| Chain sequence(s) |
A: EIVLTKSPATLSLSPGERATLSCSASQSVSYMNWYKQKPGLAPRLLIYDTSNLAYGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSNNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVQKPGASVKVSCKASGYTFNRYTMHWVRQAPGQLLWMGYINPSRGYYNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
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 (00:20:46)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/efa1bea8bc0c145/tmp/folded.pdb (00:20:46)
[INFO] Main: Simulation completed successfully. (00:29:16)
|
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 | -1.8628 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.8752 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.3002 | |
| 6 | K | A | -0.5747 | |
| 7 | S | A | -0.5221 | |
| 8 | P | A | -0.4062 | |
| 9 | A | A | -0.5840 | |
| 10 | T | A | -0.4911 | |
| 11 | L | A | -0.3953 | |
| 12 | S | A | -0.7602 | |
| 13 | L | A | -1.0750 | |
| 14 | S | A | -1.6031 | |
| 15 | P | A | -1.8486 | |
| 16 | G | A | -2.1556 | |
| 17 | E | A | -2.8391 | |
| 18 | R | A | -3.2238 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5445 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.7108 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.9580 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.7044 | |
| 27 | Q | A | -1.6975 | |
| 28 | S | A | -1.3932 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.8506 | |
| 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 | -0.3602 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -0.7589 | |
| 39 | P | A | -0.2408 | |
| 40 | G | A | -0.0749 | |
| 41 | L | A | 0.7230 | |
| 42 | A | A | 0.0681 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -0.4295 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.0998 | |
| 49 | D | A | -0.7450 | |
| 50 | T | A | -0.5107 | |
| 51 | S | A | -0.5134 | |
| 52 | N | A | -0.2227 | |
| 53 | L | A | 0.2336 | |
| 54 | A | A | 0.0000 | |
| 55 | Y | A | 1.2412 | |
| 56 | G | A | 0.0206 | |
| 57 | I | A | -0.0251 | |
| 58 | P | A | -0.7729 | |
| 59 | D | A | -1.8844 | |
| 60 | R | A | -1.8858 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.6705 | |
| 63 | G | A | 0.0000 | |
| 64 | S | A | -0.8734 | |
| 65 | G | A | -1.1451 | |
| 66 | S | A | -1.0628 | |
| 67 | G | A | -1.1825 | |
| 68 | T | A | -1.5602 | |
| 69 | D | A | -2.2682 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7427 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.8021 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.3705 | |
| 76 | R | A | -3.2712 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.4113 | |
| 79 | P | A | -1.7976 | |
| 80 | E | A | -2.6463 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | 0.0000 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.6704 | |
| 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 | -1.0663 | |
| 92 | N | A | -2.0612 | |
| 93 | N | A | -1.6245 | |
| 94 | P | A | -1.3655 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.1733 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -1.3669 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.2320 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.1333 | |
| 105 | I | A | -1.0022 | |
| 106 | K | A | -1.9423 | |
| 107 | G | A | -1.5041 | |
| 108 | G | A | -1.3043 | |
| 109 | G | A | -1.2341 | |
| 110 | G | A | -1.5363 | |
| 111 | S | A | -1.0487 | |
| 112 | G | A | -1.6832 | |
| 113 | G | A | -1.5818 | |
| 114 | G | A | -1.5621 | |
| 115 | G | A | -1.5175 | |
| 116 | S | A | -1.0892 | |
| 117 | G | A | -1.2680 | |
| 118 | G | A | -1.2080 | |
| 119 | G | A | -1.3368 | |
| 120 | G | A | -1.3978 | |
| 121 | S | A | -1.1662 | |
| 122 | Q | A | -1.7625 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.3943 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | 0.1738 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.5729 | |
| 129 | G | A | -0.6488 | |
| 130 | A | A | -0.0965 | |
| 131 | E | A | -0.1862 | |
| 132 | V | A | 0.8681 | |
| 133 | Q | A | -0.8969 | |
| 134 | K | A | -2.1608 | |
| 135 | P | A | -2.2928 | |
| 136 | G | A | -1.6323 | |
| 137 | A | A | -1.2727 | |
