| Chain sequence(s) |
A: EIVLTKSPATLSLSPGERATLSCSASSSVSYMNWYKQKPGLAPRLLIYDTSNLATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSSNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVQKPGASVKVSCKASGYTFNRYTMHWVRQAPGQLLWMGYINPSRGYYNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
B: MQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMGSADDAKKDAAKKDDAKKDDAKKDGSDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARV 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 (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:11:13)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/17303d531bbb659/tmp/folded.pdb (00:11:13)
[INFO] Main: Simulation completed successfully. (00:20:53)
|
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 | E | A | -1.6306 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 1.0769 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.2174 | |
| 6 | K | A | -0.4411 | |
| 7 | S | A | -0.4547 | |
| 8 | P | A | -0.3667 | |
| 9 | A | A | -0.4745 | |
| 10 | T | A | -0.5390 | |
| 11 | L | A | -0.5095 | |
| 12 | S | A | -0.9520 | |
| 13 | L | A | -1.2801 | |
| 14 | S | A | -1.7907 | |
| 15 | P | A | -1.9845 | |
| 16 | G | A | -2.4606 | |
| 17 | E | A | -3.0786 | |
| 18 | R | A | -3.3175 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5523 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.6838 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.8080 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.2681 | |
| 27 | S | A | -0.5707 | |
| 28 | S | A | -0.7676 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.6119 | |
| 31 | Y | A | 0.0000 | |
| 32 | M | A | 0.0000 | |
| 33 | N | A | 0.0000 | |
| 34 | W | A | 0.0000 | |
| 35 | Y | A | 0.0000 | |
| 36 | K | A | -0.3815 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -0.7762 | |
| 39 | P | A | -0.2799 | |
| 40 | G | A | -0.0842 | |
| 41 | L | A | 0.7028 | |
| 42 | A | A | 0.0575 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -0.4088 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.3445 | |
| 49 | D | A | -0.8267 | |
| 50 | T | A | -0.5174 | |
| 51 | S | A | -0.5262 | |
| 52 | N | A | -0.4317 | |
| 53 | L | A | -0.0750 | |
| 54 | A | A | 0.0000 | |
| 55 | T | A | -0.1878 | |
| 56 | G | A | -0.6633 | |
| 57 | I | A | -0.3910 | |
| 58 | P | A | -0.9412 | |
| 59 | D | A | -1.8723 | |
| 60 | R | A | -1.8601 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.6625 | |
| 63 | G | A | 0.0000 | |
| 64 | S | A | -0.8770 | |
| 65 | G | A | -1.1548 | |
| 66 | S | A | -1.0767 | |
| 67 | G | A | -1.0147 | |
| 68 | T | A | -1.2970 | |
| 69 | D | A | -2.1663 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7378 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.7994 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.4327 | |
| 76 | R | A | -3.3744 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.2871 | |
| 79 | P | A | -1.7845 | |
| 80 | E | A | -2.3420 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | 0.0000 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.7400 | |
| 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 | W | A | 0.0000 | |
| 91 | S | A | -0.5152 | |
| 92 | S | A | -1.0641 | |
| 93 | N | A | -1.4254 | |
| 94 | P | A | -1.2942 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.2274 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -1.0517 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.2087 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.5756 | |
