| Chain sequence(s) |
A: EIVLTQSPATLSLSPGERATLSCSASQSVSYMNWYQQKPGQAPRLLIYDTSNLATGIPARFSGSGSGRDFTLTISSLEPEDFAVYYCQQWSNNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVKKPGASVKVSCKASGYTFNRYTMHWVRQAPGQGLWMGYINPSRGYTNYNQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
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. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:11:43)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/5a7c7caa4d7cbf7/tmp/folded.pdb (00:11:43)
[INFO] Main: Simulation completed successfully. (00:21:35)
|
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 | -1.8021 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.9878 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.0325 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.4160 | |
| 8 | P | A | -0.2902 | |
| 9 | A | A | -0.3399 | |
| 10 | T | A | -0.5128 | |
| 11 | L | A | -0.4544 | |
| 12 | S | A | -0.9983 | |
| 13 | L | A | -1.2800 | |
| 14 | S | A | -1.6490 | |
| 15 | P | A | -1.7998 | |
| 16 | G | A | -1.9477 | |
| 17 | E | A | -2.5794 | |
| 18 | R | A | -2.8190 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.6537 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.6305 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -1.3905 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.9855 | |
| 27 | Q | A | -2.0596 | |
| 28 | S | A | -1.9769 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.9715 | |
| 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 | -0.4712 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -1.5438 | |
| 39 | P | A | -1.1615 | |
| 40 | G | A | -1.4225 | |
| 41 | Q | A | -2.0497 | |
| 42 | A | A | -1.2287 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -0.6785 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.3812 | |
| 49 | D | A | -0.8868 | |
| 50 | T | A | -0.5549 | |
| 51 | S | A | -0.5693 | |
| 52 | N | A | -0.4834 | |
| 53 | L | A | 0.2445 | |
| 54 | A | A | 0.0000 | |
| 55 | T | A | -0.1924 | |
| 56 | G | A | -0.4353 | |
| 57 | I | A | 0.0256 | |
| 58 | P | A | -0.0835 | |
| 59 | A | A | -0.0777 | |
| 60 | R | A | -0.7343 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.3112 | |
| 63 | G | A | 0.0000 | |
| 64 | S | A | -0.8923 | |
| 65 | G | A | -1.4276 | |
| 66 | S | A | -1.5136 | |
| 67 | G | A | -1.9649 | |
| 68 | R | A | -3.1984 | |
| 69 | D | A | -3.0664 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7118 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.6291 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -1.5586 | |
| 76 | S | A | -1.9235 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.5700 | |
| 79 | P | A | -1.9915 | |
| 80 | E | A | -2.7298 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -1.2028 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.4608 | |
| 85 | Y | A | 0.0000 | |
| 86 | Y | A | -0.1312 | |
| 87 | C | A | 0.0000 | |
| 88 | Q | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | W | A | 0.0000 | |
| 91 | S | A | -0.8445 | |
| 92 | N | A | -1.6833 | |
| 93 | N | A | -1.5532 | |
| 94 | P | A | -1.3417 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | -0.1219 | |
| 97 | F | A | 0.2648 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -0.9274 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.1209 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.7075 | |
| 105 | I | A | -1.1747 | |
| 106 | K | A | -2.1061 | |
| 107 | G | A | -1.6046 | |
| 108 | G | A | -1.4410 | |
| 109 | G | A | -1.3406 | |
| 110 | G | A | -1.4195 | |
| 111 | S | A | -0.9660 | |
| 112 | G | A | -1.6386 | |
| 113 | G | A | -1.6273 | |
| 114 | G | A | -1.8134 | |
| 115 | G | A | -1.6545 | |
| 116 | S | A | -1.1989 | |
| 117 | G | A | -1.4393 | |
| 118 | G | A | -1.2109 | |
| 119 | G | A | -1.3517 | |
| 120 | G | A | -1.4395 | |
| 121 | S | A | -1.3864 | |
| 122 | Q | A | -1.8074 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.5579 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | 0.2478 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.6525 | |
| 129 | G | A | -0.7106 | |
| 130 | A | A | -0.2661 | |
| 131 | E | A | -0.5627 | |
| 132 | V | A | 0.6923 | |
| 133 | K | A | -0.9994 | |
| 134 | K | A | -2.1376 | |
| 135 | P | A | -2.2230 | |
