| Chain sequence(s) |
A: EIVLTKSPATLSLSPGERATLSCSASQSVSYMNWYKQKPGLAPRLLIYDTSNLATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSSNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVQKPGASVKVSCKASGYTFNRYTMHWVRQAPGQLLWMGYINPSRGYYNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
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] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:02)
[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. (00:00:05)
[INFO] FoldX: Starting FoldX energy minimization (00:00:05)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:11:46)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/8036b576102f1f4/tmp/folded.pdb (00:11:46)
[INFO] Main: Simulation completed successfully. (00:21:54)
|
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 | -1.7227 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.9133 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.2284 | |
| 6 | K | A | -0.4970 | |
| 7 | S | A | -0.5135 | |
| 8 | P | A | -0.4175 | |
| 9 | A | A | -0.5309 | |
| 10 | T | A | -0.4892 | |
| 11 | L | A | -0.3493 | |
| 12 | S | A | -0.6737 | |
| 13 | L | A | -0.9700 | |
| 14 | S | A | -1.6026 | |
| 15 | P | A | -1.8419 | |
| 16 | G | A | -2.4519 | |
| 17 | E | A | -2.9293 | |
| 18 | R | A | -3.2260 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5309 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.7119 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.9617 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.7278 | |
| 27 | Q | A | -1.5714 | |
| 28 | S | A | -1.2554 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.6669 | |
| 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 | -0.6037 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -0.5425 | |
| 39 | P | A | -0.1128 | |
| 40 | G | A | -0.0150 | |
| 41 | L | A | 0.6505 | |
| 42 | A | A | -0.1382 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -1.4474 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.3960 | |
| 49 | D | A | -0.8565 | |
| 50 | T | A | -0.5656 | |
| 51 | S | A | -0.5624 | |
| 52 | N | A | -0.4206 | |
| 53 | L | A | -0.0917 | |
| 54 | A | A | 0.0000 | |
| 55 | T | A | -0.2411 | |
| 56 | G | A | -0.7919 | |
| 57 | I | A | -0.6735 | |
| 58 | P | A | -0.9662 | |
| 59 | D | A | -1.9180 | |
| 60 | R | A | -1.9321 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.7141 | |
| 63 | G | A | -0.4363 | |
| 64 | S | A | -0.9050 | |
| 65 | G | A | -1.1564 | |
| 66 | S | A | -1.0661 | |
| 67 | G | A | -1.1870 | |
| 68 | T | A | -1.5597 | |
| 69 | D | A | -2.2658 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7481 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.7967 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.5346 | |
| 76 | R | A | -3.4184 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.2427 | |
| 79 | P | A | -1.5609 | |
| 80 | E | A | -1.6867 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -0.5889 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.5067 | |
| 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 | -0.9940 | |
| 93 | N | A | -1.3018 | |
| 94 | P | A | -1.1859 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.2532 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -0.9659 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.1504 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -0.9669 | |
| 105 | I | A | -0.8746 | |
| 106 | K | A | -1.9094 | |
| 107 | G | A | -1.4983 | |
| 108 | G | A | -1.3289 | |
| 109 | G | A | -1.1820 | |
| 110 | G | A | -1.2957 | |
| 111 | S | A | -1.0702 | |
| 112 | G | A | -1.4276 | |
| 113 | G | A | -1.4588 | |
| 114 | G | A | -1.3865 | |
| 115 | G | A | -1.4643 | |
| 116 | S | A | -1.0573 | |
| 117 | G | A | -1.2747 | |
| 118 | G | A | -1.2326 | |
| 119 | G | A | -1.3359 | |
| 120 | G | A | -1.4322 | |
| 121 | S | A | -1.3827 | |
| 122 | Q | A | -1.7822 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.4812 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | 0.4776 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.4656 | |
| 129 | G | A | -0.5613 | |
| 130 | A | A | -0.0339 | |
| 131 | E | A | -0.0465 | |
| 132 | V | A | 0.9217 | |
| 133 | Q | A | -0.8690 | |
| 134 | K | A | -2.1036 | |
| 135 | P | A | -2.1363 | |