| 105 | I | A | -1.2286 | |
| 106 | K | A | -2.0933 | |
| 107 | G | A | -1.6043 | |
| 108 | G | A | -1.4536 | |
| 109 | G | A | -1.2144 | |
| 110 | G | A | -1.4061 | |
| 111 | S | A | -1.0787 | |
| 112 | G | A | -1.5894 | |
| 113 | G | A | -1.5669 | |
| 114 | G | A | -1.5891 | |
| 115 | G | A | -1.5701 | |
| 116 | S | A | -1.0884 | |
| 117 | G | A | -1.2681 | |
| 118 | G | A | -1.2189 | |
| 119 | G | A | -1.3548 | |
| 120 | G | A | -1.4205 | |
| 121 | S | A | -1.3867 | |
| 122 | Q | A | -1.7894 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.5448 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | 0.3107 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.5514 | |
| 129 | G | A | -0.5883 | |
| 130 | A | A | -0.0317 | |
| 131 | E | A | -0.0604 | |
| 132 | V | A | 0.9618 | |
| 133 | Q | A | -0.7693 | |
| 134 | K | A | -2.0762 | |
| 135 | P | A | -2.1661 | |
| 136 | G | A | -1.5340 | |
| 137 | A | A | -1.1929 | |
| 138 | S | A | -1.2630 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -1.8015 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.5927 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -0.9892 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.8231 | |
| 147 | G | A | -0.9535 | |
| 148 | Y | A | -0.6580 | |
| 149 | T | A | -0.6677 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -1.7656 | |
| 152 | R | A | -2.6091 | |
| 153 | Y | A | -0.7858 | |
| 154 | T | A | 0.0000 | |
| 155 | M | A | 0.0000 | |
| 156 | H | A | 0.0000 | |
| 157 | W | A | 0.0000 | |
| 158 | V | A | 0.0000 | |
| 159 | R | A | -0.1600 | |
| 160 | Q | A | -0.3313 | |
| 161 | A | A | -0.7181 | |
| 162 | P | A | -0.7173 | |
| 163 | G | A | -1.0387 | |
| 164 | Q | A | -1.0393 | |
| 165 | L | A | 0.0000 | |
| 166 | L | A | -0.2149 | |
| 167 | W | A | 0.0000 | |
| 168 | M | A | 0.0000 | |
| 169 | G | A | 0.0000 | |
| 170 | Y | A | 0.0000 | |
| 171 | I | A | 0.0000 | |
| 172 | N | A | 0.0000 | |
| 173 | P | A | 0.0000 | |
| 174 | S | A | -1.3479 | |
| 175 | R | A | -1.1256 | |
| 176 | G | A | -0.1690 | |
| 177 | Y | A | 0.3746 | |
| 178 | Y | A | 1.1884 | |
| 179 | N | A | 0.0630 | |
| 180 | Y | A | -0.9840 | |
| 181 | A | A | -1.7260 | |
| 182 | Q | A | -2.7717 | |
| 183 | K | A | -2.8921 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.0813 | |
| 186 | D | A | -2.9934 | |
| 187 | R | A | -1.9831 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -0.8051 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.3432 | |
| 192 | R | A | -1.2031 | |
| 193 | D | A | -1.2418 | |
| 194 | T | A | -0.8232 | |
| 195 | S | A | -0.5768 | |
| 196 | T | A | -0.6963 | |
| 197 | S | A | -0.8539 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.7655 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.3551 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.2193 | |
| 205 | S | A | -1.2818 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.9198 | |
| 208 | S | A | -2.3052 | |
| 209 | E | A | -2.5043 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.8568 | |
| 212 | A | A | -0.3039 | |
| 213 | V | A | 0.0973 | |
| 214 | Y | A | 0.0000 | |
| 215 | Y | A | 0.0000 | |
| 216 | C | A | 0.0000 | |
| 217 | A | A | 0.0000 | |
| 218 | R | A | 0.0000 | |
| 219 | Y | A | 0.0000 | |
