| Chain sequence(s) |
A: EIVLTQSPATLSLSPGERATLSCSASQSVSYMNWYKQKPGLAPRLLIYDTSKLATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSSNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVQKPGASVKVSCKASGYTFNRYTMHWVRQAPGQLLWMGYINPSRGYYNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
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 (00:16:58)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/afd462ffcebe7af/tmp/folded.pdb (00:16:58)
[INFO] Main: Simulation completed successfully. (00:26:59)
|
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 | -1.7362 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.9612 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.0554 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.4704 | |
| 8 | P | A | -0.3581 | |
| 9 | A | A | -0.4167 | |
| 10 | T | A | -0.5989 | |
| 11 | L | A | -0.4954 | |
| 12 | S | A | -0.9564 | |
| 13 | L | A | -1.1919 | |
| 14 | S | A | -1.6878 | |
| 15 | P | A | -1.9905 | |
| 16 | G | A | -2.2606 | |
| 17 | E | A | -2.9658 | |
| 18 | R | A | -3.2920 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5676 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.6587 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.8853 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.7090 | |
| 27 | Q | A | -1.5673 | |
| 28 | S | A | -1.2607 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.6863 | |
| 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 | -0.7393 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -1.0684 | |
| 39 | P | A | -0.6099 | |
| 40 | G | A | -0.6466 | |
| 41 | L | A | -0.5218 | |
| 42 | A | A | 0.0000 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -1.4833 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.4792 | |
| 49 | D | A | -0.9288 | |
| 50 | T | A | -0.7099 | |
| 51 | S | A | -0.9766 | |
| 52 | K | A | -1.3489 | |
| 53 | L | A | -0.5790 | |
| 54 | A | A | -0.3901 | |
| 55 | T | A | -0.2595 | |
| 56 | G | A | -0.6083 | |
| 57 | I | A | -0.5222 | |
| 58 | P | A | -0.9008 | |
| 59 | D | A | -1.8709 | |
| 60 | R | A | -1.8799 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.8933 | |
| 63 | G | A | -0.6274 | |
| 64 | S | A | -1.0028 | |
| 65 | G | A | -1.1806 | |
| 66 | S | A | -1.0766 | |
| 67 | G | A | -1.1905 | |
| 68 | T | A | -1.5693 | |
| 69 | D | A | -2.2811 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7514 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.8285 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.3985 | |
| 76 | R | A | -3.3483 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.4569 | |
| 79 | P | A | -1.6853 | |
| 80 | E | A | -2.3847 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -1.1275 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.5981 | |
| 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 | -0.5496 | |
| 92 | S | A | -1.0344 | |
| 93 | N | A | -1.3344 | |
| 94 | P | A | -1.2251 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.2124 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -0.9116 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.3398 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.6200 | |
| 105 | I | A | -1.2070 | |
| 106 | K | A | -2.0508 | |
| 107 | G | A | -1.5587 | |
| 108 | G | A | -1.3754 | |
| 109 | G | A | -1.3053 | |
| 110 | G | A | -1.3721 | |
| 111 | S | A | -1.0005 | |
| 112 | G | A | -1.4695 | |
| 113 | G | A | -1.5850 | |
| 114 | G | A | -1.3781 | |
| 115 | G | A | -1.3357 | |
| 116 | S | A | -1.1380 | |
| 117 | G | A | -1.1409 | |
| 118 | G | A | -1.2520 | |
| 119 | G | A | -1.3122 | |
| 120 | G | A | -1.4993 | |
| 121 | S | A | -1.3469 | |
| 122 | Q | A | -1.8690 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.6264 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | -0.0717 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.5557 | |
| 129 | G | A | -0.6015 | |
| 130 | A | A | 0.0334 | |
| 131 | E | A | 0.1248 | |
| 132 | V | A | 1.0154 | |
| 133 | Q | A | -0.7575 | |
| 134 | K | A | -2.0726 | |
| 135 | P | A | -2.1361 | |
| 136 | G | A | -1.4906 | |
| 137 | A | A | -1.1786 | |
