | B | 0.0000 | |
| 92 | A | B | 0.0000 | |
| 93 | I | B | 0.4704 | |
| 94 | Y | B | 0.0000 | |
| 95 | F | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | R | B | 0.0000 | |
| 99 | K | B | -0.1290 | |
| 100 | S | B | -0.1836 | |
| 101 | T | B | -0.2654 | |
| 102 | D | B | -0.4696 | |
| 103 | G | B | 0.0000 | |
| 104 | V | B | 0.0000 | |
| 105 | D | B | 0.0000 | |
| 106 | Y | B | -0.1879 | |
| 107 | W | B | -0.6175 | |
| 108 | G | B | 0.0000 | |
| 109 | Q | B | -1.8426 | |
| 110 | G | B | -0.8562 | |
| 111 | T | B | 0.0000 | |
| 112 | S | B | 0.0004 | |
| 113 | V | B | 0.0000 | |
| 114 | T | B | -0.1023 | |
| 115 | V | B | 0.0000 | |
| 116 | S | B | -0.4506 | |
| 117 | S | B | 0.0892 | |
| 118 | V | B | 0.8471 | |
| 119 | A | B | 0.0378 | |
| 120 | A | B | -0.0618 | |
| 121 | P | B | 0.0000 | |
| 122 | S | B | -0.1810 | |
| 123 | V | B | 0.0000 | |
| 124 | F | B | 0.0000 | |
| 125 | I | B | 0.0000 | |
| 126 | F | B | 0.0000 | |
| 127 | P | B | -0.7715 | |
| 128 | P | B | -0.8441 | |
| 129 | S | B | -1.8375 | |
| 130 | D | B | -3.0217 | |
| 131 | E | B | -3.1784 | |
| 132 | Q | B | 0.0000 | |
| 133 | L | B | -2.2762 | |
| 134 | K | B | -2.8846 | |
| 135 | S | B | -1.7890 | |
| 136 | G | B | -1.2403 | |
| 137 | T | B | -1.2566 | |
| 138 | A | B | 0.0000 | |
| 139 | S | B | 0.0000 | |
| 140 | V | B | 0.0000 | |
| 141 | V | B | 0.0000 | |
| 142 | C | B | 0.0000 | |
| 143 | L | B | 0.0000 | |
| 144 | L | B | 0.0000 | |
| 145 | N | B | 0.0000 | |
| 146 | N | B | -1.0276 | |
| 147 | F | B | 0.0000 | |
| 148 | Y | B | 0.0000 | |
| 149 | P | B | -1.3122 | |
| 150 | R | B | -3.0844 | |
| 151 | E | B | -3.2771 | |
| 152 | A | B | -2.3494 | |
| 153 | K | B | -2.4636 | |
| 154 | V | B | -1.1779 | |
| 155 | Q | B | -0.8115 | |
| 156 | W | B | 0.0000 | |
| 157 | K | B | -0.7729 | |
| 158 | V | B | 0.0000 | |
| 159 | D | B | -2.0583 | |
| 160 | N | B | -1.6566 | |
| 161 | A | B | -0.4592 | |
| 162 | L | B | 0.3409 | |
| 163 | Q | B | -0.4962 | |
| 164 | S | B | -0.8307 | |
| 165 | G | B | -1.2986 | |
| 166 | N | B | -1.6324 | |
| 167 | S | B | -1.4483 | |
| 168 | Q | B | -1.4381 | |
| 169 | E | B | -1.4803 | |
| 170 | S | B | -0.7271 | |
| 171 | V | B | -0.5501 | |
| 172 | T | B | -1.1271 | |
| 173 | E | B | -2.2190 | |
| 174 | Q | B | 0.0000 | |
| 175 | D | B | -2.3025 | |
| 176 | S | B | -2.5713 | |
| 177 | K | B | -2.8838 | |
| 178 | D | B | -2.3091 | |
| 179 | S | B | 0.0000 | |
| 180 | T | B | 0.0000 | |
| 181 | Y | B | 0.0000 | |
| 182 | S | B | 0.0000 | |
| 183 | L | B | 0.0000 | |
| 184 | S | B | 0.0000 | |
| 185 | S | B | 0.0000 | |
| 186 | T | B | -0.7109 | |
| 187 | L | B | 0.0000 | |
| 188 | T | B | -0.7046 | |
| 189 | L | B | -0.9515 | |
| 190 | S | B | -1.1872 | |
| 191 | K | B | -2.2078 | |
| 192 | A | B | -2.0857 | |
| 193 | D | B | -2.9348 | |
| 194 | Y | B | 0.0000 | |
| 195 | E | B | -3.7309 | |
| 196 | K | B | -3.8119 | |
| 197 | H | B | -3.1685 | |
| 198 | K | B | -3.4179 | |
| 199 | V | B | -1.7910 | |
| 200 | Y | B | 0.0000 | |
| 201 | A | B | 0.0000 | |
| 202 | C | B | 0.0000 | |
| 203 | E | B | -0.9203 | |
| 204 | V | B | 0.0000 | |
| 205 | T | B | -1.2686 | |
| 206 | H | B | 0.0000 | |
| 207 | Q | B | -1.7133 | |
| 208 | G | B | -0.3745 | |
| 209 | L | B | -0.2068 | |
| 210 | S | B | -0.4571 | |
| 211 | S | B | -0.4552 | |
| 212 | P | B | -0.6197 | |
| 213 | V | B | -0.0360 | |
| 214 | T | B | -0.4118 | |
| 215 | K | B | -0.5149 | |
| 216 | S | B | -0.5768 | |
| 217 | F | B | 0.0000 | |
| 218 | N | B | -2.0631 | |
| 219 | R | B | -2.6610 | |
| 220 | G | B | -2.0502 | |
| 221 | E | B | -2.2752 | |
| 222 | C | B | -0.7742 |
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 | -0.7538 | 3.8511 | View | CSV | PDB |
| 4.5 | -0.7988 | 3.8519 | View | CSV | PDB |
| 5.0 | -0.8507 | 3.8545 | View | CSV | PDB |
| 5.5 | -0.8989 | 3.8614 | View | CSV | PDB |
| 6.0 | -0.9313 | 3.8769 | View | CSV | PDB |
| 6.5 | -0.9386 | 3.9011 | View | CSV | PDB |
| 7.0 | -0.9217 | 3.9252 | View | CSV | PDB |
| 7.5 | -0.8896 | 3.9406 | View | CSV | PDB |
| 8.0 | -0.8492 | 3.9474 | View | CSV | PDB |
| 8.5 | -0.8025 | 3.9499 | View | CSV | PDB |
| 9.0 | -0.7496 | 3.9507 | 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