| Chain sequence(s) |
A: EIVLTKSPATLSLSPGERATLSCSASSSVSYMNWYQQKPGQAPRLLIYDTSNLATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSSNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVKKPGASVKVSCKASGYTFTRYTMHWVRQAPGQGLWMGYINPSRGYTNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTLVTVSS
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 (00:16:06)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/f7c0723d896d79c/tmp/folded.pdb (00:16:06)
[INFO] Main: Simulation completed successfully. (00:26:25)
|
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 | -1.7198 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 1.0856 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.1530 | |
| 6 | K | A | 0.0000 | |
| 7 | S | A | -0.4588 | |
| 8 | P | A | -0.2985 | |
| 9 | A | A | -0.3281 | |
| 10 | T | A | -0.4049 | |
| 11 | L | A | -0.4130 | |
| 12 | S | A | -0.8402 | |
| 13 | L | A | -1.1465 | |
| 14 | S | A | -1.9640 | |
| 15 | P | A | -2.3145 | |
| 16 | G | A | -2.5537 | |
| 17 | E | A | -2.8974 | |
| 18 | R | A | -3.0752 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5646 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.6457 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.7650 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.2669 | |
| 27 | S | A | -0.5700 | |
| 28 | S | A | -0.7647 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.7306 | |
| 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 | Q | A | -0.5116 | |
| 37 | Q | A | -0.9194 | |
| 38 | K | A | -1.6146 | |
| 39 | P | A | -1.1003 | |
| 40 | G | A | -1.4626 | |
| 41 | Q | A | -2.1587 | |
| 42 | A | A | -1.3269 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -0.8129 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.1443 | |
| 49 | D | A | -0.7805 | |
| 50 | T | A | -0.5430 | |
| 51 | S | A | -0.5615 | |
| 52 | N | A | -0.4451 | |
| 53 | L | A | -0.1193 | |
| 54 | A | A | 0.0000 | |
| 55 | T | A | -0.2179 | |
| 56 | G | A | -0.8152 | |
| 57 | I | A | -0.5277 | |
| 58 | P | A | -1.0221 | |
| 59 | D | A | -1.9094 | |
| 60 | R | A | -1.8649 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.6924 | |
| 63 | G | A | -0.4362 | |
| 64 | S | A | -0.9055 | |
| 65 | G | A | -1.1638 | |
| 66 | S | A | -1.0709 | |
| 67 | G | A | -1.0100 | |
| 68 | T | A | -1.2953 | |
| 69 | D | A | -2.1680 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7355 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.7757 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.4949 | |
| 76 | R | A | -3.3701 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.3422 | |
| 79 | P | A | -2.1407 | |
| 80 | E | A | -2.4732 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -0.6623 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.2603 | |
| 85 | Y | A | 0.0000 | |
| 86 | Y | A | -0.1980 | |
| 87 | C | A | 0.0000 | |
| 88 | Q | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | W | A | 0.0000 | |
| 91 | S | A | -0.6021 | |
| 92 | S | A | -1.1127 | |
| 93 | N | A | -1.7418 | |
| 94 | P | A | -1.4864 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.1320 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -1.3758 | |
| 100 | G | A | -0.9115 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -0.7216 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.2384 | |
| 105 | I | A | -1.7680 | |
| 106 | K | A | -2.3494 | |
| 107 | G | A | -1.7886 | |
| 108 | G | A | -1.7631 | |
| 109 | G | A | -1.4223 | |
| 110 | G | A | -1.6190 | |
| 111 | S | A | -1.1109 | |
| 112 | G | A | -1.6395 | |
| 113 | G | A | -1.6051 | |
| 114 | G | A | -1.7086 | |
| 115 | G | A | -1.5656 | |
| 116 | S | A | -1.1684 | |
| 117 | G | A | -1.2976 | |
| 118 | G | A | -1.3031 | |
| 119 | G | A | -1.3597 | |
| 120 | G | A | -1.5380 | |
| 121 | S | A | -1.3860 | |
| 122 | Q | A | -1.7968 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.4544 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | 0.5536 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.3845 | |
| 129 | G | A | -0.3792 | |
| 130 | A | A | 0.3445 | |
| 131 | E | A | 0.0838 | |
| 132 | V | A | 1.0526 | |
| 133 | K | A | -0.8249 | |
| 134 | K | A | -2.0409 | |
| 135 | P | A | -2.0239 | |
| 136 | G | A | -1.4357 | |
| 137 | A | A | -1.1448 | |
