| Chain sequence(s) |
A: EVQLQESGGGLVQPGGSLRLSCAASGFTFSIYSMNWVRQAPGKGLEWVSSIGSSGGTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAGSQYLYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCD
B: DIQMTQSPSSLSASVGDRVTITCRSSQRIMTYLNWYQQKPGKAPKLLIYVGSHSQSGVPSRFRGSGSETDFTLTISGLQPEDSATYYCQQSFFTPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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. (00:00:02)
[INFO] FoldX: Starting FoldX energy minimization (00:00:02)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:04:14)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/2545c77932a93f3/tmp/folded.pdb (00:04:14)
[INFO] Main: Simulation completed successfully. (00:06:22)
|
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 | -1.6638 | |
| 2 | V | A | -0.4505 | |
| 3 | Q | A | -1.3248 | |
| 4 | L | A | 0.0000 | |
| 5 | Q | A | -1.7369 | |
| 6 | E | A | 0.0000 | |
| 7 | S | A | -0.9810 | |
| 8 | G | A | -0.7737 | |
| 9 | G | A | -0.3915 | |
| 10 | G | A | -0.1665 | |
| 11 | L | A | -0.0849 | |
| 12 | V | A | -0.5136 | |
| 13 | Q | A | -1.5199 | |
| 14 | P | A | -1.6339 | |
| 15 | G | A | -1.4397 | |
| 16 | G | A | -1.1549 | |
| 17 | S | A | -1.1971 | |
| 18 | L | A | -0.9245 | |
| 19 | R | A | -1.6999 | |
| 20 | L | A | 0.0000 | |
| 21 | S | A | -0.7402 | |
| 22 | C | A | 0.0000 | |
| 23 | A | A | -1.0478 | |
| 24 | A | A | 0.0000 | |
| 25 | S | A | -1.0793 | |
| 26 | G | A | -0.8084 | |
| 27 | F | A | -0.1450 | |
| 28 | T | A | 0.2023 | |
| 29 | F | A | 0.0000 | |
| 30 | S | A | 0.0816 | |
| 31 | I | A | 1.3842 | |
| 32 | Y | A | 0.0000 | |
| 33 | S | A | 0.0000 | |
| 34 | M | A | 0.0000 | |
| 35 | N | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | V | A | 0.0000 | |
| 38 | R | A | 0.0000 | |
| 39 | Q | A | -0.9879 | |
| 40 | A | A | -1.3172 | |
| 41 | P | A | -1.1054 | |
| 42 | G | A | -1.4733 | |
| 43 | K | A | -2.3321 | |
| 44 | G | A | -1.5316 | |
| 45 | L | A | 0.0000 | |
| 46 | E | A | -1.3656 | |
| 47 | W | A | 0.0000 | |
| 48 | V | A | 0.0000 | |
| 49 | S | A | 0.0000 | |
| 50 | S | A | 0.0000 | |
| 51 | I | A | 0.0000 | |
| 52 | G | A | 0.1437 | |
| 53 | S | A | 0.1991 | |
| 54 | S | A | -0.4214 | |
| 55 | G | A | -0.8201 | |
| 56 | G | A | -0.7049 | |
| 57 | T | A | -0.3410 | |
| 58 | T | A | -0.0067 | |
| 59 | Y | A | -0.0070 | |
| 60 | Y | A | -0.7055 | |
| 61 | A | A | -1.3996 | |
| 62 | D | A | -2.3848 | |
| 63 | S | A | -1.6977 | |
| 64 | V | A | 0.0000 | |
| 65 | K | A | -2.4469 | |
| 66 | G | A | -1.6359 | |
| 67 | R | A | 0.0000 | |
| 68 | F | A | 0.0000 | |
| 69 | T | A | -0.6732 | |
| 70 | I | A | 0.0000 | |
| 71 | S | A | -0.4864 | |
| 72 | R | A | -1.1381 | |
