| Chain sequence(s) |
A: EIVLTKSPATLSLSPGERATLSCSASQSVSYMNWYKQKPGLAPRLLIYDTSNLAYGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSSNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVQKPGASVKVSCKASGYTFNRYTMHWVRQAPGQLLWMGYINPSRGYYNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
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 (00:18:58)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/ab7cd1f915d4ccf/tmp/folded.pdb (00:18:58)
[INFO] Main: Simulation completed successfully. (00:28:16)
|
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 | -1.7854 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.8783 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.3013 | |
| 6 | K | A | -0.5812 | |
| 7 | S | A | -0.5181 | |
| 8 | P | A | -0.4286 | |
| 9 | A | A | -0.5599 | |
| 10 | T | A | -0.5468 | |
| 11 | L | A | -0.4688 | |
| 12 | S | A | -0.9312 | |
| 13 | L | A | -1.1290 | |
| 14 | S | A | -1.5905 | |
| 15 | P | A | -1.9034 | |
| 16 | G | A | -2.3377 | |
| 17 | E | A | -2.8288 | |
| 18 | R | A | -3.2142 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5384 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.6662 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.9137 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.7014 | |
| 27 | Q | A | -1.5520 | |
| 28 | S | A | -1.2110 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.4400 | |
| 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 | -0.3340 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -0.5934 | |
| 39 | P | A | -0.3774 | |
| 40 | G | A | -0.3049 | |
| 41 | L | A | 0.1542 | |
| 42 | A | A | -0.1892 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -0.4708 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.4008 | |
| 49 | D | A | -1.0653 | |
| 50 | T | A | -0.6545 | |
| 51 | S | A | -0.8097 | |
| 52 | N | A | -0.7996 | |
| 53 | L | A | -0.0370 | |
| 54 | A | A | 0.0000 | |
| 55 | Y | A | 1.1905 | |
| 56 | G | A | 0.0869 | |
| 57 | I | A | -0.0664 | |
| 58 | P | A | -0.7547 | |
| 59 | D | A | -1.8808 | |
| 60 | R | A | -1.8987 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.7618 | |
| 63 | G | A | 0.0000 | |
| 64 | S | A | -0.7025 | |
| 65 | G | A | -0.7562 | |
| 66 | S | A | -0.5514 | |
| 67 | G | A | -0.7902 | |
| 68 | T | A | -1.4720 | |
| 69 | D | A | -2.1566 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.6606 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.7940 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.3951 | |
| 76 | R | A | -3.3149 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.2539 | |
| 79 | P | A | -1.6112 | |
| 80 | E | A | -2.1814 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -0.8874 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.5574 | |
| 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 | -0.5046 | |
| 92 | S | A | -1.1035 | |
| 93 | N | A | -1.4995 | |
| 94 | P | A | -1.3586 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.1839 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -1.2988 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.2215 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.1988 | |
| 105 | I | A | -1.0715 | |
| 106 | K | A | -2.0017 | |
| 107 | G | A | -1.5315 | |
| 108 | G | A | -1.3522 | |
| 109 | G | A | -1.2736 | |
| 110 | G | A | -1.3203 | |
| 111 | S | A | -1.0126 | |
| 112 | G | A | -1.5203 | |
| 113 | G | A | -1.5243 | |
| 114 | G | A | -1.3709 | |
| 115 | G | A | -1.4191 | |
| 116 | S | A | -1.0188 | |
| 117 | G | A | -1.1733 | |
| 118 | G | A | -1.1861 | |
| 119 | G | A | -1.3414 | |
| 120 | G | A | -1.4036 | |
| 121 | S | A | -1.2790 | |
| 122 | Q | A | -1.8429 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.6122 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | -0.3097 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.6562 | |
| 129 | G | A | -0.6321 | |
| 130 | A | A | -0.0032 | |
| 131 | E | A | 0.0539 | |
| 132 | V | A | 0.9807 | |
| 133 | Q | A | -0.7231 | |
| 134 | K | A | -1.9991 | |
| 135 | P | A | -1.9809 | |
| 136 | G | A | -1.4096 | |
| 137 | A | A | -1.1251 | |
| 138 | S | A | -1.1812 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -1.5161 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.6810 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -1.4059 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -1.0695 | |
