| Chain sequence(s) |
A: EIVLTKSPATLSLSPGERATLSCSASSSVSYMNWYKQKPGLAPRLLIYDTSNLAYGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSSNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVQKPGASVKVSCKASGYTFNRYTMHWVRQAPGQLLWMGYINPSRGYYNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
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 (00:17:25)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/b79d7b1c00f0ad5/tmp/folded.pdb (00:17:25)
[INFO] Main: Simulation completed successfully. (00:27:47)
|
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 | -1.5450 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 1.0611 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.2607 | |
| 6 | K | A | -0.5041 | |
| 7 | S | A | -0.4950 | |
| 8 | P | A | -0.4191 | |
| 9 | A | A | -0.5791 | |
| 10 | T | A | -0.5342 | |
| 11 | L | A | -0.4006 | |
| 12 | S | A | -0.7378 | |
| 13 | L | A | -0.8476 | |
| 14 | S | A | -1.4265 | |
| 15 | P | A | -1.9094 | |
| 16 | G | A | -2.3195 | |
| 17 | E | A | -2.7040 | |
| 18 | R | A | -3.1696 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5253 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.6962 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.8183 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.2689 | |
| 27 | S | A | -0.5735 | |
| 28 | S | A | -0.7621 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.6560 | |
| 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 | -0.7293 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -1.0370 | |
| 39 | P | A | -0.5400 | |
| 40 | G | A | -0.5122 | |
| 41 | L | A | -0.2562 | |
| 42 | A | A | -0.5287 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -1.5855 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.5184 | |
| 49 | D | A | -0.8709 | |
| 50 | T | A | -0.6277 | |
| 51 | S | A | -0.7853 | |
| 52 | N | A | -0.7788 | |
| 53 | L | A | -0.0203 | |
| 54 | A | A | 0.0000 | |
| 55 | Y | A | 1.0979 | |
| 56 | G | A | 0.0045 | |
| 57 | I | A | -0.1301 | |
| 58 | P | A | -0.7819 | |
| 59 | D | A | -1.9111 | |
| 60 | R | A | -1.9663 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.8008 | |
| 63 | G | A | -0.5279 | |
| 64 | S | A | -0.9496 | |
| 65 | G | A | -1.1470 | |
| 66 | S | A | -1.0590 | |
| 67 | G | A | -1.0011 | |
| 68 | T | A | -1.2913 | |
| 69 | D | A | -2.1610 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7377 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.8171 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.4145 | |
| 76 | R | A | -3.3455 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.6505 | |
| 79 | P | A | -1.7002 | |
| 80 | E | A | -2.5988 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -0.9428 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.5809 | |
| 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 | -0.4589 | |
| 92 | S | A | -0.7499 | |
| 93 | N | A | -1.0450 | |
| 94 | P | A | -1.0559 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.2054 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -1.2256 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.2401 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -0.9838 | |
| 105 | I | A | -0.6596 | |
| 106 | K | A | -1.7840 | |
| 107 | G | A | -1.4845 | |
| 108 | G | A | -1.3621 | |
| 109 | G | A | -1.2637 | |
| 110 | G | A | -1.0781 | |
| 111 | S | A | -0.9687 | |
| 112 | G | A | -1.4953 | |
| 113 | G | A | -1.6150 | |
| 114 | G | A | -1.4658 | |
| 115 | G | A | -1.5425 | |
| 116 | S | A | -0.9701 | |
| 117 | G | A | -1.4286 | |
| 118 | G | A | -1.1945 | |
| 119 | G | A | -1.1872 | |
| 120 | G | A | -1.3920 | |
| 121 | S | A | -1.2177 | |
| 122 | Q | A | -1.7942 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.5625 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | 0.1515 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.5738 | |
| 129 | G | A | -0.6118 | |
| 130 | A | A | -0.0350 | |
| 131 | E | A | -0.0499 | |
| 132 | V | A | 0.9597 | |
| 133 | Q | A | -0.7666 | |
| 134 | K | A | -2.0658 | |
| 135 | P | A | -2.1281 | |
| 136 | G | A | -1.4824 | |
| 137 | A | A | -1.1672 | |