| 73 | D | A | -1.7476 | |
| 74 | N | A | -1.5355 | |
| 75 | S | A | -1.6241 | |
| 76 | K | A | -2.3991 | |
| 77 | N | A | -1.7272 | |
| 78 | T | A | 0.0000 | |
| 79 | L | A | 0.0000 | |
| 80 | Y | A | -0.4753 | |
| 81 | L | A | 0.0000 | |
| 82 | Q | A | -0.9551 | |
| 83 | M | A | 0.0000 | |
| 84 | N | A | -1.3484 | |
| 85 | S | A | -1.2403 | |
| 86 | L | A | 0.0000 | |
| 87 | R | A | -2.2502 | |
| 88 | A | A | -1.6986 | |
| 89 | E | A | -2.2150 | |
| 90 | D | A | 0.0000 | |
| 91 | T | A | -0.7610 | |
| 92 | A | A | 0.0000 | |
| 93 | V | A | 0.0288 | |
| 94 | Y | A | 0.0000 | |
| 95 | Y | A | 0.0000 | |
| 96 | C | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | G | A | 0.0000 | |
| 99 | S | A | 0.0000 | |
| 100 | Q | A | -0.0869 | |
| 101 | Y | A | 1.1380 | |
| 102 | L | A | 2.0899 | |
| 103 | Y | A | 0.0000 | |
| 104 | G | A | 0.0000 | |
| 105 | M | A | 0.0000 | |
| 106 | D | A | -0.8835 | |
| 107 | V | A | 0.0000 | |
| 108 | W | A | -0.7746 | |
| 109 | G | A | 0.0000 | |
| 110 | Q | A | -1.9000 | |
| 111 | G | A | -1.0506 | |
| 112 | T | A | -0.5057 | |
| 113 | T | A | -0.1361 | |
| 114 | V | A | 0.0000 | |
| 115 | T | A | -0.5024 | |
| 116 | V | A | 0.0000 | |
| 117 | S | A | -0.8763 | |
| 118 | S | A | -0.6353 | |
| 119 | A | A | -0.4315 | |
| 120 | S | A | -0.6290 | |
| 121 | T | A | -1.0513 | |
| 122 | K | A | -1.5325 | |
| 123 | G | A | -1.7092 | |
| 124 | P | A | 0.0000 | |
| 125 | S | A | -0.6068 | |
| 126 | V | A | 0.0000 | |
| 127 | F | A | 0.0000 | |
| 128 | P | A | -1.1628 | |
| 129 | L | A | 0.0000 | |
| 130 | A | A | -0.8810 | |
| 131 | P | A | 0.0000 | |
| 132 | S | A | -1.3532 | |
| 133 | S | A | -1.5552 | |
| 134 | K | A | -2.1065 | |
| 135 | S | A | -1.1584 | |
| 136 | T | A | -0.8581 | |
| 137 | S | A | -0.8319 | |
| 138 | G | A | -0.8749 | |
| 139 | G | A | -0.8902 | |
| 140 | T | A | -0.6130 | |
| 141 | A | A | 0.0000 | |
| 142 | A | A | 0.0000 | |
| 143 | L | A | 0.0000 | |
| 144 | G | A | 0.0000 | |
| 145 | C | A | 0.0000 | |
| 146 | L | A | 0.0000 | |
| 147 | V | A | 0.0000 | |
| 148 | K | A | -0.3893 | |
| 149 | D | A | -0.6154 | |
| 150 | Y | A | 0.0000 | |
| 151 | F | A | -0.3695 | |
| 152 | P | A | 0.0000 | |
| 153 | E | A | -0.6600 | |
| 154 | P | A | -0.8049 | |
| 155 | V | A | -0.7503 | |
| 156 | T | A | -0.7034 | |
| 157 | V | A | -0.4274 | |
| 158 | S | A | -0.4715 | |
| 159 | W | A | 0.0000 | |
| 160 | N | A | -0.8210 | |
| 161 | S | A | -0.7134 | |
| 162 | G | A | -0.5161 | |
| 163 | A | A | -0.2558 | |
| 164 | L | A | -0.0070 | |
| 165 | T | A | -0.1755 | |
| 166 | S | A | -0.1646 | |
| 167 | G | A | -0.1674 | |
| 168 | V | A | 0.1732 | |