| 147 | G | A | -1.1488 | |
| 148 | Y | A | -0.7459 | |
| 149 | T | A | -0.7044 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -1.8268 | |
| 152 | R | A | -2.5466 | |
| 153 | Y | A | -0.7697 | |
| 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 | -0.2280 | |
| 161 | A | A | -0.6768 | |
| 162 | P | A | -0.7359 | |
| 163 | G | A | -1.1236 | |
| 164 | Q | A | -0.9638 | |
| 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 | -1.5004 | |
| 175 | R | A | -1.0313 | |
| 176 | G | A | -0.2392 | |
| 177 | Y | A | 0.1129 | |
| 178 | Y | A | 1.1590 | |
| 179 | N | A | -0.0319 | |
| 180 | Y | A | -1.0184 | |
| 181 | A | A | -1.7870 | |
| 182 | Q | A | -2.8112 | |
| 183 | K | A | -2.9226 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.1509 | |
| 186 | D | A | -3.0648 | |
| 187 | R | A | -2.1434 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -0.8292 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.3492 | |
| 192 | R | A | -1.2057 | |
| 193 | D | A | -1.1533 | |
| 194 | T | A | -0.7042 | |
| 195 | S | A | -0.5350 | |
| 196 | T | A | -0.7313 | |
| 197 | S | A | -0.8893 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.7265 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.2796 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.1777 | |
| 205 | S | A | -1.1960 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.4868 | |
| 208 | S | A | -2.1010 | |
| 209 | E | A | -2.3531 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.7641 | |
| 212 | A | A | -0.2719 | |
| 213 | V | A | 0.1271 | |
| 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 | -0.5671 | |
| 221 | D | A | -1.3111 | |
| 222 | D | A | -2.1052 | |
| 223 | H | A | -1.1847 | |
| 224 | Y | A | -0.6164 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | 0.0000 | |
| 228 | Y | A | -0.1457 | |
| 229 | W | A | -0.2623 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -0.9586 | |
| 232 | G | A | -0.3687 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | 0.0360 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.2185 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.7760 | |
| 239 | S | A | -0.9125 | |
| 1 | M | B | 0.6425 | |
| 2 | Q | B | -0.5533 | |
| 3 | S | B | -0.1281 | |
| 4 | I | B | 0.6242 | |
| 5 | K | B | -1.3360 | |
| 6 | G | B | 0.0000 | |
| 7 | N | B | -1.2652 | |
| 8 | H | B | -1.3625 | |
| 9 | L | B | -1.2985 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -1.2228 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.4081 | |
| 14 | D | B | -0.1520 | |
| 15 | Y | B | 0.4618 | |
| 16 | Q | B | -1.3435 | |
| 17 | E | B | -2.6949 | |
| 18 | D | B | -2.8004 | |
| 19 | G | B | -1.6002 | |
| 20 | S | B | -1.3575 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.6410 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.6411 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.6017 | |
| 27 | A | B | -2.6660 | |
| 28 | E | B | -3.2731 | |
| 29 | A | B | -2.8739 | |
| 30 | K | B | -3.5537 | |
| 31 | N | B | -2.2408 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.6914 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | -0.3372 | |
| 36 | K | B | -1.4220 | |
| 37 | D | B | -2.1325 | |
| 38 | G | B | -1.5231 | |
| 39 | K | B | -1.5759 | |
| 40 | M | B | 0.5285 | |
| 41 | I | B | 0.8721 | |
| 42 | G | B | 1.4005 | |
| 43 | F | B | 1.7123 | |
| 44 | L | B | -0.9308 | |
| 45 | T | B | -2.4895 | |
| 46 | E | B | -4.5396 | |
| 47 | D | B | -4.2551 | |
| 48 | K | B | -4.1243 | |
| 49 | K | B | -4.1431 | |
| 50 | K | B | -2.9249 | |
| 51 | W | B | -1.0968 | |
| 52 | N | B | -1.6245 | |
| 53 | L | B | -0.9839 | |
| 54 | G | B | -1.1173 | |
| 55 | S | B | -1.4122 | |
| 56 | N | B | -1.3859 | |
| 57 | A | B | -1.1926 | |
| 58 | K | B | -2.1825 | |
| 59 | D | B | -1.6852 | |
| 60 | P | B | -1.2435 | |
| 61 | R | B | -1.4099 | |
| 62 | G | B | -0.9919 | |
| 63 | M | B | 0.0000 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | -0.9218 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.7343 | |
| 68 | G | B | 0.0000 | |
| 69 | S | B | -1.9462 | |
| 70 | Q | B | -2.4324 | |
| 71 | N | B | -2.5195 | |