| 138 | S | A | -1.3238 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -1.7065 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.5641 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -0.8386 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.8019 | |
| 147 | G | A | -0.9427 | |
| 148 | Y | A | -0.6761 | |
| 149 | T | A | -0.7201 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -1.7305 | |
| 152 | R | A | -2.3703 | |
| 153 | Y | A | -0.9191 | |
| 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 | -0.1638 | |
| 160 | Q | A | -0.3433 | |
| 161 | A | A | -0.7700 | |
| 162 | P | A | -0.7822 | |
| 163 | G | A | -1.1851 | |
| 164 | Q | A | -1.1721 | |
| 165 | L | A | 0.0000 | |
| 166 | L | A | -0.2101 | |
| 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 | -1.2130 | |
| 175 | R | A | -0.7946 | |
| 176 | G | A | -0.1282 | |
| 177 | Y | A | 0.2474 | |
| 178 | Y | A | 1.2309 | |
| 179 | N | A | -0.0583 | |
| 180 | Y | A | -1.1556 | |
| 181 | A | A | 0.0000 | |
| 182 | Q | A | -2.9463 | |
| 183 | K | A | -3.0273 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.5529 | |
| 186 | D | A | -3.2666 | |
| 187 | R | A | -2.2968 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -0.9167 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.3828 | |
| 192 | R | A | -1.2480 | |
| 193 | D | A | -1.2553 | |
| 194 | T | A | -0.8566 | |
| 195 | S | A | -0.5865 | |
| 196 | T | A | -0.6702 | |
| 197 | S | A | -0.8350 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.7441 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.3664 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.3111 | |
| 205 | S | A | -1.4184 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -3.1469 | |
| 208 | S | A | -2.4179 | |
| 209 | E | A | -2.5651 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.9237 | |
| 212 | A | A | -0.3138 | |
| 213 | V | A | 0.0775 | |
| 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 | -0.5267 | |
| 221 | D | A | -1.1687 | |
| 222 | D | A | -2.0572 | |
| 223 | H | A | -1.0648 | |
| 224 | Y | A | -0.5593 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | 0.0000 | |
| 228 | Y | A | -0.0163 | |
| 229 | W | A | 0.0009 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -0.7502 | |
| 232 | G | A | -0.2500 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | -0.0369 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.3618 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8885 | |
| 239 | S | A | -1.0019 | |
| 1 | M | B | 0.7316 | |
| 2 | Q | B | -0.5746 | |
| 3 | S | B | -1.0314 | |
| 4 | I | B | 0.0000 | |
| 5 | K | B | -2.4836 | |
| 6 | G | B | -1.9362 | |
| 7 | N | B | -1.8322 | |
| 8 | H | B | 0.0000 | |
| 9 | L | B | -1.1406 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | 0.0000 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.5561 | |
| 14 | D | B | -0.1456 | |
| 15 | Y | B | 0.3580 | |
| 16 | Q | B | -1.5006 | |
| 17 | E | B | -2.7423 | |
| 18 | D | B | -2.8336 | |
| 19 | G | B | -1.6277 | |
| 20 | S | B | 0.0000 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.5278 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | 0.0000 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.4375 | |
| 27 | A | B | -2.6678 | |
| 28 | E | B | -3.3213 | |
| 29 | A | B | -3.0204 | |
| 30 | K | B | -3.7029 | |
| 31 | N | B | -2.6057 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.4518 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | 0.0000 | |
| 36 | K | B | -1.8149 | |
| 37 | D | B | -2.6179 | |
| 38 | G | B | -1.8072 | |
| 39 | K | B | -2.0548 | |
| 40 | M | B | -0.1678 | |
| 41 | I | B | 0.3671 | |
| 42 | G | B | 1.1054 | |
| 43 | F | B | 1.4735 | |
| 44 | L | B | -0.9880 | |
| 45 | T | B | -2.5808 | |
| 46 | E | B | -4.5364 | |
| 47 | D | B | -4.1384 | |
| 48 | K | B | -3.8465 | |
| 49 | K | B | -3.9543 | |
| 50 | K | B | -2.5946 | |
| 51 | W | B | -0.9818 | |
| 52 | N | B | -1.5668 | |
| 53 | L | B | -0.9814 | |
| 54 | G | B | -1.1197 | |
| 55 | S | B | -1.4412 | |
| 56 | N | B | -1.4564 | |
| 57 | A | B | -1.1750 | |
| 58 | K | B | -2.1721 | |
| 59 | D | B | -1.6425 | |
| 60 | P | B | -1.2615 | |
| 61 | R | B | -1.5365 | |
| 62 | G | B | -1.1153 | |