| 138 | S | A | -1.2418 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -1.5823 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.5607 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -0.9278 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.9426 | |
| 147 | G | A | -1.1112 | |
| 148 | Y | A | -0.6426 | |
| 149 | T | A | -0.5112 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -1.3359 | |
| 152 | R | A | -1.7369 | |
| 153 | Y | A | -0.5114 | |
| 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 | -0.4141 | |
| 161 | A | A | -0.7853 | |
| 162 | P | A | -0.7517 | |
| 163 | G | A | -1.3322 | |
| 164 | Q | A | -1.4461 | |
| 165 | L | A | 0.0000 | |
| 166 | L | A | -0.3346 | |
| 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 | -0.9919 | |
| 175 | R | A | -0.7733 | |
| 176 | G | A | -0.0965 | |
| 177 | Y | A | 0.2064 | |
| 178 | Y | A | 1.1662 | |
| 179 | N | A | 0.0031 | |
| 180 | Y | A | -0.9911 | |
| 181 | A | A | -1.7538 | |
| 182 | Q | A | -2.7965 | |
| 183 | K | A | -2.9271 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.1285 | |
| 186 | D | A | -3.0609 | |
| 187 | R | A | -2.1518 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -0.8510 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.3536 | |
| 192 | R | A | -1.1152 | |
| 193 | D | A | -1.2044 | |
| 194 | T | A | -0.8303 | |
| 195 | S | A | -0.5783 | |
| 196 | T | A | -0.6647 | |
| 197 | S | A | -0.8202 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.6919 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.3518 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.2429 | |
| 205 | S | A | -1.2672 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.8563 | |
| 208 | S | A | -2.2745 | |
| 209 | E | A | -2.4766 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.8329 | |
| 212 | A | A | 0.0000 | |
| 213 | V | A | 0.1123 | |
| 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 | -0.5072 | |
| 221 | D | A | -1.1808 | |
| 222 | D | A | -2.1161 | |
| 223 | H | A | -1.3752 | |
| 224 | Y | A | -0.6891 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | -0.3602 | |
| 228 | Y | A | -0.3964 | |
| 229 | W | A | 0.0000 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -1.0741 | |
| 232 | G | A | -0.4560 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | 0.0607 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.2385 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8375 | |
| 239 | S | A | -0.9657 | |
| 1 | M | B | 0.4573 | |
| 2 | Q | B | -1.1824 | |
| 3 | S | B | -1.0245 | |
| 4 | I | B | 0.0000 | |
| 5 | K | B | -2.0420 | |
| 6 | G | B | -1.9447 | |
| 7 | N | B | -2.2605 | |
| 8 | H | B | 0.0000 | |
| 9 | L | B | -1.4230 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | 0.0000 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.6239 | |
| 14 | D | B | 0.0000 | |
| 15 | Y | B | 0.5489 | |
| 16 | Q | B | -1.1313 | |
| 17 | E | B | -2.5596 | |
| 18 | D | B | -2.6889 | |
| 19 | G | B | -1.4304 | |
| 20 | S | B | 0.0000 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.4037 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.1678 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.5667 | |
| 27 | A | B | -2.9411 | |
| 28 | E | B | -3.1432 | |
| 29 | A | B | -2.8869 | |
| 30 | K | B | -3.4845 | |
| 31 | N | B | -2.1537 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.6817 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | -0.4600 | |
| 36 | K | B | -1.5355 | |
| 37 | D | B | -2.1943 | |
| 38 | G | B | -1.5785 | |
| 39 | K | B | -1.7672 | |
| 40 | M | B | 0.3623 | |
| 41 | I | B | 0.7603 | |
| 42 | G | B | 1.3548 | |
| 43 | F | B | 1.7796 | |
| 44 | L | B | -0.6633 | |
| 45 | T | B | -2.2528 | |
| 46 | E | B | -4.2771 | |
| 47 | D | B | -3.9549 | |
| 48 | K | B | -3.4045 | |
| 49 | K | B | -3.2288 | |
| 50 | K | B | -2.5370 | |
| 51 | W | B | -0.8539 | |
| 52 | N | B | -1.2695 | |
| 53 | L | B | -0.8998 | |
| 54 | G | B | -1.0578 | |
| 55 | S | B | -1.2779 | |
| 56 | N | B | -1.2773 | |
| 57 | A | B | -1.1173 | |
| 58 | K | B | -2.1123 | |
| 59 | D | B | -1.5735 | |
| 60 | P | B | -1.2062 | |
| 61 | R | B | -1.4211 | |
| 62 | G | B | -1.0018 | |
| 63 | M | B | -1.1695 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | -0.9005 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.8258 | |