| 136 | G | A | -1.5467 | |
| 137 | A | A | -1.2224 | |
| 138 | S | A | -1.3447 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -2.1812 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.6633 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -1.0212 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.8272 | |
| 147 | G | A | -0.9245 | |
| 148 | Y | A | -0.6413 | |
| 149 | T | A | -0.6624 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -1.6507 | |
| 152 | R | A | -2.4972 | |
| 153 | Y | A | -0.9138 | |
| 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 | -0.3774 | |
| 161 | A | A | -0.7474 | |
| 162 | P | A | -0.7941 | |
| 163 | G | A | -1.2620 | |
| 164 | Q | A | -1.2948 | |
| 165 | G | A | -0.6177 | |
| 166 | L | A | -0.3659 | |
| 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 | -1.4226 | |
| 175 | R | A | -1.4437 | |
| 176 | G | A | -0.7786 | |
| 177 | Y | A | -0.3809 | |
| 178 | T | A | -0.1688 | |
| 179 | N | A | -0.5875 | |
| 180 | Y | A | -1.3147 | |
| 181 | N | A | 0.0000 | |
| 182 | Q | A | -2.9270 | |
| 183 | K | A | -2.9551 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.4491 | |
| 186 | D | A | -3.0805 | |
| 187 | R | A | 0.0000 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -1.0760 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.6079 | |
| 192 | R | A | -1.3582 | |
| 193 | D | A | -1.2442 | |
| 194 | T | A | -0.8120 | |
| 195 | S | A | -0.5763 | |
| 196 | T | A | -0.7196 | |
| 197 | S | A | -0.8654 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.8103 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.5941 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.2427 | |
| 205 | S | A | -1.2534 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -3.0146 | |
| 208 | S | A | -2.3488 | |
| 209 | E | A | -2.5297 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.9244 | |
| 212 | A | A | 0.0000 | |
| 213 | V | A | 0.1323 | |
| 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 | -0.6087 | |
| 221 | D | A | -1.3241 | |
| 222 | D | A | -2.1994 | |
| 223 | H | A | -1.3125 | |
| 224 | Y | A | -0.7261 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | 0.0000 | |
| 228 | Y | A | -0.1282 | |
| 229 | W | A | -0.3106 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -1.3383 | |
| 232 | G | A | -0.6416 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | -0.0792 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.4209 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8744 | |
| 239 | S | A | -0.9340 | |
| 1 | M | B | 0.7184 | |
| 2 | Q | B | -0.6913 | |
| 3 | S | B | -0.9589 | |
| 4 | I | B | 0.0000 | |
| 5 | K | B | -2.6429 | |
| 6 | G | B | -2.1395 | |
| 7 | N | B | -2.4084 | |
| 8 | H | B | 0.0000 | |
| 9 | L | B | -1.5631 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | 0.0000 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.6717 | |
| 14 | D | B | 0.0000 | |
| 15 | Y | B | 0.5606 | |
| 16 | Q | B | -1.1647 | |
| 17 | E | B | -2.5919 | |
| 18 | D | B | -2.7081 | |
| 19 | G | B | -1.4550 | |
| 20 | S | B | 0.0000 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.4038 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.1850 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.5020 | |
| 27 | A | B | 0.0000 | |
| 28 | E | B | -3.1045 | |
| 29 | A | B | -2.8455 | |
| 30 | K | B | -3.4373 | |
| 31 | N | B | -2.0927 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.7162 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | -0.3428 | |
| 36 | K | B | -1.4248 | |
| 37 | D | B | -2.0946 | |
| 38 | G | B | -1.4212 | |
| 39 | K | B | -1.8125 | |
| 40 | M | B | 0.5057 | |
| 41 | I | B | 0.8641 | |
| 42 | G | B | 1.3903 | |
| 43 | F | B | 1.9661 | |
| 44 | L | B | -0.7118 | |
| 45 | T | B | -2.2167 | |
| 46 | E | B | -4.4433 | |
| 47 | D | B | -3.9553 | |
| 48 | K | B | -3.5429 | |
| 49 | K | B | -3.5583 | |
| 50 | K | B | -2.4106 | |
| 51 | W | B | -0.8912 | |
| 52 | N | B | -1.5089 | |
| 53 | L | B | -0.9048 | |
| 54 | G | B | -1.0793 | |
| 55 | S | B | -1.3152 | |
| 56 | N | B | -1.2525 | |
| 57 | A | B | -1.1393 | |
| 58 | K | B | -2.1301 | |
| 59 | D | B | -1.6055 | |
| 60 | P | B | -1.1965 | |
| 61 | R | B | -1.3589 | |
| 62 | G | B | -0.9520 | |
