| Chain sequence(s) |
A: EIVLTKSPATLSLSPGERATLSCSASSSVSYMNWYKQKPGLAPRLLIYDTSNLAYGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSNNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVQKPGASVKVSCKASGYTFNRYTMHWVRQAPGQLLWMGYINPSRGYYNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
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] (00:00:03)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:03)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:03)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:03)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:06)
[INFO] FoldX: Starting FoldX energy minimization (00:00:07)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:21:36)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/d6d541d01f99948/tmp/folded.pdb (00:21:36)
[INFO] Main: Simulation completed successfully. (00:30:24)
|
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 | -1.7289 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 1.0353 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.3246 | |
| 6 | K | A | -0.6003 | |
| 7 | S | A | -0.5519 | |
| 8 | P | A | -0.4686 | |
| 9 | A | A | -0.6230 | |
| 10 | T | A | -0.6284 | |
| 11 | L | A | -0.4892 | |
| 12 | S | A | -0.9068 | |
| 13 | L | A | -1.0685 | |
| 14 | S | A | -1.5726 | |
| 15 | P | A | -1.9281 | |
| 16 | G | A | -2.3656 | |
| 17 | E | A | -2.8629 | |
| 18 | R | A | -3.2292 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5603 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.7298 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.8227 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.2489 | |
| 27 | S | A | -0.6663 | |
| 28 | S | A | -0.8840 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.8940 | |
| 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 | -0.3498 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -0.6162 | |
| 39 | P | A | -0.2653 | |
| 40 | G | A | -0.1354 | |
| 41 | L | A | 0.5042 | |
| 42 | A | A | -0.0260 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -0.4320 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.1332 | |
| 49 | D | A | -0.7378 | |
| 50 | T | A | -0.5457 | |
| 51 | S | A | -0.5857 | |
| 52 | N | A | -0.3214 | |
| 53 | L | A | 0.1654 | |
| 54 | A | A | 0.0000 | |
| 55 | Y | A | 1.1687 | |
| 56 | G | A | -0.0703 | |
| 57 | I | A | -0.0220 | |
| 58 | P | A | -0.7796 | |
| 59 | D | A | -1.8927 | |
| 60 | R | A | -1.8996 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.7198 | |
| 63 | G | A | -0.4520 | |
| 64 | S | A | -0.9096 | |
| 65 | G | A | -1.1612 | |
| 66 | S | A | -1.0650 | |
| 67 | G | A | -0.9938 | |
| 68 | T | A | -1.2758 | |
| 69 | D | A | -2.1598 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7679 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.8109 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.3895 | |
| 76 | R | A | -3.3557 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.4320 | |
| 79 | P | A | -1.5884 | |
| 80 | E | A | -2.1644 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -0.9130 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.7532 | |
| 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 | -1.0361 | |
| 92 | N | A | -1.9075 | |
| 93 | N | A | -1.5880 | |
| 94 | P | A | -1.3704 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.1573 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -1.4360 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.4725 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.1745 | |
| 105 | I | A | -0.9273 | |
| 106 | K | A | -1.8861 | |
| 107 | G | A | -1.5134 | |
| 108 | G | A | -1.3504 | |
| 109 | G | A | -1.2581 | |
| 110 | G | A | -1.0802 | |
| 111 | S | A | -0.9905 | |
| 112 | G | A | -1.4352 | |
| 113 | G | A | -1.5105 | |
| 114 | G | A | -1.3583 | |
| 115 | G | A | -1.5620 | |
| 116 | S | A | -1.0596 | |
| 117 | G | A | -1.2477 | |
| 118 | G | A | -1.1882 | |
| 119 | G | A | -1.1956 | |
| 120 | G | A | -1.4298 | |
| 121 | S | A | -1.2264 | |
| 122 | Q | A | -1.7935 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.4856 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | 0.4615 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.5256 | |
| 129 | G | A | -0.5585 | |
| 130 | A | A | -0.0164 | |
| 131 | E | A | -0.0462 | |
| 132 | V | A | 0.9831 | |
