| Chain sequence(s) |
A: QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEINGGGGSGGGGSGGGGSQVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPQGLEWIGYINPSRGYTNTNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS
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] (00:00:01)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:01)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:01)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:01)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:03)
[INFO] FoldX: Starting FoldX energy minimization (00:00:03)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:08:30)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/1141e10a0f13a18/tmp/folded.pdb (00:08:30)
[INFO] Main: Simulation completed successfully. (00:12:10)
|
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 | Q | A | -0.9454 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 1.3052 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | 0.1759 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.0919 | |
| 8 | P | A | 0.1808 | |
| 9 | A | A | 0.4164 | |
| 10 | I | A | 0.8988 | |
| 11 | M | A | -0.0086 | |
| 12 | S | A | -1.0300 | |
| 13 | A | A | 0.0000 | |
| 14 | S | A | -1.8378 | |
| 15 | P | A | -1.8246 | |
| 16 | G | A | -2.0783 | |
| 17 | E | A | -2.8538 | |
| 18 | K | A | -2.6746 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.8681 | |
| 21 | M | A | 0.0000 | |
| 22 | T | A | -0.2454 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.1496 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.0025 | |
| 27 | S | A | -0.3105 | |
| 28 | S | A | -0.5303 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.5791 | |
| 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 | Q | A | 0.0000 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -1.5836 | |
| 39 | S | A | -0.8128 | |
| 40 | G | A | -0.9270 | |
| 41 | T | A | -1.0812 | |
| 42 | S | A | -1.0244 | |
| 43 | P | A | 0.0000 | |
| 44 | K | A | -1.8083 | |
| 45 | R | A | -0.8546 | |
| 46 | W | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.4303 | |
| 49 | D | A | -0.8353 | |
| 50 | T | A | -0.8007 | |
| 51 | S | A | -1.2550 | |
| 52 | K | A | -1.6027 | |
| 53 | L | A | -0.7054 | |
| 54 | A | A | 0.0000 | |
| 55 | S | A | -0.4732 | |
| 56 | G | A | -0.5404 | |
| 57 | V | A | -0.4152 | |
| 58 | P | A | -0.3549 | |
| 59 | A | A | -0.4065 | |
| 60 | H | A | -1.0420 | |
| 61 | F | A | 0.0000 | |
| 62 | R | A | -2.1227 | |
| 63 | G | A | 0.0000 | |
| 64 | S | A | -1.0078 | |
| 65 | G | A | -0.5846 | |
| 66 | S | A | -0.5830 | |
| 67 | G | A | -0.5567 | |
| 68 | T | A | -0.5337 | |
| 69 | S | A | -0.5749 | |
| 70 | Y | A | 0.0000 | |
| 71 | S | A | -0.5902 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -1.1494 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -1.7548 | |
| 76 | G | A | -1.9784 | |
| 77 | M | A | 0.0000 | |
| 78 | E | A | -2.3665 | |
| 79 | A | A | -2.2101 | |
| 80 | E | A | -2.6248 | |
| 81 | D | A | 0.0000 | |
| 82 | A | A | -1.8963 | |
| 83 | A | A | -1.4225 | |
| 84 | T | A | 0.0000 | |
| 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 | -0.4525 | |
| 92 | S | A | -0.7256 | |
| 93 | N | A | -1.0352 | |