| 68 | G | B | -2.5195 | |
| 69 | S | B | -2.0435 | |
| 70 | Q | B | -2.5251 | |
| 71 | N | B | -2.5343 | |
| 72 | K | B | -2.1189 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.5079 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.5608 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.0852 | |
| 82 | M | B | 0.0000 | |
| 83 | G | B | -1.5313 | |
| 84 | S | B | -1.5530 | |
| 85 | A | B | -2.0404 | |
| 86 | D | B | -3.6224 | |
| 87 | D | B | -3.8049 | |
| 88 | A | B | -3.1746 | |
| 89 | K | B | -4.2291 | |
| 90 | K | B | -4.7922 | |
| 91 | D | B | -4.7324 | |
| 92 | A | B | -3.7015 | |
| 93 | A | B | -3.7437 | |
| 94 | K | B | -5.0367 | |
| 95 | K | B | -5.1281 | |
| 96 | D | B | -5.0212 | |
| 97 | D | B | -5.0149 | |
| 98 | A | B | -4.4639 | |
| 99 | K | B | -5.1565 | |
| 100 | K | B | -5.0631 | |
| 101 | D | B | -4.7243 | |
| 102 | D | B | -4.3917 | |
| 103 | A | B | -3.5060 | |
| 104 | K | B | -4.0388 | |
| 105 | K | B | -4.1022 | |
| 106 | D | B | -3.5102 | |
| 107 | G | B | -2.5692 | |
| 108 | S | B | -2.3547 | |
| 109 | D | B | -3.0919 | |
| 110 | G | B | -2.9061 | |
| 111 | N | B | -3.3255 | |
| 112 | E | B | -3.4795 | |
| 113 | E | B | -2.8722 | |
| 114 | M | B | -0.9531 | |
| 115 | G | B | -0.5837 | |
| 116 | G | B | -0.3801 | |
| 117 | I | B | 1.4321 | |
| 118 | T | B | 0.2826 | |
| 119 | Q | B | -0.5234 | |
| 120 | T | B | -0.5536 | |
| 121 | P | B | -0.8354 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.6059 | |
| 124 | V | B | -0.5601 | |
| 125 | S | B | -0.2525 | |
| 126 | I | B | -0.1867 | |
| 127 | S | B | -0.2837 | |
| 128 | G | B | -0.7152 | |
| 129 | T | B | -1.2310 | |
| 130 | T | B | -1.1020 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.2507 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | -1.5369 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | -1.3752 | |
| 137 | Q | B | -1.5723 | |
| 138 | Y | B | -0.7466 | |
| 139 | P | B | -1.0449 | |
| 140 | G | B | -0.9955 | |
| 141 | S | B | -0.8127 | |
| 142 | E | B | 0.0000 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.6984 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | 0.0000 | |
| 147 | H | B | -1.4722 | |
| 148 | N | B | -2.0779 | |
| 149 | D | B | -2.9755 | |
| 150 | K | B | -2.9280 | |
| 151 | N | B | -2.6624 | |
| 152 | I | B | -1.5994 | |
| 153 | G | B | -1.8113 | |
| 154 | G | B | -2.3590 | |
| 155 | D | B | -2.9535 | |
| 156 | E | B | -3.9672 | |
| 157 | D | B | -3.8713 | |
| 158 | D | B | -3.6093 | |
| 159 | K | B | -3.3289 | |
| 160 | N | B | -2.5446 | |
| 161 | I | B | -2.0423 | |
| 162 | G | B | -1.9413 | |
| 163 | S | B | -1.8063 | |
| 164 | D | B | -3.1945 | |
| 165 | E | B | -3.2478 | |
| 166 | D | B | -2.5959 | |
| 167 | H | B | -2.1330 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.9348 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.8133 | |
| 172 | E | B | -2.5904 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.3148 | |
| 175 | E | B | -1.0861 | |
| 176 | L | B | 0.0412 | |
| 177 | E | B | -1.3247 | |
| 178 | Q | B | -1.0681 | |
| 179 | S | B | -0.7805 | |
| 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 | -0.4693 | |
| 187 | R | B | -0.3123 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -0.7010 | |
| 190 | K | B | -1.2076 | |
| 191 | P | B | 0.0000 | |
| 192 | E | B | -2.3225 | |
| 193 | D | B | -2.3889 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.9026 | |
| 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 | -0.7106 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.4453 | |
| 204 | V | B | -0.3647 |
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 | -0.9326 | 4.072 | View | CSV | PDB |
| 4.5 | -1.0162 | 4.0444 | View | CSV | PDB |
| 5.0 | -1.1136 | 4.0103 | View | CSV | PDB |
| 5.5 | -1.2081 | 3.9836 | View | CSV | PDB |
| 6.0 | -1.2813 | 3.9811 | View | CSV | PDB |
| 6.5 | -1.3196 | 4.0127 | View | CSV | PDB |
| 7.0 | -1.3236 | 4.0746 | View | CSV | PDB |
| 7.5 | -1.3053 | 4.1545 | View | CSV | PDB |
| 8.0 | -1.2738 | 4.2422 | View | CSV | PDB |
| 8.5 | -1.2305 | 4.3323 | View | CSV | PDB |
| 9.0 | -1.1721 | 4.4221 | 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