| 133 | Q | A | -0.7359 | |
| 134 | K | A | -2.0458 | |
| 135 | P | A | -2.1028 | |
| 136 | G | A | -1.4872 | |
| 137 | A | A | -1.1686 | |
| 138 | S | A | -1.3332 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -2.0141 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.6300 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -0.9445 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.7895 | |
| 147 | G | A | -0.9316 | |
| 148 | Y | A | -0.6414 | |
| 149 | T | A | -0.6513 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -1.5477 | |
| 152 | R | A | -2.3214 | |
| 153 | Y | A | -0.8688 | |
| 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 | -0.1932 | |
| 160 | Q | A | -0.4183 | |
| 161 | A | A | -0.6872 | |
| 162 | P | A | -0.7551 | |
| 163 | G | A | -1.2723 | |
| 164 | Q | A | -1.1749 | |
| 165 | L | A | 0.0000 | |
| 166 | L | A | -0.2768 | |
| 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 | -1.1346 | |
| 175 | R | A | -0.6429 | |
| 176 | G | A | -0.0477 | |
| 177 | Y | A | 0.2529 | |
| 178 | Y | A | 1.1835 | |
| 179 | N | A | -0.0636 | |
| 180 | Y | A | 0.0000 | |
| 181 | A | A | -1.8772 | |
| 182 | Q | A | -2.9324 | |
| 183 | K | A | -3.0689 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.6125 | |
| 186 | D | A | -3.3130 | |
| 187 | R | A | -2.2096 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -0.9783 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.4557 | |
| 192 | R | A | -1.3526 | |
| 193 | D | A | -1.3380 | |
| 194 | T | A | -0.8712 | |
| 195 | S | A | -0.6029 | |
| 196 | T | A | -0.7196 | |
| 197 | S | A | -0.8865 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.8601 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.5132 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.3021 | |
| 205 | S | A | -1.3026 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.8170 | |
| 208 | S | A | -2.2574 | |
| 209 | E | A | -2.4597 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.8511 | |
| 212 | A | A | 0.0000 | |
| 213 | V | A | 0.0299 | |
| 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 | -0.5564 | |
| 221 | D | A | -1.3329 | |
| 222 | D | A | -2.0774 | |
| 223 | H | A | -1.0823 | |
| 224 | Y | A | -0.5635 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | 0.0000 | |
| 228 | Y | A | -0.1234 | |
| 229 | W | A | -0.0362 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -0.7329 | |
| 232 | G | A | -0.2375 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | -0.0015 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.2656 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8366 | |
| 239 | S | A | -0.9551 | |
| 1 | M | B | 0.4515 | |
| 2 | Q | B | -1.0096 | |
| 3 | S | B | -0.9457 | |
| 4 | I | B | -1.2009 | |
| 5 | K | B | -2.3296 | |
| 6 | G | B | -1.9000 | |
| 7 | N | B | -2.3581 | |
| 8 | H | B | 0.0000 | |
| 9 | L | B | -1.4052 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -0.4867 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.5470 | |
| 14 | D | B | -0.0771 | |
| 15 | Y | B | 0.4813 | |
| 16 | Q | B | -1.2421 | |
| 17 | E | B | -2.6444 | |
| 18 | D | B | -2.7535 | |
| 19 | G | B | -1.5245 | |
| 20 | S | B | -1.3410 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.3571 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.0978 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.5793 | |
| 27 | A | B | 0.0000 | |
| 28 | E | B | -3.2129 | |
| 29 | A | B | -2.8448 | |
| 30 | K | B | -3.2615 | |
| 31 | N | B | -2.1384 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.0000 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | -0.4973 | |
| 36 | K | B | -1.5685 | |
| 37 | D | B | -2.4533 | |
| 38 | G | B | -1.6149 | |
| 39 | K | B | -1.8725 | |
| 40 | M | B | 0.4558 | |
| 41 | I | B | 0.8152 | |
| 42 | G | B | 1.3930 | |
| 43 | F | B | 1.7958 | |
| 44 | L | B | -0.6611 | |
| 45 | T | B | -2.1944 | |
| 46 | E | B | -4.2063 | |
| 47 | D | B | -3.9179 | |
| 48 | K | B | -3.1843 | |
| 49 | K | B | -3.4276 | |
| 50 | K | B | -2.3925 | |
| 51 | W | B | -0.7880 | |
| 52 | N | B | -1.3793 | |
| 53 | L | B | 0.0000 | |
| 54 | G | B | -1.1153 | |
| 55 | S | B | -1.4017 | |
| 56 | N | B | -1.3517 | |
| 57 | A | B | -1.1394 | |
| 58 | K | B | -2.1583 | |
| 59 | D | B | -1.6189 | |
| 60 | P | B | 0.0000 | |
| 61 | R | B | -1.4627 | |