| 94 | P | A | -0.9659 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.0000 | |
| 98 | G | A | 0.0000 | |
| 99 | S | A | -0.5131 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.4408 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -2.2358 | |
| 105 | I | A | -1.7709 | |
| 106 | N | A | -1.5925 | |
| 107 | G | A | -1.4498 | |
| 108 | G | A | -1.5679 | |
| 109 | G | A | -1.2324 | |
| 110 | G | A | -1.2353 | |
| 111 | S | A | -1.0604 | |
| 112 | G | A | -1.5929 | |
| 113 | G | A | -1.2207 | |
| 114 | G | A | -1.5873 | |
| 115 | G | A | -1.2222 | |
| 116 | S | A | -1.1089 | |
| 117 | G | A | -1.2296 | |
| 118 | G | A | -1.2870 | |
| 119 | G | A | -1.3265 | |
| 120 | G | A | -1.3873 | |
| 121 | S | A | -1.2702 | |
| 122 | Q | A | -1.6959 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.7635 | |
| 125 | L | A | 0.0000 | |
| 126 | Q | A | -2.1133 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -1.1392 | |
| 129 | G | A | -0.7702 | |
| 130 | A | A | -0.1492 | |
| 131 | E | A | -0.2457 | |
| 132 | L | A | 0.7463 | |
| 133 | A | A | -0.5336 | |
| 134 | R | A | -1.8862 | |
| 135 | P | A | -1.6144 | |
| 136 | G | A | -1.1670 | |
| 137 | A | A | -0.9747 | |
| 138 | S | A | -1.1425 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -1.9585 | |
| 141 | M | A | 0.0000 | |
| 142 | S | A | -0.9366 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -1.6831 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -1.0813 | |
| 147 | G | A | -0.8647 | |
| 148 | Y | A | -0.5538 | |
| 149 | T | A | -0.7125 | |
| 150 | F | A | 0.0000 | |
| 151 | T | A | -1.7078 | |
| 152 | R | A | -2.1908 | |
| 153 | Y | A | -0.6550 | |
| 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 | K | A | 0.0000 | |
| 160 | Q | A | -0.7112 | |
| 161 | R | A | -1.3801 | |
| 162 | P | A | -1.1135 | |
| 163 | Q | A | -1.6759 | |
| 164 | G | A | -1.1241 | |
| 165 | L | A | 0.0000 | |
| 166 | E | A | -0.9644 | |
| 167 | W | A | 0.0000 | |
| 168 | I | 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 | -1.5125 | |
| 175 | R | A | -1.4214 | |
| 176 | G | A | -0.8544 | |
| 177 | Y | A | -0.6770 | |
| 178 | T | A | -0.3188 | |
| 179 | N | A | -0.7573 | |
| 180 | T | A | -1.5295 | |
| 181 | N | A | 0.0000 | |
| 182 | Q | A | -2.9538 | |
| 183 | K | A | -3.1581 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.5924 | |
| 186 | D | A | -3.2677 | |
| 187 | K | A | -2.2749 | |
| 188 | A | A | 0.0000 | |
| 189 | T | A | -1.1466 | |
| 190 | L | A | 0.0000 | |
| 191 | T | A | -0.4413 | |
| 192 | T | A | -0.9644 | |
| 193 | D | A | -1.6778 | |
| 194 | K | A | -2.2128 | |
| 195 | S | A | -1.2889 | |
| 196 | S | A | -1.1459 | |
| 197 | S | A | -1.2609 | |
| 198 | T | A | 0.0000 | |
| 199 | A | A | 0.0000 | |
| 200 | Y | A | -0.5780 | |
| 201 | M | A | 0.0000 | |
| 202 | Q | A | -1.3945 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.1376 | |
| 205 | S | A | -1.0149 | |
| 206 | L | A | 0.0000 | |
| 207 | T | A | -1.3464 | |
| 208 | S | A | -1.4953 | |
| 209 | E | A | -2.0231 | |
| 210 | D | A | 0.0000 | |
| 211 | S | A | -0.6505 | |
| 212 | A | A | 0.0000 | |
| 213 | V | A | 0.0485 | |
| 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 | -0.4983 | |
| 221 | D | A | -1.2295 | |
| 222 | D | A | -2.0075 | |