| 63 | M | B | 0.0000 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | 0.0000 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.6664 | |
| 68 | G | B | -2.4693 | |
| 69 | S | B | -1.9797 | |
| 70 | Q | B | -2.3162 | |
| 71 | N | B | -2.3161 | |
| 72 | K | B | -1.7078 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.0939 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.5676 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.0914 | |
| 82 | M | B | -1.1193 | |
| 83 | G | B | -1.6020 | |
| 84 | S | B | -1.4448 | |
| 85 | A | B | -1.8739 | |
| 86 | D | B | -3.4810 | |
| 87 | D | B | -4.1799 | |
| 88 | A | B | -3.2972 | |
| 89 | K | B | -4.2475 | |
| 90 | K | B | -4.7947 | |
| 91 | D | B | -4.3393 | |
| 92 | A | B | -3.2493 | |
| 93 | A | B | -3.3796 | |
| 94 | K | B | -4.6153 | |
| 95 | K | B | -4.6777 | |
| 96 | D | B | -4.5220 | |
| 97 | D | B | -4.3882 | |
| 98 | A | B | -3.6844 | |
| 99 | K | B | -4.3606 | |
| 100 | K | B | -4.3361 | |
| 101 | D | B | -4.0976 | |
| 102 | D | B | -3.9368 | |
| 103 | A | B | -2.9912 | |
| 104 | K | B | -3.8254 | |
| 105 | K | B | -3.7733 | |
| 106 | D | B | -3.6245 | |
| 107 | G | B | -2.7744 | |
| 108 | S | B | -2.3744 | |
| 109 | D | B | -3.1329 | |
| 110 | G | B | -2.8852 | |
| 111 | N | B | -3.4843 | |
| 112 | E | B | -3.7340 | |
| 113 | E | B | -3.2589 | |
| 114 | M | B | -2.1008 | |
| 115 | G | B | -1.4274 | |
| 116 | G | B | -1.3663 | |
| 117 | I | B | -0.9466 | |
| 118 | T | B | -0.5869 | |
| 119 | Q | B | -0.8288 | |
| 120 | T | B | -0.6507 | |
| 121 | P | B | -0.7327 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.4475 | |
| 124 | V | B | -0.4520 | |
| 125 | S | B | -0.1299 | |
| 126 | I | B | 0.0459 | |
| 127 | S | B | -0.2400 | |
| 128 | G | B | -0.6985 | |
| 129 | T | B | -1.1927 | |
| 130 | T | B | -1.0156 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.1361 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | 0.0000 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | -0.9575 | |
| 137 | Q | B | -0.8814 | |
| 138 | Y | B | -0.4632 | |
| 139 | P | B | -0.8752 | |
| 140 | G | B | -1.0407 | |
| 141 | S | B | -0.7751 | |
| 142 | E | B | 0.0000 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.6936 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | -1.5800 | |
| 147 | H | B | -1.3865 | |
| 148 | N | B | -1.4074 | |
| 149 | D | B | -2.3139 | |
| 150 | K | B | -2.7840 | |
| 151 | N | B | -2.7691 | |
| 152 | I | B | 0.0000 | |
| 153 | G | B | 0.0000 | |
| 154 | G | B | -2.2310 | |
| 155 | D | B | -2.7032 | |
| 156 | E | B | -3.2950 | |
| 157 | D | B | -3.4695 | |
| 158 | D | B | -3.3636 | |
| 159 | K | B | -3.1087 | |
| 160 | N | B | -2.5918 | |
| 161 | I | B | -1.9090 | |
| 162 | G | B | -1.7564 | |
| 163 | S | B | 0.0000 | |
| 164 | D | B | -3.0517 | |
| 165 | E | B | -3.1338 | |
| 166 | D | B | -2.2888 | |
| 167 | H | B | -1.8810 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.8106 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.6300 | |
| 172 | E | B | -2.4758 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.1521 | |
| 175 | E | B | -0.7672 | |
| 176 | L | B | 0.2010 | |
| 177 | E | B | -1.2384 | |
| 178 | Q | B | -0.9573 | |
| 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 | -0.4654 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -0.8866 | |
| 190 | K | B | -1.2621 | |
| 191 | P | B | 0.0000 | |
| 192 | E | B | -1.9876 | |
| 193 | D | B | -2.3283 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.2663 | |
| 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 | -0.4985 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.3210 | |
| 204 | V | B | -0.3751 |
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 | -0.8971 | 3.6902 | View | CSV | PDB |
| 4.5 | -0.9737 | 3.671 | View | CSV | PDB |
| 5.0 | -1.0631 | 3.6419 | View | CSV | PDB |
| 5.5 | -1.1491 | 3.6146 | View | CSV | PDB |
| 6.0 | -1.215 | 3.6066 | View | CSV | PDB |
| 6.5 | -1.2492 | 3.6311 | View | CSV | PDB |
| 7.0 | -1.2534 | 3.69 | View | CSV | PDB |
| 7.5 | -1.2375 | 3.7748 | View | CSV | PDB |
| 8.0 | -1.2095 | 3.8733 | View | CSV | PDB |
| 8.5 | -1.1704 | 3.9769 | View | CSV | PDB |
| 9.0 | -1.1175 | 4.0814 | 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