| 169 | H | A | -0.2221 | |
| 170 | T | A | 0.0758 | |
| 171 | F | A | 0.0000 | |
| 172 | P | A | -0.0855 | |
| 173 | A | A | 0.5088 | |
| 174 | V | A | 0.7323 | |
| 175 | L | A | 1.4944 | |
| 176 | Q | A | 0.3992 | |
| 177 | S | A | -0.0188 | |
| 178 | S | A | -0.2253 | |
| 179 | G | A | 0.0857 | |
| 180 | L | A | 0.0516 | |
| 181 | Y | A | 0.3946 | |
| 182 | S | A | 0.0000 | |
| 183 | L | A | 0.0000 | |
| 184 | S | A | 0.0000 | |
| 185 | S | A | 0.0000 | |
| 186 | V | A | 0.0000 | |
| 187 | V | A | 0.0000 | |
| 188 | T | A | -0.0904 | |
| 189 | V | A | 0.0000 | |
| 190 | P | A | -0.5490 | |
| 191 | S | A | -0.6136 | |
| 192 | S | A | -0.6914 | |
| 193 | S | A | -0.7499 | |
| 194 | L | A | -0.9182 | |
| 195 | G | A | -1.4848 | |
| 196 | T | A | -1.1726 | |
| 197 | Q | A | -1.5522 | |
| 198 | T | A | -1.1833 | |
| 199 | Y | A | 0.0000 | |
| 200 | I | A | -1.2543 | |
| 201 | C | A | 0.0000 | |
| 202 | N | A | -1.5653 | |
| 203 | V | A | 0.0000 | |
| 204 | N | A | -2.3295 | |
| 205 | H | A | 0.0000 | |
| 206 | K | A | -2.8113 | |
| 207 | P | A | -1.6111 | |
| 208 | S | A | -1.9193 | |
| 209 | N | A | -2.7376 | |
| 210 | T | A | -2.2510 | |
| 211 | K | A | -2.8930 | |
| 212 | V | A | -1.7264 | |
| 213 | D | A | -2.5611 | |
| 214 | K | A | -2.1085 | |
| 215 | R | A | -2.2186 | |
| 216 | V | A | 0.0000 | |
| 217 | E | A | -2.8418 | |
| 218 | P | A | -1.7535 | |
| 219 | K | A | -2.6007 | |
| 220 | S | A | -1.3425 | |
| 221 | C | A | -0.8191 | |
| 222 | D | A | -1.6161 | |
| 1 | D | B | -1.9328 | |
| 2 | I | B | -1.6403 | |
| 3 | Q | B | -2.0346 | |
| 4 | M | B | 0.0000 | |
| 5 | T | B | -1.0555 | |
| 6 | Q | B | -0.7172 | |
| 7 | S | B | -0.4966 | |
| 8 | P | B | -0.5163 | |
| 9 | S | B | -0.7102 | |
| 10 | S | B | -0.6624 | |
| 11 | L | B | -0.4105 | |
| 12 | S | B | -0.6855 | |
| 13 | A | B | 0.0000 | |
| 14 | S | B | -1.0596 | |
| 15 | V | B | -0.3767 | |
| 16 | G | B | -1.1218 | |
| 17 | D | B | -2.3589 | |
| 18 | R | B | -2.5635 | |
| 19 | V | B | 0.0000 | |
| 20 | T | B | -0.6755 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.7484 | |
| 23 | C | B | 0.0000 | |
| 24 | R | B | -2.3609 | |
| 25 | S | B | 0.0000 | |
| 26 | S | B | -2.3135 | |
| 27 | Q | B | -2.8075 | |
| 28 | R | B | -2.9645 | |
| 29 | I | B | 0.0000 | |
| 30 | M | B | -0.2481 | |
| 31 | T | B | -0.0218 | |
| 32 | Y | B | 1.1482 | |
| 33 | L | B | 0.0000 | |
| 34 | N | B | 0.0000 | |
| 35 | W | B | 0.0000 | |
| 36 | Y | B | 0.0000 | |
| 37 | Q | B | 0.0000 | |
| 38 | Q | B | -1.3278 | |
| 39 | K | B | -1.9243 | |
| 40 | P | B | -1.5683 | |
| 41 | G | B | -1.6717 | |
| 42 | K | B | -2.5469 | |
| 43 | A | B | -1.6985 | |