| 220 | Y | A | -0.5518 | |
| 221 | D | A | -1.1983 | |
| 222 | D | A | -2.1222 | |
| 223 | H | A | -1.2327 | |
| 224 | Y | A | -0.6576 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | 0.0000 | |
| 228 | Y | A | -0.1294 | |
| 229 | W | A | -0.1898 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -0.7211 | |
| 232 | G | A | -0.2073 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | 0.0066 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.2824 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8402 | |
| 239 | S | A | -0.9593 | |
| 1 | M | B | 0.1706 | |
| 2 | Q | B | -1.5589 | |
| 3 | S | B | -1.2784 | |
| 4 | I | B | -1.5263 | |
| 5 | K | B | -2.5942 | |
| 6 | G | B | -2.0010 | |
| 7 | N | B | -2.3466 | |
| 8 | H | B | 0.0000 | |
| 9 | L | B | -1.5661 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -0.8373 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.4286 | |
| 14 | D | B | -0.2026 | |
| 15 | Y | B | 0.4177 | |
| 16 | Q | B | -1.3468 | |
| 17 | E | B | -2.6796 | |
| 18 | D | B | -2.7868 | |
| 19 | G | B | -1.5783 | |
| 20 | S | B | -1.4037 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.6545 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.4342 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.5683 | |
| 27 | A | B | -2.7315 | |
| 28 | E | B | -3.1031 | |
| 29 | A | B | -2.8359 | |
| 30 | K | B | -3.5399 | |
| 31 | N | B | -2.2430 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.6263 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | -0.3067 | |
| 36 | K | B | -1.2590 | |
| 37 | D | B | -1.7889 | |
| 38 | G | B | 0.0000 | |
| 39 | K | B | -1.4564 | |
| 40 | M | B | 0.5813 | |
| 41 | I | B | 0.8322 | |
| 42 | G | B | 1.3463 | |
| 43 | F | B | 1.8955 | |
| 44 | L | B | -0.8324 | |
| 45 | T | B | -2.3739 | |
| 46 | E | B | -4.5261 | |
| 47 | D | B | -4.0671 | |
| 48 | K | B | -3.7534 | |
| 49 | K | B | -3.5134 | |
| 50 | K | B | -2.7032 | |
| 51 | W | B | -1.0328 | |
| 52 | N | B | -1.6739 | |
| 53 | L | B | 0.0000 | |
| 54 | G | B | -1.1546 | |
| 55 | S | B | -1.4446 | |
| 56 | N | B | -1.3871 | |
| 57 | A | B | -1.1642 | |
| 58 | K | B | -2.1755 | |
| 59 | D | B | -1.6433 | |
| 60 | P | B | 0.0000 | |
| 61 | R | B | -1.4169 | |
| 62 | G | B | -0.9056 | |
| 63 | M | B | 0.0000 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | -0.8495 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.8660 | |
| 68 | G | B | -2.2822 | |
| 69 | S | B | -1.9369 | |
| 70 | Q | B | -2.3446 | |
| 71 | N | B | -2.6120 | |
| 72 | K | B | -2.3334 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.4568 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.5836 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.1606 | |
| 82 | M | B | -1.1106 | |
| 83 | G | B | -1.5815 | |
| 84 | S | B | -1.4213 | |
| 85 | A | B | -1.8568 | |
| 86 | D | B | -3.4800 | |
| 87 | D | B | -4.1568 | |
| 88 | A | B | -3.3066 | |
| 89 | K | B | -4.2377 | |
| 90 | K | B | -4.7397 | |
| 91 | D | B | -4.3073 | |
| 92 | A | B | -3.2373 | |
| 93 | A | B | -3.3328 | |
| 94 | K | B | -4.5375 | |
| 95 | K | B | -4.6490 | |
| 96 | D | B | -4.5411 | |
| 97 | D | B | -4.5369 | |
| 98 | A | B | -3.6325 | |
| 99 | K | B | -4.4149 | |
| 100 | K | B | -4.3986 | |
| 101 | D | B | -4.2790 | |
| 102 | D | B | -3.9550 | |
| 103 | A | B | -3.0184 | |
| 104 | K | B | -3.7833 | |
| 105 | K | B | -3.7996 | |