| 223 | H | A | -1.1976 | |
| 224 | Y | A | -0.5489 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | 0.0000 | |
| 228 | Y | A | -0.2235 | |
| 229 | W | A | -0.6982 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -1.6018 | |
| 232 | G | A | -0.8286 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | -0.0595 | |
| 235 | L | A | 0.0000 | |
| 236 | T | A | -0.2031 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.6588 | |
| 239 | S | A | -0.9835 | |
| 1 | M | B | 0.6073 | |
| 2 | Q | B | -0.9193 | |
| 3 | S | B | -1.2350 | |
| 4 | I | B | 0.0000 | |
| 5 | K | B | -2.6974 | |
| 6 | G | B | -2.2112 | |
| 7 | N | B | -2.6851 | |
| 8 | H | B | 0.0000 | |
| 9 | L | B | -1.6730 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -0.4238 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.5660 | |
| 14 | D | B | 0.0000 | |
| 15 | Y | B | 0.5151 | |
| 16 | Q | B | -1.2510 | |
| 17 | E | B | -2.6056 | |
| 18 | D | B | -2.7421 | |
| 19 | G | B | -1.6913 | |
| 20 | S | B | 0.0000 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.5381 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.3571 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.5268 | |
| 27 | A | B | -2.9489 | |
| 28 | E | B | -3.1282 | |
| 29 | A | B | -2.8643 | |
| 30 | K | B | -3.5153 | |
| 31 | N | B | -2.1913 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.6980 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | -0.4799 | |
| 36 | K | B | -1.5579 | |
| 37 | D | B | -2.2721 | |
| 38 | G | B | -1.6291 | |
| 39 | K | B | -1.9260 | |
| 40 | M | B | 0.3835 | |
| 41 | I | B | 0.7845 | |
| 42 | G | B | 1.3878 | |
| 43 | F | B | 1.7804 | |
| 44 | L | B | -0.7194 | |
| 45 | T | B | -2.3120 | |
| 46 | E | B | -4.3911 | |
| 47 | D | B | -4.1445 | |
| 48 | K | B | -3.8493 | |
| 49 | K | B | -3.6123 | |
| 50 | K | B | -2.7655 | |
| 51 | W | B | -1.0652 | |
| 52 | N | B | -1.4408 | |
| 53 | L | B | -0.9649 | |
| 54 | G | B | -1.1369 | |
| 55 | S | B | -1.4230 | |
| 56 | N | B | -1.4285 | |
| 57 | A | B | -1.1938 | |
| 58 | K | B | -2.1813 | |
| 59 | D | B | -1.6418 | |
| 60 | P | B | -1.1874 | |
| 61 | R | B | -1.2773 | |
| 62 | G | B | -0.9488 | |
| 63 | M | B | -1.1657 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | -0.9093 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.8291 | |
| 68 | G | B | -2.5901 | |
| 69 | S | B | -2.0099 | |
| 70 | Q | B | -2.4901 | |
| 71 | N | B | -2.6397 | |
| 72 | K | B | -2.2009 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.4979 | |
| 75 | P | B | -0.9765 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.4962 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.0443 | |
| 82 | M | B | -1.1432 | |
| 83 | G | B | -1.5411 | |
| 84 | S | B | -1.3860 | |
| 85 | A | B | -1.8467 | |
| 86 | D | B | -3.4088 | |
| 87 | D | B | -4.1140 | |
| 88 | A | B | -3.2321 | |
| 89 | K | B | -4.1879 | |
| 90 | K | B | -4.7096 | |
| 91 | D | B | -4.2907 | |
| 92 | A | B | -3.2361 | |
| 93 | A | B | -3.3690 | |
| 94 | K | B | -4.5598 | |
| 95 | K | B | -4.7189 | |
| 96 | D | B | -4.6076 | |
| 97 | D | B | -4.6628 | |
| 98 | A | B | -3.9754 | |
| 99 | K | B | -4.5491 | |
| 100 | K | B | -4.4725 | |
| 101 | D | B | -4.4063 | |