| 44 | P | B | 0.0000 | |
| 45 | K | B | -1.6452 | |
| 46 | L | B | 0.0000 | |
| 47 | L | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | Y | B | -0.1294 | |
| 50 | V | B | 0.5193 | |
| 51 | G | B | 0.0000 | |
| 52 | S | B | -1.0543 | |
| 53 | H | B | -1.4585 | |
| 54 | S | B | -1.5221 | |
| 55 | Q | B | -1.6856 | |
| 56 | S | B | -1.1184 | |
| 57 | G | B | -0.9043 | |
| 58 | V | B | -0.8537 | |
| 59 | P | B | -0.8067 | |
| 60 | S | B | -1.0026 | |
| 61 | R | B | -1.2360 | |
| 62 | F | B | 0.0000 | |
| 63 | R | B | -2.2467 | |
| 64 | G | B | -1.3529 | |
| 65 | S | B | -1.2184 | |
| 66 | G | B | -1.1935 | |
| 67 | S | B | -1.4586 | |
| 68 | E | B | -2.5940 | |
| 69 | T | B | -2.7151 | |
| 70 | D | B | -2.7909 | |
| 71 | F | B | 0.0000 | |
| 72 | T | B | -1.0354 | |
| 73 | L | B | 0.0000 | |
| 74 | T | B | -1.1627 | |
| 75 | I | B | 0.0000 | |
| 76 | S | B | -1.7502 | |
| 77 | G | B | -1.3283 | |
| 78 | L | B | 0.0000 | |
| 79 | Q | B | -1.0268 | |
| 80 | P | B | -1.6565 | |
| 81 | E | B | -2.0115 | |
| 82 | D | B | 0.0000 | |
| 83 | S | B | 0.0000 | |
| 84 | A | B | 0.0000 | |
| 85 | T | B | -0.6975 | |
| 86 | Y | B | 0.0000 | |
| 87 | Y | B | 0.0000 | |
| 88 | C | B | 0.0000 | |
| 89 | Q | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | S | B | 0.0000 | |
| 92 | F | B | 1.4965 | |
| 93 | F | B | 2.0741 | |
| 94 | T | B | 0.7247 | |
| 95 | P | B | -0.2795 | |
| 96 | L | B | 0.0000 | |
| 97 | T | B | -0.4897 | |
| 98 | F | B | -0.4046 | |
| 99 | G | B | 0.0000 | |
| 100 | G | B | -1.1625 | |
| 101 | G | B | -0.8705 | |
| 102 | T | B | 0.0000 | |
| 103 | K | B | -1.1633 | |
| 104 | V | B | 0.0000 | |
| 105 | E | B | 0.0000 | |
| 106 | I | B | 0.0000 | |
| 107 | K | B | -1.2070 | |
| 108 | R | B | -0.6396 | |
| 109 | T | B | 0.2442 | |
| 110 | V | B | 1.0715 | |
| 111 | A | B | 0.3520 | |
| 112 | A | B | 0.0205 | |
| 113 | P | B | 0.0000 | |
| 114 | S | B | -0.2837 | |
| 115 | V | B | 0.0000 | |
| 116 | F | B | 0.0000 | |
| 117 | I | B | 0.0000 | |
| 118 | F | B | 0.0000 | |
| 119 | P | B | -0.4552 | |
| 120 | P | B | -0.8517 | |
| 121 | S | B | -1.9467 | |
| 122 | D | B | -3.2713 | |
| 123 | E | B | -3.2821 | |
| 124 | Q | B | 0.0000 | |
| 125 | L | B | -2.3590 | |
| 126 | K | B | -2.9347 | |
| 127 | S | B | -1.8329 | |
| 128 | G | B | -1.5314 | |
| 129 | T | B | -1.1434 | |
| 130 | A | B | 0.0000 | |
| 131 | S | B | 0.0000 | |
| 132 | V | B | 0.0000 | |
| 133 | V | B | 0.0000 | |
| 134 | C | B | 0.0000 | |
| 135 | L | B | 0.0000 | |
| 136 | L | B | 0.0000 | |
| 137 | N | B | 0.0000 | |
| 138 | N | B | -0.7908 | |
| 139 | F | B | 0.0000 | |
| 140 | Y | B | 0.0000 | |