| 106 | D | B | -3.6535 | |
| 107 | G | B | -2.8204 | |
| 108 | S | B | -2.4184 | |
| 109 | D | B | -3.1880 | |
| 110 | G | B | -2.9162 | |
| 111 | N | B | -3.4269 | |
| 112 | E | B | -3.5563 | |
| 113 | E | B | -2.9351 | |
| 114 | M | B | -1.3361 | |
| 115 | G | B | -1.1707 | |
| 116 | G | B | -1.0489 | |
| 117 | I | B | -0.6264 | |
| 118 | T | B | -0.4655 | |
| 119 | Q | B | -0.7667 | |
| 120 | T | B | -0.7462 | |
| 121 | P | B | -0.8209 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.6632 | |
| 124 | V | B | -0.5935 | |
| 125 | S | B | -0.2666 | |
| 126 | I | B | -0.0047 | |
| 127 | S | B | -0.2610 | |
| 128 | G | B | -0.6801 | |
| 129 | T | B | -1.1818 | |
| 130 | T | B | 0.0000 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.2468 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | -1.3923 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | 0.0000 | |
| 137 | Q | B | -1.6277 | |
| 138 | Y | B | -0.7713 | |
| 139 | P | B | -0.8326 | |
| 140 | G | B | -0.7318 | |
| 141 | S | B | -0.7202 | |
| 142 | E | B | 0.0000 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.6278 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | -1.7112 | |
| 147 | H | B | 0.0000 | |
| 148 | N | B | -1.8177 | |
| 149 | D | B | -3.2477 | |
| 150 | K | B | -3.1280 | |
| 151 | N | B | -2.7691 | |
| 152 | I | B | -1.8148 | |
| 153 | G | B | 0.0000 | |
| 154 | G | B | -2.9655 | |
| 155 | D | B | -4.0519 | |
| 156 | E | B | -4.6298 | |
| 157 | D | B | -4.1330 | |
| 158 | D | B | -3.8582 | |
| 159 | K | B | -3.5301 | |
| 160 | N | B | -2.7726 | |
| 161 | I | B | -2.1862 | |
| 162 | G | B | -2.1232 | |
| 163 | S | B | -1.7516 | |
| 164 | D | B | -3.0502 | |
| 165 | E | B | -3.0732 | |
| 166 | D | B | -2.0260 | |
| 167 | H | B | -1.9548 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.9155 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.8252 | |
| 172 | E | B | -2.5387 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.1564 | |
| 175 | E | B | -0.7676 | |
| 176 | L | B | 0.1996 | |
| 177 | E | B | -1.2401 | |
| 178 | Q | B | -0.9532 | |
| 179 | S | B | 0.0000 | |
| 180 | G | B | 0.0000 | |
| 181 | Y | B | 0.0000 | |
| 182 | Y | B | 0.0000 | |
| 183 | V | B | 0.0000 | |
| 184 | C | B | 0.0000 | |
| 185 | Y | B | 0.0000 | |
| 186 | P | B | -0.4788 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | 0.0000 | |
| 190 | K | B | -0.9073 | |
| 191 | P | B | 0.0000 | |
| 192 | E | B | -1.9570 | |
| 193 | D | B | -2.0165 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.4778 | |
| 196 | F | B | 0.0000 | |
| 197 | Y | B | 0.0000 | |
| 198 | L | B | 0.0000 | |
| 199 | Y | B | 0.0000 | |
| 200 | L | B | 0.0000 | |
| 201 | R | B | -0.6284 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.2787 | |
| 204 | V | B | -0.1877 |
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 | -0.9199 | 4.0424 | View | CSV | PDB |
| 4.5 | -0.999 | 4.0443 | View | CSV | PDB |
| 5.0 | -1.0923 | 4.0499 | View | CSV | PDB |
| 5.5 | -1.1835 | 4.0654 | View | CSV | PDB |
| 6.0 | -1.2547 | 4.1011 | View | CSV | PDB |
| 6.5 | -1.2936 | 4.1635 | View | CSV | PDB |
| 7.0 | -1.3004 | 4.2478 | View | CSV | PDB |
| 7.5 | -1.2852 | 4.3436 | View | CSV | PDB |
| 8.0 | -1.2564 | 4.4437 | View | CSV | PDB |
| 8.5 | -1.2154 | 4.5451 | View | CSV | PDB |
| 9.0 | -1.1596 | 4.6461 | 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