| 138 | S | A | -1.3524 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -2.1501 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.5607 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -0.7610 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.7637 | |
| 147 | G | A | -0.9212 | |
| 148 | Y | A | -0.5824 | |
| 149 | T | A | -0.5284 | |
| 150 | F | A | 0.0000 | |
| 151 | T | A | -1.5112 | |
| 152 | R | A | -2.3140 | |
| 153 | Y | A | -0.6869 | |
| 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 | -0.1858 | |
| 160 | Q | A | -0.4463 | |
| 161 | A | A | -0.8083 | |
| 162 | P | A | -0.9409 | |
| 163 | G | A | -1.4815 | |
| 164 | Q | A | -1.8529 | |
| 165 | G | A | -0.9395 | |
| 166 | L | A | -0.5794 | |
| 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 | -0.7387 | |
| 173 | P | A | 0.0000 | |
| 174 | S | A | -1.6787 | |
| 175 | R | A | -1.4136 | |
| 176 | G | A | -0.7872 | |
| 177 | Y | A | -0.3971 | |
| 178 | T | A | -0.1629 | |
| 179 | N | A | -0.6216 | |
| 180 | Y | A | -1.2825 | |
| 181 | A | A | 0.0000 | |
| 182 | Q | A | -2.9142 | |
| 183 | K | A | -3.0255 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.5263 | |
| 186 | D | A | -3.2612 | |
| 187 | R | A | -2.3116 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -1.1623 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.5062 | |
| 192 | R | A | -1.1728 | |
| 193 | D | A | -1.1258 | |
| 194 | T | A | -0.7955 | |
| 195 | S | A | -0.5531 | |
| 196 | T | A | -0.6643 | |
| 197 | S | A | -0.7270 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.7292 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.6816 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.3111 | |
| 205 | S | A | -1.2085 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.5194 | |
| 208 | S | A | -2.1076 | |
| 209 | E | A | -2.3543 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.6158 | |
| 212 | A | A | 0.0000 | |
| 213 | V | A | 0.5589 | |
| 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 | -0.5979 | |
| 221 | D | A | -1.2877 | |
| 222 | D | A | -2.1531 | |
| 223 | H | A | -1.2191 | |
| 224 | Y | A | -0.5997 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | 0.0000 | |
| 228 | Y | A | -0.1182 | |
| 229 | W | A | -0.2773 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -1.1639 | |
| 232 | G | A | -0.3606 | |
| 233 | T | A | 0.0000 | |
| 234 | L | A | 1.1201 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | 0.0076 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8173 | |
| 239 | S | A | -0.9494 | |
| 1 | M | B | 0.1611 | |
| 2 | Q | B | -1.2692 | |
| 3 | S | B | -1.2155 | |
| 4 | I | B | -1.5571 | |
| 5 | K | B | -2.4957 | |
| 6 | G | B | -2.2751 | |
| 7 | N | B | -2.4906 | |
| 8 | H | B | -2.4874 | |
| 9 | L | B | 0.0000 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -0.3652 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.6254 | |
| 14 | D | B | 0.0000 | |
| 15 | Y | B | 0.4901 | |
| 16 | Q | B | -1.3748 | |
| 17 | E | B | -2.7103 | |
| 18 | D | B | -2.7862 | |
| 19 | G | B | -1.5361 | |
| 20 | S | B | 0.0000 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.4867 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.1924 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.3541 | |
| 27 | A | B | 0.0000 | |
| 28 | E | B | -3.1310 | |
| 29 | A | B | -2.9890 | |
| 30 | K | B | -3.7259 | |
| 31 | N | B | -2.6629 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.5409 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | 0.0000 | |
| 36 | K | B | -1.5822 | |
| 37 | D | B | -2.3034 | |
| 38 | G | B | -1.8094 | |
| 39 | K | B | -1.8385 | |
| 40 | M | B | 0.3818 | |
| 41 | I | B | 0.7721 | |
| 42 | G | B | 1.3472 | |
| 43 | F | B | 1.5405 | |
| 44 | L | B | -1.0297 | |
| 45 | T | B | -2.6668 | |
| 46 | E | B | -4.5726 | |
| 47 | D | B | -4.2230 | |
| 48 | K | B | -4.0263 | |
| 49 | K | B | -3.6614 | |
| 50 | K | B | -2.6258 | |
| 51 | W | B | -0.9865 | |
| 52 | N | B | -1.6430 | |
| 53 | L | B | 0.0000 | |
| 54 | G | B | -1.1313 | |
| 55 | S | B | -1.3872 | |
| 56 | N | B | -1.2797 | |
| 57 | A | B | -1.1084 | |
| 58 | K | B | -2.1428 | |
| 59 | D | B | -1.6048 | |
| 60 | P | B | 0.0000 | |
| 61 | R | B | -1.4628 | |
| 62 | G | B | -1.0226 | |
| 63 | M | B | -1.2216 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | -1.0690 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.9283 | |
