| Chain sequence(s) |
A: EIVLTQSPATLSLSPGERATLSCSASSSVSYMNWYKQKPGLAPRLLIYDTSKLATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSSNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVQKPGASVKVSCKASGYTFNRYTMHWVRQAPGQLLWMGYINPSRGYYNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
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. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:19:21)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/f882793bc01ae61/tmp/folded.pdb (00:19:21)
[INFO] Main: Simulation completed successfully. (00:29:18)
|
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 | -1.7152 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 1.1112 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.0968 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.4544 | |
| 8 | P | A | -0.3309 | |
| 9 | A | A | -0.3881 | |
| 10 | T | A | -0.5377 | |
| 11 | L | A | -0.4396 | |
| 12 | S | A | -0.9207 | |
| 13 | L | A | -1.1794 | |
| 14 | S | A | -1.7069 | |
| 15 | P | A | -1.8854 | |
| 16 | G | A | -2.4508 | |
| 17 | E | A | -2.9588 | |
| 18 | R | A | -3.2776 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5627 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.6529 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.7492 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.2620 | |
| 27 | S | A | -0.5508 | |
| 28 | S | A | -0.7548 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.8905 | |
| 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 | -0.4028 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -0.7336 | |
| 39 | P | A | -0.4331 | |
| 40 | G | A | -0.4111 | |
| 41 | L | A | 0.0910 | |
| 42 | A | A | -0.2293 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -0.6586 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.4398 | |
| 49 | D | A | -0.8989 | |
| 50 | T | A | -0.7019 | |
| 51 | S | A | -0.9565 | |
| 52 | K | A | -1.2801 | |
| 53 | L | A | -0.5564 | |
| 54 | A | A | 0.0000 | |
| 55 | T | A | -0.2785 | |
| 56 | G | A | -0.5877 | |
| 57 | I | A | -0.5760 | |
| 58 | P | A | -0.9711 | |
| 59 | D | A | -1.9068 | |
| 60 | R | A | -1.9280 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.8760 | |
| 63 | G | A | -0.6113 | |
| 64 | S | A | -0.9995 | |
| 65 | G | A | -1.1836 | |
| 66 | S | A | -1.0755 | |
| 67 | G | A | -1.0013 | |
| 68 | T | A | -1.2882 | |
| 69 | D | A | -2.1726 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7470 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.8181 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.4245 | |
| 76 | R | A | -3.4059 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.3785 | |
| 79 | P | A | -1.4110 | |
| 80 | E | A | -1.8524 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -0.8144 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.5226 | |
| 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 | -0.7292 | |
| 92 | S | A | -1.1680 | |
| 93 | N | A | -1.8369 | |
| 94 | P | A | -1.4932 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | -0.0891 | |
| 97 | F | A | 0.1749 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -1.0638 | |
| 100 | G | A | -0.9520 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.1469 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.4724 | |
| 105 | I | A | -1.0404 | |
| 106 | K | A | -1.9731 | |
| 107 | G | A | -1.5483 | |
| 108 | G | A | -1.3583 | |
| 109 | G | A | -1.2932 | |
| 110 | G | A | -1.1289 | |
| 111 | S | A | -1.0042 | |
| 112 | G | A | -1.2396 | |
| 113 | G | A | -1.5697 | |
| 114 | G | A | -1.4023 | |
| 115 | G | A | -1.3097 | |
| 116 | S | A | -1.2350 | |
| 117 | G | A | -1.2038 | |
| 118 | G | A | -1.2126 | |
| 119 | G | A | -1.3375 | |
| 120 | G | A | -1.4413 | |
| 121 | S | A | -1.3586 | |
| 122 | Q | A | -1.7523 | |
| 123 | V | A | -1.1370 | |
| 124 | Q | A | -1.6306 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | -0.3457 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.7608 | |
| 129 | G | A | -0.7594 | |
| 130 | A | A | -0.2164 | |
| 131 | E | A | -0.4505 | |
| 132 | V | A | 0.7706 | |
| 133 | Q | A | -0.8663 | |
| 134 | K | A | -2.0489 | |
| 135 | P | A | -2.0877 | |
| 136 | G | A | -1.4078 | |
| 137 | A | A | -1.1385 | |