| 141 | P | B | -1.1573 | |
| 142 | R | B | -1.8989 | |
| 143 | E | B | -2.4048 | |
| 144 | A | B | -1.6808 | |
| 145 | K | B | -1.6196 | |
| 146 | V | B | -0.6578 | |
| 147 | Q | B | -0.3677 | |
| 148 | W | B | 0.0000 | |
| 149 | K | B | -0.5489 | |
| 150 | V | B | 0.0000 | |
| 151 | D | B | -1.8844 | |
| 152 | N | B | -1.5153 | |
| 153 | A | B | -0.2886 | |
| 154 | L | B | 0.7667 | |
| 155 | Q | B | -0.2635 | |
| 156 | S | B | -0.6203 | |
| 157 | G | B | -1.2427 | |
| 158 | N | B | -1.5424 | |
| 159 | S | B | -1.3097 | |
| 160 | Q | B | -1.3484 | |
| 161 | E | B | -1.4141 | |
| 162 | S | B | -0.5612 | |
| 163 | V | B | -0.1521 | |
| 164 | T | B | -0.7194 | |
| 165 | E | B | -1.8664 | |
| 166 | Q | B | 0.0000 | |
| 167 | D | B | -1.9949 | |
| 168 | S | B | -2.2901 | |
| 169 | K | B | -2.7101 | |
| 170 | D | B | -2.1212 | |
| 171 | S | B | 0.0000 | |
| 172 | T | B | 0.0000 | |
| 173 | Y | B | -0.9510 | |
| 174 | S | B | 0.0000 | |
| 175 | L | B | 0.0000 | |
| 176 | S | B | 0.0000 | |
| 177 | S | B | 0.0000 | |
| 178 | T | B | 0.0000 | |
| 179 | L | B | 0.0000 | |
| 180 | T | B | -0.6200 | |
| 181 | L | B | -0.8351 | |
| 182 | S | B | -1.1463 | |
| 183 | K | B | -2.0977 | |
| 184 | A | B | -1.9564 | |
| 185 | D | B | -2.9096 | |
| 186 | Y | B | 0.0000 | |
| 187 | E | B | -3.1549 | |
| 188 | K | B | -3.5365 | |
| 189 | H | B | -3.0031 | |
| 190 | K | B | -3.1118 | |
| 191 | V | B | -1.2547 | |
| 192 | Y | B | 0.0000 | |
| 193 | A | B | 0.0000 | |
| 194 | C | B | 0.0000 | |
| 195 | E | B | -0.6079 | |
| 196 | V | B | 0.0000 | |
| 197 | T | B | -0.9105 | |
| 198 | H | B | 0.0000 | |
| 199 | Q | B | -1.2998 | |
| 200 | G | B | -0.2455 | |
| 201 | L | B | -0.1532 | |
| 202 | S | B | -0.4507 | |
| 203 | S | B | -0.4504 | |
| 204 | P | B | -0.4673 | |
| 205 | V | B | 0.0778 | |
| 206 | T | B | -0.3035 | |
| 207 | K | B | -0.4508 | |
| 208 | S | B | -0.6928 | |
| 209 | F | B | 0.0000 | |
| 210 | N | B | -2.0763 | |
| 211 | R | B | -2.3753 | |
| 212 | G | B | -2.0039 | |
| 213 | E | B | -2.6516 | |
| 214 | C | B | -1.4724 |
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 | -0.7387 | 4.9422 | View | CSV | PDB |
| 4.5 | -0.7857 | 4.8883 | View | CSV | PDB |
| 5.0 | -0.8401 | 4.828 | View | CSV | PDB |
| 5.5 | -0.8913 | 4.7654 | View | CSV | PDB |
| 6.0 | -0.9274 | 4.7019 | View | CSV | PDB |
| 6.5 | -0.9404 | 4.6384 | View | CSV | PDB |
| 7.0 | -0.9315 | 4.5751 | View | CSV | PDB |
| 7.5 | -0.9088 | 4.5129 | View | CSV | PDB |
| 8.0 | -0.8785 | 4.4538 | View | CSV | PDB |
| 8.5 | -0.8421 | 4.4028 | View | CSV | PDB |
| 9.0 | -0.7986 | 4.3666 | 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