| 62 | G | B | -1.0351 | |
| 63 | M | B | -1.2527 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | -1.1576 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.9866 | |
| 68 | G | B | 0.0000 | |
| 69 | S | B | -2.0499 | |
| 70 | Q | B | -2.5713 | |
| 71 | N | B | -2.7470 | |
| 72 | K | B | -2.5758 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.9090 | |
| 75 | P | B | -1.1387 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.5497 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.0659 | |
| 82 | M | B | -1.0519 | |
| 83 | G | B | -1.5125 | |
| 84 | S | B | -1.3865 | |
| 85 | A | B | -1.6169 | |
| 86 | D | B | -3.4118 | |
| 87 | D | B | -4.1125 | |
| 88 | A | B | -3.2307 | |
| 89 | K | B | -4.1917 | |
| 90 | K | B | -4.6969 | |
| 91 | D | B | -4.4776 | |
| 92 | A | B | -3.2781 | |
| 93 | A | B | -3.3891 | |
| 94 | K | B | -4.5695 | |
| 95 | K | B | -4.7341 | |
| 96 | D | B | -4.7841 | |
| 97 | D | B | -4.6111 | |
| 98 | A | B | -3.8889 | |
| 99 | K | B | -4.4852 | |
| 100 | K | B | -4.3923 | |
| 101 | D | B | -4.3095 | |
| 102 | D | B | -3.9928 | |
| 103 | A | B | -3.0538 | |
| 104 | K | B | -3.8559 | |
| 105 | K | B | -3.7841 | |
| 106 | D | B | -3.6056 | |
| 107 | G | B | -2.7316 | |
| 108 | S | B | -2.3716 | |
| 109 | D | B | -3.1312 | |
| 110 | G | B | -2.8891 | |
| 111 | N | B | -3.4190 | |
| 112 | E | B | -3.4770 | |
| 113 | E | B | -2.9025 | |
| 114 | M | B | -0.7820 | |
| 115 | G | B | -0.5199 | |
| 116 | G | B | -0.2509 | |
| 117 | I | B | 1.5776 | |
| 118 | T | B | 0.2317 | |
| 119 | Q | B | -0.1268 | |
| 120 | T | B | -0.5049 | |
| 121 | P | B | -0.8889 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.6557 | |
| 124 | V | B | -0.5468 | |
| 125 | S | B | -0.2051 | |
| 126 | I | B | 0.1000 | |
| 127 | S | B | -0.2464 | |
| 128 | G | B | -0.7048 | |
| 129 | T | B | -1.2224 | |
| 130 | T | B | -1.1153 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.2399 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | -1.4045 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | 0.0000 | |
| 137 | Q | B | -1.3904 | |
| 138 | Y | B | -0.7301 | |
| 139 | P | B | -0.8055 | |
| 140 | G | B | -0.7021 | |
| 141 | S | B | -0.7825 | |
| 142 | E | B | 0.0000 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.5844 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | 0.0000 | |
| 147 | H | B | -1.0988 | |
| 148 | N | B | -1.4160 | |
| 149 | D | B | -2.0453 | |
| 150 | K | B | -2.4481 | |
| 151 | N | B | -2.3673 | |
| 152 | I | B | -1.3078 | |
| 153 | G | B | 0.0000 | |
| 154 | G | B | -2.0902 | |
| 155 | D | B | -2.6829 | |
| 156 | E | B | -3.3862 | |
| 157 | D | B | -3.4767 | |
| 158 | D | B | -3.1421 | |
| 159 | K | B | -3.1991 | |
| 160 | N | B | -2.6520 | |
| 161 | I | B | -1.8779 | |
| 162 | G | B | -1.7920 | |
| 163 | S | B | -1.6437 | |
| 164 | D | B | -3.0257 | |
| 165 | E | B | -2.9354 | |
| 166 | D | B | -2.1192 | |
| 167 | H | B | -1.8807 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.9266 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.7772 | |
| 172 | E | B | -2.6051 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.1657 | |
| 175 | E | B | -0.7250 | |
| 176 | L | B | 0.2173 | |
| 177 | E | B | -1.2414 | |
| 178 | Q | B | -0.9549 | |
| 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 | -0.6191 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -0.9503 | |
| 190 | K | B | -1.3717 | |
| 191 | P | B | 0.0000 | |
| 192 | E | B | -2.2882 | |
| 193 | D | B | -2.4406 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.4634 | |
| 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 | -0.5826 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.2077 | |
| 204 | V | B | -0.2696 |
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 | -0.9113 | 4.081 | View | CSV | PDB |
| 4.5 | -0.9903 | 4.053 | View | CSV | PDB |
| 5.0 | -1.0815 | 4.0179 | View | CSV | PDB |
| 5.5 | -1.1694 | 3.9895 | View | CSV | PDB |
| 6.0 | -1.2366 | 3.9848 | View | CSV | PDB |
| 6.5 | -1.2707 | 4.0143 | View | CSV | PDB |
| 7.0 | -1.2723 | 4.0751 | View | CSV | PDB |
| 7.5 | -1.252 | 4.1552 | View | CSV | PDB |
| 8.0 | -1.2184 | 4.2438 | View | CSV | PDB |
| 8.5 | -1.1726 | 4.335 | View | CSV | PDB |
| 9.0 | -1.112 | 4.4261 | 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