| 136 | G | A | -1.4809 | |
| 137 | A | A | -1.1812 | |
| 138 | S | A | -1.2091 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -1.4995 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.5176 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -1.0056 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.7974 | |
| 147 | G | A | -0.9155 | |
| 148 | Y | A | -0.6826 | |
| 149 | T | A | -0.7630 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -2.1590 | |
| 152 | R | A | -2.5900 | |
| 153 | Y | A | -0.8911 | |
| 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 | -0.1710 | |
| 160 | Q | A | -0.3245 | |
| 161 | A | A | -0.6924 | |
| 162 | P | A | -0.6863 | |
| 163 | G | A | -0.9968 | |
| 164 | Q | A | -0.9513 | |
| 165 | L | A | 0.0000 | |
| 166 | L | A | -0.2140 | |
| 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 | -1.5148 | |
| 175 | R | A | -1.1608 | |
| 176 | G | A | -0.0975 | |
| 177 | Y | A | 0.1691 | |
| 178 | Y | A | 1.1865 | |
| 179 | N | A | -0.1037 | |
| 180 | Y | A | -1.0165 | |
| 181 | A | A | -1.7454 | |
| 182 | Q | A | -2.7712 | |
| 183 | K | A | -2.9191 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.1548 | |
| 186 | D | A | -3.0601 | |
| 187 | R | A | -1.9974 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -0.8297 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.3822 | |
| 192 | R | A | -1.2079 | |
| 193 | D | A | -1.1826 | |
| 194 | T | A | -0.8430 | |
| 195 | S | A | -0.5608 | |
| 196 | T | A | -0.7108 | |
| 197 | S | A | -0.9236 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.7212 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.2817 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.1878 | |
| 205 | S | A | -1.2172 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.7711 | |
| 208 | S | A | -2.2650 | |
| 209 | E | A | -2.4460 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.8433 | |
| 212 | A | A | -0.3066 | |
| 213 | V | A | 0.0859 | |
| 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 | -0.6448 | |
| 221 | D | A | -1.2602 | |
| 222 | D | A | -2.0956 | |
| 223 | H | A | -1.2973 | |
| 224 | Y | A | -0.6843 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | -0.3943 | |
| 228 | Y | A | -0.4507 | |
| 229 | W | A | -0.4235 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -0.6714 | |
| 232 | G | A | -0.1798 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | -0.0010 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.3067 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8420 | |
| 239 | S | A | -1.1446 | |
| 1 | M | B | 0.0670 | |
| 2 | Q | B | -1.4576 | |
| 3 | S | B | -1.5482 | |
| 4 | I | B | 0.0000 | |
| 5 | K | B | -2.4826 | |
| 6 | G | B | -1.8500 | |
| 7 | N | B | -1.8107 | |
| 8 | H | B | 0.0000 | |
| 9 | L | B | -1.4603 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -0.2983 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.7752 | |
| 14 | D | B | 0.0000 | |
| 15 | Y | B | 0.4887 | |
| 16 | Q | B | -1.4750 | |
| 17 | E | B | -2.7712 | |
| 18 | D | B | -2.8361 | |
| 19 | G | B | -1.6021 | |
| 20 | S | B | -1.3604 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.4835 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.2977 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.5000 | |
| 27 | A | B | 0.0000 | |
| 28 | E | B | -3.1519 | |
| 29 | A | B | -2.9416 | |
| 30 | K | B | -3.6594 | |
| 31 | N | B | -2.4427 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.6460 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | -0.3077 | |
| 36 | K | B | -1.4683 | |
| 37 | D | B | -2.3963 | |
| 38 | G | B | -1.5749 | |
| 39 | K | B | -1.7796 | |
| 40 | M | B | 0.4860 | |
| 41 | I | B | 0.8407 | |
| 42 | G | B | 1.4020 | |
| 43 | F | B | 1.8429 | |
| 44 | L | B | -0.9664 | |
| 45 | T | B | -2.5278 | |
| 46 | E | B | -4.6921 | |
| 47 | D | B | -4.2411 | |
| 48 | K | B | -4.1123 | |
| 49 | K | B | -3.8868 | |
| 50 | K | B | -2.8110 | |
| 51 | W | B | -1.1013 | |
| 52 | N | B | -1.6939 | |
| 53 | L | B | 0.0000 | |
| 54 | G | B | -1.1483 | |
| 55 | S | B | -1.3865 | |
| 56 | N | B | -1.2248 | |
| 57 | A | B | -1.0654 | |
| 58 | K | B | -2.0493 | |
| 59 | D | B | -1.4069 | |
| 60 | P | B | 0.0000 | |
| 61 | R | B | -1.2194 | |
| 62 | G | B | -0.9306 | |