| 138 | S | A | -1.2803 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -1.8157 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.6166 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -0.9544 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.8223 | |
| 147 | G | A | -0.9495 | |
| 148 | Y | A | -0.6501 | |
| 149 | T | A | -0.6447 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -1.9028 | |
| 152 | R | A | -2.5928 | |
| 153 | Y | A | -0.8068 | |
| 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 | -0.1547 | |
| 160 | Q | A | -0.3418 | |
| 161 | A | A | -0.7369 | |
| 162 | P | A | -0.7598 | |
| 163 | G | A | -1.1499 | |
| 164 | Q | A | -1.0992 | |
| 165 | L | A | 0.0000 | |
| 166 | L | A | -0.1730 | |
| 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 | -1.4967 | |
| 175 | R | A | -1.2828 | |
| 176 | G | A | -0.0140 | |
| 177 | Y | A | 0.3970 | |
| 178 | Y | A | 1.2107 | |
| 179 | N | A | 0.0902 | |
| 180 | Y | A | -1.0259 | |
| 181 | A | A | -1.6987 | |
| 182 | Q | A | -2.8055 | |
| 183 | K | A | -2.9251 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.1681 | |
| 186 | D | A | -3.0753 | |
| 187 | R | A | -2.1168 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -0.8827 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.4274 | |
| 192 | R | A | -1.2510 | |
| 193 | D | A | -1.2946 | |
| 194 | T | A | -0.8506 | |
| 195 | S | A | -0.5972 | |
| 196 | T | A | -0.6919 | |
| 197 | S | A | -0.8423 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.8051 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.4840 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.2352 | |
| 205 | S | A | -1.2085 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.8032 | |
| 208 | S | A | -2.2553 | |
| 209 | E | A | -2.4666 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.8455 | |
| 212 | A | A | -0.3143 | |
| 213 | V | A | 0.0649 | |
| 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 | -0.6269 | |
| 221 | D | A | -1.2447 | |
| 222 | D | A | -2.0425 | |
| 223 | H | A | -1.1999 | |
| 224 | Y | A | -0.6171 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | -0.1511 | |
| 228 | Y | A | -0.3992 | |
| 229 | W | A | -0.3760 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -0.9348 | |
| 232 | G | A | -0.3793 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | -0.0095 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.2844 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8542 | |
| 239 | S | A | -0.9737 | |
| 1 | M | B | 0.3644 | |
| 2 | Q | B | -1.5908 | |
| 3 | S | B | -1.2362 | |
| 4 | I | B | -1.4079 | |
| 5 | K | B | -2.3422 | |
| 6 | G | B | -1.8175 | |
| 7 | N | B | -1.7106 | |
| 8 | H | B | 0.0000 | |
| 9 | L | B | -0.9604 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -0.3120 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.1378 | |
| 14 | D | B | -0.1757 | |
| 15 | Y | B | 0.3487 | |
| 16 | Q | B | -1.4206 | |
| 17 | E | B | -2.6846 | |
| 18 | D | B | -2.7857 | |
| 19 | G | B | -1.5712 | |
| 20 | S | B | 0.0000 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.6323 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | 0.0000 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -1.8410 | |
| 27 | A | B | 0.0000 | |
| 28 | E | B | -3.0147 | |
| 29 | A | B | -2.6669 | |
| 30 | K | B | -3.4192 | |
| 31 | N | B | -2.0763 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.7490 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | 0.0000 | |
| 36 | K | B | -1.3194 | |
| 37 | D | B | -1.9427 | |
| 38 | G | B | -1.2520 | |
| 39 | K | B | -1.5262 | |
| 40 | M | B | 0.5245 | |
| 41 | I | B | 0.8554 | |
| 42 | G | B | 1.3037 | |
| 43 | F | B | 1.8963 | |
| 44 | L | B | 0.0000 | |
| 45 | T | B | -2.2239 | |
| 46 | E | B | -4.3341 | |
| 47 | D | B | -3.8770 | |
| 48 | K | B | -3.4243 | |
| 49 | K | B | -3.1161 | |
| 50 | K | B | -2.4513 | |
| 51 | W | B | -0.9905 | |
| 52 | N | B | -1.6182 | |
| 53 | L | B | 0.0000 | |
| 54 | G | B | -1.1452 | |
| 55 | S | B | -1.4336 | |
| 56 | N | B | -1.3973 | |
| 57 | A | B | -1.1096 | |
| 58 | K | B | -2.0833 | |
| 59 | D | B | -1.4717 | |
| 60 | P | B | 0.0000 | |
| 61 | R | B | -1.1240 | |
| 62 | G | B | -0.8342 | |