| 68 | G | B | -2.3902 | |
| 69 | S | B | -2.1069 | |
| 70 | Q | B | -2.6070 | |
| 71 | N | B | -2.6549 | |
| 72 | K | B | -2.1987 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.7322 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.5716 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.0096 | |
| 82 | M | B | -1.0104 | |
| 83 | G | B | -1.4562 | |
| 84 | S | B | -1.4797 | |
| 85 | A | B | -1.9563 | |
| 86 | D | B | -3.5897 | |
| 87 | D | B | -3.8756 | |
| 88 | A | B | -3.1243 | |
| 89 | K | B | -4.1439 | |
| 90 | K | B | -4.6450 | |
| 91 | D | B | -4.3956 | |
| 92 | A | B | -3.4821 | |
| 93 | A | B | -3.6266 | |
| 94 | K | B | -4.8903 | |
| 95 | K | B | -4.9687 | |
| 96 | D | B | -4.9283 | |
| 97 | D | B | -4.8832 | |
| 98 | A | B | -4.2542 | |
| 99 | K | B | -5.0238 | |
| 100 | K | B | -4.7801 | |
| 101 | D | B | -4.4380 | |
| 102 | D | B | -4.2686 | |
| 103 | A | B | -3.4532 | |
| 104 | K | B | -3.8572 | |
| 105 | K | B | -3.9005 | |
| 106 | D | B | -3.5748 | |
| 107 | G | B | -2.7517 | |
| 108 | S | B | -2.2747 | |
| 109 | D | B | -3.1763 | |
| 110 | G | B | -2.9021 | |
| 111 | N | B | -3.3586 | |
| 112 | E | B | -3.4889 | |
| 113 | E | B | -2.8686 | |
| 114 | M | B | -0.7457 | |
| 115 | G | B | -0.5131 | |
| 116 | G | B | 0.1911 | |
| 117 | I | B | 1.6538 | |
| 118 | T | B | 0.3617 | |
| 119 | Q | B | -0.2919 | |
| 120 | T | B | -0.3420 | |
| 121 | P | B | -0.7487 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.6689 | |
| 124 | V | B | -0.5788 | |
| 125 | S | B | -0.2729 | |
| 126 | I | B | 0.0348 | |
| 127 | S | B | -0.2485 | |
| 128 | G | B | -0.6625 | |
| 129 | T | B | -1.1329 | |
| 130 | T | B | -1.0729 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.2141 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | -1.3764 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | -0.8623 | |
| 137 | Q | B | -0.5808 | |
| 138 | Y | B | -0.3982 | |
| 139 | P | B | -0.8306 | |
| 140 | G | B | -1.0005 | |
| 141 | S | B | -0.9934 | |
| 142 | E | B | -1.0176 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.6337 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | -1.7226 | |
| 147 | H | B | 0.0000 | |
| 148 | N | B | -1.9873 | |
| 149 | D | B | -3.0065 | |
| 150 | K | B | -3.1743 | |
| 151 | N | B | -2.7602 | |
| 152 | I | B | -1.9080 | |
| 153 | G | B | 0.0000 | |
| 154 | G | B | -2.5756 | |
| 155 | D | B | -3.4884 | |
| 156 | E | B | -3.6836 | |
| 157 | D | B | -3.4527 | |
| 158 | D | B | -3.7207 | |
| 159 | K | B | -3.4549 | |
| 160 | N | B | -2.6415 | |
| 161 | I | B | -2.1469 | |
| 162 | G | B | -2.0236 | |
| 163 | S | B | -1.8521 | |
| 164 | D | B | -3.0843 | |
| 165 | E | B | -3.2097 | |
| 166 | D | B | -2.3308 | |
| 167 | H | B | -2.0183 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.9054 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.9116 | |
| 172 | E | B | -2.5234 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.0877 | |
| 175 | E | B | -0.6320 | |
| 176 | L | B | 0.2202 | |
| 177 | E | B | -1.2378 | |
| 178 | Q | B | -1.0036 | |
| 179 | S | B | -0.6737 | |
| 180 | G | B | 0.0000 | |
| 181 | Y | B | -0.6147 | |
| 182 | Y | B | 0.0000 | |
| 183 | V | B | 0.0000 | |
| 184 | C | B | 0.0000 | |
| 185 | Y | B | 0.0000 | |
| 186 | P | B | -0.3715 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -0.7232 | |
| 190 | K | B | 0.0000 | |
| 191 | P | B | 0.0000 | |
| 192 | E | B | -2.3724 | |
| 193 | D | B | -2.2991 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.5694 | |
| 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 | -0.4631 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.0470 | |
| 204 | V | B | 0.0535 |
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 | -0.9444 | 3.7665 | View | CSV | PDB |
| 4.5 | -1.0264 | 3.7401 | View | CSV | PDB |
| 5.0 | -1.1219 | 3.7058 | View | CSV | PDB |
| 5.5 | -1.2144 | 3.6782 | View | CSV | PDB |
| 6.0 | -1.286 | 3.6769 | View | CSV | PDB |
| 6.5 | -1.3231 | 3.7167 | View | CSV | PDB |
| 7.0 | -1.326 | 3.7951 | View | CSV | PDB |
| 7.5 | -1.3061 | 3.8975 | View | CSV | PDB |
| 8.0 | -1.2725 | 4.0105 | View | CSV | PDB |
| 8.5 | -1.2267 | 4.127 | View | CSV | PDB |
| 9.0 | -1.1665 | 4.2436 | 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