| 63 | M | B | -1.0977 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | 0.0000 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.7536 | |
| 68 | G | B | 0.0000 | |
| 69 | S | B | -1.9971 | |
| 70 | Q | B | -2.4956 | |
| 71 | N | B | -2.6163 | |
| 72 | K | B | -2.1906 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.3533 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.5608 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.1891 | |
| 82 | M | B | -1.1574 | |
| 83 | G | B | -1.6194 | |
| 84 | S | B | -1.4707 | |
| 85 | A | B | -2.0609 | |
| 86 | D | B | -3.4215 | |
| 87 | D | B | -4.0294 | |
| 88 | A | B | -3.1961 | |
| 89 | K | B | -4.0431 | |
| 90 | K | B | -4.3080 | |
| 91 | D | B | -4.0908 | |
| 92 | A | B | -3.1348 | |
| 93 | A | B | -3.2293 | |
| 94 | K | B | -4.4729 | |
| 95 | K | B | -4.3470 | |
| 96 | D | B | -4.2018 | |
| 97 | D | B | -4.2112 | |
| 98 | A | B | -3.4444 | |
| 99 | K | B | -4.0131 | |
| 100 | K | B | -4.0651 | |
| 101 | D | B | -4.1648 | |
| 102 | D | B | -3.9599 | |
| 103 | A | B | -3.0238 | |
| 104 | K | B | -3.7893 | |
| 105 | K | B | -3.7833 | |
| 106 | D | B | -3.6336 | |
| 107 | G | B | -2.7821 | |
| 108 | S | B | -2.3861 | |
| 109 | D | B | -3.1306 | |
| 110 | G | B | -2.9345 | |
| 111 | N | B | -3.3555 | |
| 112 | E | B | -3.4760 | |
| 113 | E | B | -2.8600 | |
| 114 | M | B | -0.7890 | |
| 115 | G | B | -0.5061 | |
| 116 | G | B | -0.2499 | |
| 117 | I | B | 1.3749 | |
| 118 | T | B | 0.2924 | |
| 119 | Q | B | -0.3603 | |
| 120 | T | B | -0.5811 | |
| 121 | P | B | -0.8963 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.6539 | |
| 124 | V | B | -0.5643 | |
| 125 | S | B | -0.1954 | |
| 126 | I | B | 0.0198 | |
| 127 | S | B | -0.2432 | |
| 128 | G | B | -0.6872 | |
| 129 | T | B | -1.1932 | |
| 130 | T | B | 0.0000 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.1790 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | -1.3931 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | 0.0000 | |
| 137 | Q | B | -1.6102 | |
| 138 | Y | B | -0.7897 | |
| 139 | P | B | -0.8984 | |
| 140 | G | B | -0.8824 | |
| 141 | S | B | -1.0552 | |
| 142 | E | B | -0.9118 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.6577 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | -1.6809 | |
| 147 | H | B | -1.5529 | |
| 148 | N | B | -1.7909 | |
| 149 | D | B | -2.7752 | |
| 150 | K | B | -2.9733 | |
| 151 | N | B | -2.9800 | |
| 152 | I | B | -1.7942 | |
| 153 | G | B | 0.0000 | |
| 154 | G | B | -2.6758 | |
| 155 | D | B | -3.5586 | |
| 156 | E | B | -4.2853 | |
| 157 | D | B | -3.9373 | |
| 158 | D | B | -3.5788 | |
| 159 | K | B | -3.2050 | |
| 160 | N | B | -2.6863 | |
| 161 | I | B | -2.0666 | |
| 162 | G | B | -1.9134 | |
| 163 | S | B | -1.6332 | |
| 164 | D | B | -3.1172 | |
| 165 | E | B | -3.0842 | |
| 166 | D | B | -2.1735 | |
| 167 | H | B | -1.8151 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.8621 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.7412 | |
| 172 | E | B | -2.5135 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.1662 | |
| 175 | E | B | -0.7814 | |
| 176 | L | B | 0.2034 | |
| 177 | E | B | -1.2331 | |
| 178 | Q | B | -1.0058 | |
| 179 | S | B | -0.7091 | |
| 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 | -0.6299 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -0.7748 | |
| 190 | K | B | -1.1669 | |
| 191 | P | B | -1.3644 | |
| 192 | E | B | -2.0539 | |
| 193 | D | B | -2.2331 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.3250 | |
| 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 | -0.6752 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.3415 | |
| 204 | V | B | -0.2720 |
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 | -0.8933 | 4.1438 | View | CSV | PDB |
| 4.5 | -0.9696 | 4.1458 | View | CSV | PDB |
| 5.0 | -1.0606 | 4.1518 | View | CSV | PDB |
| 5.5 | -1.1507 | 4.1685 | View | CSV | PDB |
| 6.0 | -1.2225 | 4.2063 | View | CSV | PDB |
| 6.5 | -1.2627 | 4.2707 | View | CSV | PDB |
| 7.0 | -1.2704 | 4.3543 | View | CSV | PDB |
| 7.5 | -1.2556 | 4.4469 | View | CSV | PDB |
| 8.0 | -1.2272 | 4.5427 | View | CSV | PDB |
| 8.5 | -1.1874 | 4.6393 | View | CSV | PDB |
| 9.0 | -1.134 | 4.7352 | 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