| 63 | M | B | 0.0000 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | 0.0000 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.5518 | |
| 68 | G | B | 0.0000 | |
| 69 | S | B | -1.8648 | |
| 70 | Q | B | -2.2723 | |
| 71 | N | B | -2.2865 | |
| 72 | K | B | -1.7157 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.1192 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.4509 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.1372 | |
| 82 | M | B | -1.2348 | |
| 83 | G | B | -1.5300 | |
| 84 | S | B | -1.4148 | |
| 85 | A | B | -2.0192 | |
| 86 | D | B | -3.6594 | |
| 87 | D | B | -4.1144 | |
| 88 | A | B | -3.2153 | |
| 89 | K | B | -4.2285 | |
| 90 | K | B | -4.6779 | |
| 91 | D | B | -4.4795 | |
| 92 | A | B | -3.2575 | |
| 93 | A | B | -3.4091 | |
| 94 | K | B | -4.5595 | |
| 95 | K | B | -4.7056 | |
| 96 | D | B | -4.8148 | |
| 97 | D | B | -4.7431 | |
| 98 | A | B | -4.1595 | |
| 99 | K | B | -4.7247 | |
| 100 | K | B | -4.7139 | |
| 101 | D | B | -4.4782 | |
| 102 | D | B | -4.4760 | |
| 103 | A | B | -3.4966 | |
| 104 | K | B | -4.2031 | |
| 105 | K | B | -3.8989 | |
| 106 | D | B | -3.8329 | |
| 107 | G | B | -2.7378 | |
| 108 | S | B | -2.3958 | |
| 109 | D | B | -3.0880 | |
| 110 | G | B | -2.8843 | |
| 111 | N | B | -3.3037 | |
| 112 | E | B | -3.4412 | |
| 113 | E | B | -2.7742 | |
| 114 | M | B | -1.0469 | |
| 115 | G | B | -0.9862 | |
| 116 | G | B | -0.8161 | |
| 117 | I | B | -0.6375 | |
| 118 | T | B | -0.3582 | |
| 119 | Q | B | -0.7810 | |
| 120 | T | B | -0.8305 | |
| 121 | P | B | -0.9169 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.6178 | |
| 124 | V | B | -0.5191 | |
| 125 | S | B | -0.0833 | |
| 126 | I | B | 0.0121 | |
| 127 | S | B | -0.1935 | |
| 128 | G | B | -0.6880 | |
| 129 | T | B | -1.2215 | |
| 130 | T | B | -1.0872 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.1568 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | -1.4087 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | 0.0000 | |
| 137 | Q | B | -1.3829 | |
| 138 | Y | B | -0.7379 | |
| 139 | P | B | -0.8298 | |
| 140 | G | B | -0.6923 | |
| 141 | S | B | -0.6838 | |
| 142 | E | B | -0.5726 | |
| 143 | I | B | -0.8250 | |
| 144 | L | B | -0.4604 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | 0.0000 | |
| 147 | H | B | -1.7058 | |
| 148 | N | B | -2.1504 | |
| 149 | D | B | -3.3302 | |
| 150 | K | B | -3.2965 | |
| 151 | N | B | -2.5422 | |
| 152 | I | B | 0.0000 | |
| 153 | G | B | 0.0000 | |
| 154 | G | B | -2.9781 | |
| 155 | D | B | -3.8616 | |
| 156 | E | B | -3.7912 | |
| 157 | D | B | -3.5404 | |
| 158 | D | B | -3.8131 | |
| 159 | K | B | -3.5438 | |
| 160 | N | B | -2.6789 | |
| 161 | I | B | -2.2695 | |
| 162 | G | B | -2.1397 | |
| 163 | S | B | -1.8265 | |
| 164 | D | B | -3.0422 | |
| 165 | E | B | -2.9717 | |
| 166 | D | B | -2.0886 | |
| 167 | H | B | -1.8738 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.9170 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.9779 | |
| 172 | E | B | -2.6089 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.2041 | |
| 175 | E | B | -0.7892 | |
| 176 | L | B | 0.1792 | |
| 177 | E | B | -1.2491 | |
| 178 | Q | B | -1.0203 | |
| 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 | -0.2630 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -0.5462 | |
| 190 | K | B | -1.0819 | |
| 191 | P | B | 0.0000 | |
| 192 | E | B | -1.9806 | |
| 193 | D | B | -2.2646 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.2924 | |
| 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 | -0.6753 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.2631 | |
| 204 | V | B | -0.2157 |
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 | -0.8967 | 4.0871 | View | CSV | PDB |
| 4.5 | -0.9786 | 4.0885 | View | CSV | PDB |
| 5.0 | -1.0727 | 4.0927 | View | CSV | PDB |
| 5.5 | -1.163 | 4.1044 | View | CSV | PDB |
| 6.0 | -1.2331 | 4.1323 | View | CSV | PDB |
| 6.5 | -1.2719 | 4.1823 | View | CSV | PDB |
| 7.0 | -1.2802 | 4.2503 | View | CSV | PDB |
| 7.5 | -1.2679 | 4.3274 | View | CSV | PDB |
| 8.0 | -1.2421 | 4.4079 | View | CSV | PDB |
| 8.5 | -1.2035 | 4.4893 | View | CSV | PDB |
| 9.0 | -1.1497 | 4.5704 | 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