| 138 | S | A | -1.3471 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -2.1555 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.7259 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -1.0982 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.8986 | |
| 147 | G | A | -0.9488 | |
| 148 | Y | A | -0.5170 | |
| 149 | T | A | -0.4108 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -1.6028 | |
| 152 | R | A | -1.8888 | |
| 153 | Y | A | -0.4045 | |
| 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 | 0.0000 | |
| 160 | Q | A | -0.4427 | |
| 161 | A | A | -0.8286 | |
| 162 | P | A | -0.8126 | |
| 163 | G | A | -1.4405 | |
| 164 | Q | A | -1.6714 | |
| 165 | L | A | 0.0000 | |
| 166 | L | A | -0.2567 | |
| 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 | -1.1881 | |
| 175 | R | A | -1.1424 | |
| 176 | G | A | -0.1505 | |
| 177 | Y | A | 0.3631 | |
| 178 | Y | A | 1.2429 | |
| 179 | N | A | 0.0372 | |
| 180 | Y | A | -1.0348 | |
| 181 | A | A | 0.0000 | |
| 182 | Q | A | -2.9480 | |
| 183 | K | A | -3.0339 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.5673 | |
| 186 | D | A | -3.2788 | |
| 187 | R | A | -2.3058 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -0.9638 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.3712 | |
| 192 | R | A | -1.2638 | |
| 193 | D | A | -1.2112 | |
| 194 | T | A | -0.8046 | |
| 195 | S | A | -0.5843 | |
| 196 | T | A | -0.6962 | |
| 197 | S | A | -0.8210 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.7632 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.6175 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.3072 | |
| 205 | S | A | -1.2366 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.7909 | |
| 208 | S | A | -2.2462 | |
| 209 | E | A | -2.4530 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.8793 | |
| 212 | A | A | 0.0000 | |
| 213 | V | A | 0.1766 | |
| 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 | -0.4769 | |
| 221 | D | A | -1.1521 | |
| 222 | D | A | -2.0531 | |
| 223 | H | A | -1.3295 | |
| 224 | Y | A | -0.6521 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | -0.0962 | |
| 228 | Y | A | -0.1873 | |
| 229 | W | A | -0.2328 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -1.0114 | |
| 232 | G | A | -0.3916 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | -0.0626 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.3625 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8411 | |
| 239 | S | A | -0.9595 | |
| 1 | M | B | 0.7049 | |
| 2 | Q | B | -0.5095 | |
| 3 | S | B | -0.1174 | |
| 4 | I | B | 0.5870 | |
| 5 | K | B | -1.5627 | |
| 6 | G | B | -1.7875 | |
| 7 | N | B | -2.5857 | |
| 8 | H | B | -2.5039 | |
| 9 | L | B | -1.1721 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -1.1490 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.1939 | |
| 14 | D | B | -0.1526 | |
| 15 | Y | B | 0.3603 | |
| 16 | Q | B | -1.4238 | |
| 17 | E | B | -2.7105 | |
| 18 | D | B | -2.8058 | |
| 19 | G | B | -1.5969 | |
| 20 | S | B | 0.0000 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.6711 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.6150 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.8521 | |
| 27 | A | B | -3.1170 | |
| 28 | E | B | -3.1593 | |
| 29 | A | B | -2.9099 | |
| 30 | K | B | -3.5599 | |
| 31 | N | B | -2.2904 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.6092 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | -0.2902 | |
| 36 | K | B | -1.3212 | |
| 37 | D | B | -1.9329 | |
| 38 | G | B | 0.0000 | |
| 39 | K | B | -1.5713 | |
| 40 | M | B | 0.3556 | |
| 41 | I | B | 0.7421 | |
| 42 | G | B | 1.2901 | |
| 43 | F | B | 1.6362 | |
| 44 | L | B | -0.9321 | |
| 45 | T | B | -2.4841 | |
| 46 | E | B | -4.5262 | |
| 47 | D | B | -4.2512 | |
| 48 | K | B | -4.1161 | |
| 49 | K | B | -3.9820 | |
| 50 | K | B | -2.8284 | |
| 51 | W | B | -1.1024 | |
| 52 | N | B | -1.5943 | |
| 53 | L | B | -0.9521 | |
| 54 | G | B | -1.1069 | |
| 55 | S | B | -1.4110 | |
| 56 | N | B | -1.3878 | |
| 57 | A | B | -1.1921 | |
| 58 | K | B | -2.1796 | |
| 59 | D | B | -1.6863 | |
| 60 | P | B | -1.2533 | |
| 61 | R | B | -1.4252 | |
| 62 | G | B | -0.9315 | |
| 63 | M | B | 0.0000 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | 0.0000 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.7550 | |
| 68 | G | B | -2.3604 | |
| 69 | S | B | -2.0132 | |
| 70 | Q | B | -2.4034 | |