| 102 | D | B | -4.1820 | |
| 103 | A | B | -3.3522 | |
| 104 | K | B | -3.8205 | |
| 105 | K | B | -3.8753 | |
| 106 | D | B | -3.4950 | |
| 107 | G | B | -2.4279 | |
| 108 | S | B | -2.2781 | |
| 109 | D | B | -3.0124 | |
| 110 | G | B | -2.8521 | |
| 111 | N | B | -3.3423 | |
| 112 | E | B | -3.4459 | |
| 113 | E | B | -2.9098 | |
| 114 | M | B | -0.6922 | |
| 115 | G | B | -0.5502 | |
| 116 | G | B | -0.4660 | |
| 117 | I | B | 1.3928 | |
| 118 | T | B | 0.1681 | |
| 119 | Q | B | -0.1638 | |
| 120 | T | B | -0.4535 | |
| 121 | P | B | -0.8057 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.6678 | |
| 124 | V | B | -0.5409 | |
| 125 | S | B | -0.1917 | |
| 126 | I | B | 0.1151 | |
| 127 | S | B | -0.2434 | |
| 128 | G | B | -0.7255 | |
| 129 | T | B | -1.2727 | |
| 130 | T | B | -1.1358 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.1887 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | -1.3982 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | 0.0000 | |
| 137 | Q | B | -1.4541 | |
| 138 | Y | B | -0.6223 | |
| 139 | P | B | -0.8004 | |
| 140 | G | B | -0.8565 | |
| 141 | S | B | -0.8481 | |
| 142 | E | B | -0.7748 | |
| 143 | I | B | -0.8730 | |
| 144 | L | B | -0.5009 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | -1.4483 | |
| 147 | H | B | 0.0000 | |
| 148 | N | B | -1.7196 | |
| 149 | D | B | -2.8505 | |
| 150 | K | B | -2.7381 | |
| 151 | N | B | -2.1560 | |
| 152 | I | B | -1.1524 | |
| 153 | G | B | -1.7216 | |
| 154 | G | B | -2.2746 | |
| 155 | D | B | -3.4060 | |
| 156 | E | B | -4.0164 | |
| 157 | D | B | -3.9295 | |
| 158 | D | B | -3.5538 | |
| 159 | K | B | -3.4959 | |
| 160 | N | B | -2.8033 | |
| 161 | I | B | -2.0498 | |
| 162 | G | B | -2.1278 | |
| 163 | S | B | -1.9120 | |
| 164 | D | B | -3.0596 | |
| 165 | E | B | -3.0845 | |
| 166 | D | B | -2.0360 | |
| 167 | H | B | -1.8684 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.9534 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.8253 | |
| 172 | E | B | -2.6514 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.2581 | |
| 175 | E | B | -0.8482 | |
| 176 | L | B | 0.1653 | |
| 177 | E | B | -1.2764 | |
| 178 | Q | B | -1.0299 | |
| 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 | -0.4073 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -0.5047 | |
| 190 | K | B | -0.9489 | |
| 191 | P | B | 0.0000 | |
| 192 | E | B | -1.9983 | |
| 193 | D | B | -2.0384 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.3837 | |
| 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 | -0.6261 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.3792 | |
| 204 | V | B | -0.4002 |
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 | -0.9732 | 4.0265 | View | CSV | PDB |
| 4.5 | -1.05 | 3.9997 | View | CSV | PDB |
| 5.0 | -1.1396 | 3.9664 | View | CSV | PDB |
| 5.5 | -1.2251 | 3.941 | View | CSV | PDB |
| 6.0 | -1.2882 | 3.9415 | View | CSV | PDB |
| 6.5 | -1.3151 | 3.9795 | View | CSV | PDB |
| 7.0 | -1.3072 | 4.0509 | View | CSV | PDB |
| 7.5 | -1.2769 | 4.1421 | View | CSV | PDB |
| 8.0 | -1.2338 | 4.2419 | View | CSV | PDB |
| 8.5 | -1.1799 | 4.3444 | View | CSV | PDB |
| 9.0 | -1.1132 | 4.4467 | 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