| 63 | M | B | -1.1295 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | -0.7715 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.7925 | |
| 68 | G | B | -2.3420 | |
| 69 | S | B | -2.0150 | |
| 70 | Q | B | -2.4374 | |
| 71 | N | B | -2.3653 | |
| 72 | K | B | -1.7037 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.2032 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.4020 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -0.9149 | |
| 82 | M | B | -0.9967 | |
| 83 | G | B | -1.2427 | |
| 84 | S | B | -1.1011 | |
| 85 | A | B | -1.5263 | |
| 86 | D | B | -3.0920 | |
| 87 | D | B | -3.3205 | |
| 88 | A | B | -2.8503 | |
| 89 | K | B | -3.7821 | |
| 90 | K | B | -4.2871 | |
| 91 | D | B | -4.0600 | |
| 92 | A | B | -3.0888 | |
| 93 | A | B | -3.2737 | |
| 94 | K | B | -4.2630 | |
| 95 | K | B | -4.4520 | |
| 96 | D | B | -4.5222 | |
| 97 | D | B | -4.3573 | |
| 98 | A | B | -3.8951 | |
| 99 | K | B | -4.4929 | |
| 100 | K | B | -4.3858 | |
| 101 | D | B | -4.1390 | |
| 102 | D | B | -4.2444 | |
| 103 | A | B | -3.3385 | |
| 104 | K | B | -3.8517 | |
| 105 | K | B | -3.9411 | |
| 106 | D | B | -3.6116 | |
| 107 | G | B | -2.8766 | |
| 108 | S | B | -2.4029 | |
| 109 | D | B | -3.1935 | |
| 110 | G | B | -2.9385 | |
| 111 | N | B | -3.5414 | |
| 112 | E | B | -3.5168 | |
| 113 | E | B | -2.9354 | |
| 114 | M | B | -0.7833 | |
| 115 | G | B | -0.4758 | |
| 116 | G | B | 0.0339 | |
| 117 | I | B | 1.6161 | |
| 118 | T | B | 0.3248 | |
| 119 | Q | B | -0.3709 | |
| 120 | T | B | -0.4658 | |
| 121 | P | B | -0.7953 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.2042 | |
| 124 | V | B | -0.2775 | |
| 125 | S | B | 0.0679 | |
| 126 | I | B | 0.3179 | |
| 127 | S | B | -0.0376 | |
| 128 | G | B | -0.5494 | |
| 129 | T | B | -1.0498 | |
| 130 | T | B | -0.9287 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.0256 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | -1.3112 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | -1.2291 | |
| 137 | Q | B | -1.5187 | |
| 138 | Y | B | -0.7176 | |
| 139 | P | B | -1.0038 | |
| 140 | G | B | -1.0982 | |
| 141 | S | B | -0.7540 | |
| 142 | E | B | 0.0000 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.6260 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | -1.7206 | |
| 147 | H | B | -1.7149 | |
| 148 | N | B | -2.1417 | |
| 149 | D | B | -3.0737 | |
| 150 | K | B | -3.0826 | |
| 151 | N | B | -2.4788 | |
| 152 | I | B | -1.3721 | |
| 153 | G | B | 0.0000 | |
| 154 | G | B | -2.5281 | |
| 155 | D | B | -3.6286 | |
| 156 | E | B | -4.3491 | |
| 157 | D | B | -4.0419 | |
| 158 | D | B | -3.6076 | |
| 159 | K | B | -3.5265 | |
| 160 | N | B | -2.7922 | |
| 161 | I | B | -2.1021 | |
| 162 | G | B | -2.1041 | |
| 163 | S | B | -1.9809 | |
| 164 | D | B | -3.1205 | |
| 165 | E | B | -3.2089 | |
| 166 | D | B | -2.3978 | |
| 167 | H | B | -1.8986 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.8479 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.6630 | |
| 172 | E | B | -2.5000 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.1113 | |
| 175 | E | B | -0.7020 | |
| 176 | L | B | 0.2048 | |
| 177 | E | B | -1.2310 | |
| 178 | Q | B | -1.0264 | |
| 179 | S | B | -0.7324 | |
| 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 | -0.5338 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -0.6148 | |
| 190 | K | B | -1.0700 | |
| 191 | P | B | 0.0000 | |
| 192 | E | B | -2.0208 | |
| 193 | D | B | -2.2771 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.6228 | |
| 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 | -0.6329 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.1381 | |
| 204 | V | B | 0.0735 |
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 | -0.8865 | 3.9528 | View | CSV | PDB |
| 4.5 | -0.9643 | 3.9552 | View | CSV | PDB |
| 5.0 | -1.0559 | 3.9621 | View | CSV | PDB |
| 5.5 | -1.1449 | 3.9813 | View | CSV | PDB |
| 6.0 | -1.2143 | 4.0248 | View | CSV | PDB |
| 6.5 | -1.2518 | 4.1003 | View | CSV | PDB |
| 7.0 | -1.2577 | 4.2019 | View | CSV | PDB |
| 7.5 | -1.242 | 4.3173 | View | CSV | PDB |
| 8.0 | -1.2135 | 4.438 | View | CSV | PDB |
| 8.5 | -1.1738 | 4.5601 | View | CSV | PDB |
| 9.0 | -1.12 | 4.6817 | 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