| 72 | K | B | -2.1041 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.0259 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.5829 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.2205 | |
| 82 | M | B | -1.1534 | |
| 83 | G | B | -1.6595 | |
| 84 | S | B | -1.4403 | |
| 85 | A | B | -2.0526 | |
| 86 | D | B | -3.6820 | |
| 87 | D | B | -4.2188 | |
| 88 | A | B | -3.3809 | |
| 89 | K | B | -4.2953 | |
| 90 | K | B | -4.8533 | |
| 91 | D | B | -4.8071 | |
| 92 | A | B | -3.6347 | |
| 93 | A | B | -3.6294 | |
| 94 | K | B | -4.9478 | |
| 95 | K | B | -4.8276 | |
| 96 | D | B | -4.8699 | |
| 97 | D | B | -4.7989 | |
| 98 | A | B | -4.1832 | |
| 99 | K | B | -4.7879 | |
| 100 | K | B | -4.4898 | |
| 101 | D | B | -4.3971 | |
| 102 | D | B | -4.0909 | |
| 103 | A | B | -3.2404 | |
| 104 | K | B | -3.9153 | |
| 105 | K | B | -3.7591 | |
| 106 | D | B | -3.5719 | |
| 107 | G | B | -2.5477 | |
| 108 | S | B | -2.1490 | |
| 109 | D | B | -3.0585 | |
| 110 | G | B | -2.8192 | |
| 111 | N | B | -3.2809 | |
| 112 | E | B | -3.4212 | |
| 113 | E | B | -2.8606 | |
| 114 | M | B | -1.1093 | |
| 115 | G | B | -0.9520 | |
| 116 | G | B | -1.0544 | |
| 117 | I | B | -0.1934 | |
| 118 | T | B | -0.3538 | |
| 119 | Q | B | -0.4608 | |
| 120 | T | B | -0.4069 | |
| 121 | P | B | -0.6295 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.3529 | |
| 124 | V | B | -0.4539 | |
| 125 | S | B | -0.1925 | |
| 126 | I | B | -0.1463 | |
| 127 | S | B | -0.2355 | |
| 128 | G | B | -0.6347 | |
| 129 | T | B | -1.0955 | |
| 130 | T | B | -0.9970 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.1313 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | -1.3068 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | -0.7698 | |
| 137 | Q | B | -0.5463 | |
| 138 | Y | B | -0.3603 | |
| 139 | P | B | -0.7830 | |
| 140 | G | B | -1.0445 | |
| 141 | S | B | -0.6740 | |
| 142 | E | B | 0.0000 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.6872 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | -1.9593 | |
| 147 | H | B | -1.9203 | |
| 148 | N | B | -2.4251 | |
| 149 | D | B | -3.3520 | |
| 150 | K | B | -3.4207 | |
| 151 | N | B | -3.0940 | |
| 152 | I | B | -1.7468 | |
| 153 | G | B | -2.1586 | |
| 154 | G | B | -2.9591 | |
| 155 | D | B | -4.4956 | |
| 156 | E | B | -4.7383 | |
| 157 | D | B | -4.3500 | |
| 158 | D | B | -3.8954 | |
| 159 | K | B | -3.6502 | |
| 160 | N | B | -2.7520 | |
| 161 | I | B | -2.1965 | |
| 162 | G | B | -2.2585 | |
| 163 | S | B | -2.0633 | |
| 164 | D | B | -3.2059 | |
| 165 | E | B | -3.2330 | |
| 166 | D | B | -2.4142 | |
| 167 | H | B | -2.0963 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.9138 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.5973 | |
| 172 | E | B | -2.4572 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.1139 | |
| 175 | E | B | -0.7010 | |
| 176 | L | B | 0.1879 | |
| 177 | E | B | -1.2666 | |
| 178 | Q | B | -1.0828 | |
| 179 | S | B | 0.0000 | |
| 180 | G | B | 0.0000 | |
| 181 | Y | B | -0.7683 | |
| 182 | Y | B | 0.0000 | |
| 183 | V | B | 0.0000 | |
| 184 | C | B | 0.0000 | |
| 185 | Y | B | 0.0000 | |
| 186 | P | B | -0.3012 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | 0.0000 | |
| 190 | K | B | -0.9491 | |
| 191 | P | B | 0.0000 | |
| 192 | E | B | -1.4435 | |
| 193 | D | B | -1.5050 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.0241 | |
| 196 | F | B | 0.0000 | |
| 197 | Y | B | -0.1753 | |
| 198 | L | B | 0.0000 | |
| 199 | Y | B | 0.0000 | |
| 200 | L | B | 0.0000 | |
| 201 | R | B | -0.6718 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.2187 | |
| 204 | V | B | 0.0040 |
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 | -0.9205 | 3.906 | View | CSV | PDB |
| 4.5 | -1.0035 | 3.8813 | View | CSV | PDB |
| 5.0 | -1.0995 | 3.8478 | View | CSV | PDB |
| 5.5 | -1.1919 | 3.8185 | View | CSV | PDB |
| 6.0 | -1.2632 | 3.8125 | View | CSV | PDB |
| 6.5 | -1.3012 | 3.8467 | View | CSV | PDB |
| 7.0 | -1.3064 | 3.9223 | View | CSV | PDB |
| 7.5 | -1.2891 | 4.0249 | View | CSV | PDB |
| 8.0 | -1.2575 | 4.1399 | View | CSV | PDB |
| 8.5 | -1.2125 | 4.2592 | View | CSV | PDB |
| 9.0 | -1.1514 | 4.379 | 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