| 71 | N | B | -2.5012 | |
| 72 | K | B | -2.0793 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.3899 | |
| 75 | P | B | -0.6226 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.6065 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.2215 | |
| 82 | M | B | -1.1466 | |
| 83 | G | B | -1.5887 | |
| 84 | S | B | -1.3513 | |
| 85 | A | B | -1.8337 | |
| 86 | D | B | -3.5017 | |
| 87 | D | B | -4.1463 | |
| 88 | A | B | -3.2639 | |
| 89 | K | B | -4.2498 | |
| 90 | K | B | -4.7499 | |
| 91 | D | B | -4.2989 | |
| 92 | A | B | -3.3138 | |
| 93 | A | B | -3.3921 | |
| 94 | K | B | -4.5398 | |
| 95 | K | B | -4.6581 | |
| 96 | D | B | -4.5280 | |
| 97 | D | B | -4.3846 | |
| 98 | A | B | -3.6805 | |
| 99 | K | B | -4.4323 | |
| 100 | K | B | -4.4272 | |
| 101 | D | B | -4.0970 | |
| 102 | D | B | -4.0045 | |
| 103 | A | B | -3.0964 | |
| 104 | K | B | -3.7387 | |
| 105 | K | B | -3.7641 | |
| 106 | D | B | -3.6020 | |
| 107 | G | B | -2.7598 | |
| 108 | S | B | -2.2696 | |
| 109 | D | B | -3.0932 | |
| 110 | G | B | -2.8759 | |
| 111 | N | B | -3.3337 | |
| 112 | E | B | -3.5544 | |
| 113 | E | B | -2.9832 | |
| 114 | M | B | -1.4388 | |
| 115 | G | B | -1.2593 | |
| 116 | G | B | -1.2376 | |
| 117 | I | B | -0.6922 | |
| 118 | T | B | -0.5048 | |
| 119 | Q | B | -0.7779 | |
| 120 | T | B | -0.5662 | |
| 121 | P | B | -0.7884 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.4750 | |
| 124 | V | B | -0.5054 | |
| 125 | S | B | -0.2366 | |
| 126 | I | B | 0.0232 | |
| 127 | S | B | -0.2239 | |
| 128 | G | B | -0.6142 | |
| 129 | T | B | -1.0704 | |
| 130 | T | B | -0.9641 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.1975 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | -1.3020 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | -0.8158 | |
| 137 | Q | B | -0.5716 | |
| 138 | Y | B | -0.2314 | |
| 139 | P | B | -0.7576 | |
| 140 | G | B | -1.0453 | |
| 141 | S | B | -0.7405 | |
| 142 | E | B | 0.0000 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.7012 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | -1.9019 | |
| 147 | H | B | -2.0579 | |
| 148 | N | B | -2.7981 | |
| 149 | D | B | -3.6324 | |
| 150 | K | B | -3.3423 | |
| 151 | N | B | -2.6739 | |
| 152 | I | B | 0.0000 | |
| 153 | G | B | -2.0220 | |
| 154 | G | B | -2.7732 | |
| 155 | D | B | -3.7760 | |
| 156 | E | B | -3.8713 | |
| 157 | D | B | -3.3152 | |
| 158 | D | B | -3.6610 | |
| 159 | K | B | -3.3511 | |
| 160 | N | B | -2.5116 | |
| 161 | I | B | -2.1530 | |
| 162 | G | B | -2.0239 | |
| 163 | S | B | -1.8658 | |
| 164 | D | B | -3.1656 | |
| 165 | E | B | -3.2294 | |
| 166 | D | B | -2.3036 | |
| 167 | H | B | -2.0134 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.8554 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.7034 | |
| 172 | E | B | -2.3999 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.0925 | |
| 175 | E | B | -0.7369 | |
| 176 | L | B | 0.1982 | |
| 177 | E | B | -1.2366 | |
| 178 | Q | B | -1.0829 | |
| 179 | S | B | 0.0000 | |
| 180 | G | B | 0.0000 | |
| 181 | Y | B | -0.9138 | |
| 182 | Y | B | 0.0000 | |
| 183 | V | B | 0.0000 | |
| 184 | C | B | 0.0000 | |
| 185 | Y | B | 0.0000 | |
| 186 | P | B | -0.6452 | |
| 187 | R | B | -0.4185 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -1.1162 | |
| 190 | K | B | -1.8620 | |
| 191 | P | B | -2.1002 | |
| 192 | E | B | -3.3597 | |
| 193 | D | B | -3.1842 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.6108 | |
| 196 | F | B | 0.0000 | |
| 197 | Y | B | -0.2662 | |
| 198 | L | B | 0.0000 | |
| 199 | Y | B | 0.0000 | |
| 200 | L | B | 0.0000 | |
| 201 | R | B | -0.7034 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.1917 | |
| 204 | V | B | 0.0596 |
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 | -0.9626 | 3.7928 | View | CSV | PDB |
| 4.5 | -1.0466 | 3.7666 | View | CSV | PDB |
| 5.0 | -1.1443 | 3.7338 | View | CSV | PDB |
| 5.5 | -1.2392 | 3.7095 | View | CSV | PDB |
| 6.0 | -1.3125 | 3.7129 | View | CSV | PDB |
| 6.5 | -1.351 | 3.7578 | View | CSV | PDB |
| 7.0 | -1.3551 | 3.8419 | View | CSV | PDB |
| 7.5 | -1.3356 | 3.9503 | View | CSV | PDB |
| 8.0 | -1.3013 | 4.0694 | View | CSV | PDB |
| 8.5 | -1.2537 | 4.1919 | View | CSV | PDB |
| 9.0 | -1.1908 | 4.3144 | 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