| Chain sequence(s) |
A: DIVMTQSPSSLSVSAGEKVTMSCKSSQSLLNSGNQKNYLAWYQQKPGQPPKLLIYGASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDHSYPYTFGGGTKLEIKVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
B: QVQLQQSGAELARPGASVKLSCKASGYTFTSYGISWVKQRTGQGLEWIGEIYPRSGNTYYNEKFKGKATLTADKSSSTAYMELRSLTSEDSAVYFCARRASTVVAPYAMDYWGQGTSVTVASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 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 (00:04:17)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/8b69f855654800f/tmp/folded.pdb (00:04:17)
[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 | D | A | -1.5468 | |
| 2 | I | A | -0.1692 | |
| 3 | V | A | 0.9239 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.4073 | |
| 6 | Q | A | -0.5350 | |
| 7 | S | A | -0.6954 | |
| 8 | P | A | -0.5222 | |
| 9 | S | A | -0.6426 | |
| 10 | S | A | -0.6311 | |
| 11 | L | A | -0.2668 | |
| 12 | S | A | -0.7252 | |
| 13 | V | A | -1.0417 | |
| 14 | S | A | -1.2922 | |
| 15 | A | A | -1.4274 | |
| 16 | G | A | -1.6463 | |
| 17 | E | A | -2.4497 | |
| 18 | K | A | -2.5979 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.4776 | |
| 21 | M | A | 0.0000 | |
| 22 | S | A | -0.8295 | |
| 23 | C | A | 0.0000 | |
| 24 | K | A | -1.7875 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -0.8325 | |
| 27 | Q | A | -1.5294 | |
| 28 | S | A | -1.1641 | |
| 29 | L | A | 0.0000 | |
| 30 | L | A | -1.1980 | |
| 31 | N | A | -1.5686 | |
| 32 | S | A | -1.4032 | |
| 33 | G | A | -1.5067 | |
| 34 | N | A | -1.9817 | |
| 35 | Q | A | -2.5183 | |
| 36 | K | A | -2.6614 | |
| 37 | N | A | -1.4333 | |
| 38 | Y | A | 0.0000 | |
| 39 | L | A | 0.0000 | |
| 40 | A | A | 0.0000 | |
| 41 | W | A | 0.0000 | |
| 42 | Y | A | 0.0000 | |
| 43 | Q | A | 0.0000 | |
| 44 | Q | A | 0.0000 | |
| 45 | K | A | -1.6527 | |
| 46 | P | A | -1.2593 | |
| 47 | G | A | -1.5011 | |
| 48 | Q | A | -1.9574 | |
| 49 | P | A | -1.3799 | |
| 50 | P | A | 0.0000 | |
| 51 | K | A | -1.7825 | |
| 52 | L | A | 0.0000 | |
| 53 | L | A | 0.0000 | |
| 54 | I | A | 0.0000 | |
| 55 | Y | A | -0.0784 | |
| 56 | G | A | -0.5700 | |
| 57 | A | A | 0.0000 | |
| 58 | S | A | -0.8085 | |
| 59 | T | A | -0.7083 | |
| 60 | R | A | -1.6402 | |
| 61 | E | A | -1.3567 | |
| 62 | S | A | -0.9452 | |
| 63 | G | A | -1.0172 | |
| 64 | V | A | -1.1869 | |
| 65 | P | A | -1.3304 | |
| 66 | D | A | -2.1768 | |
| 67 | R | A | -1.4638 | |
| 68 | F | A | 0.0000 | |
| 69 | T | A | -0.8105 | |
| 70 | G | A | 0.0000 | |
| 71 | S | A | -0.7162 | |
| 72 | G | A | -1.2015 | |
| 73 | S | A | -1.1693 | |
| 74 | G | A | -1.2923 | |
| 75 | T | A | -1.6987 | |
| 76 | D | A | -2.4863 | |
| 77 | F | A | 0.0000 | |
| 78 | T | A | -0.7889 | |
| 79 | L | A | 0.0000 | |
| 80 | T | A | -0.5134 | |
| 81 | I | A | 0.0000 | |
| 82 | S | A | -1.6290 | |
| 83 | S | A | -1.7677 | |
| 84 | V | A | 0.0000 | |
| 85 | Q | A | -1.8322 | |
| 86 | A | A | -2.1679 | |
| 87 | E | A | -2.6865 | |
| 88 | D | A | 0.0000 | |
| 89 | L | A | 0.0000 | |
| 90 | A | A | 0.0000 | |
| 91 | V | A | -0.3946 | |
| 92 | Y | A | 0.0000 | |
| 93 | Y | A | 0.0000 | |
| 94 | C | A | 0.0000 | |
| 95 | Q | A | 0.0000 | |
| 96 | N | A | 0.0000 | |
| 97 | D | A | 0.0000 | |
| 98 | H | A | -0.1834 | |
| 99 | S | A | 0.0195 | |
| 100 | Y | A | -0.0480 | |
| 101 | P | A | -0.7015 | |
| 102 | Y | A | 0.0000 | |
| 103 | T | A | 0.0215 | |
| 104 | F | A | 0.1828 | |
| 105 | G | A | 0.0000 | |
| 106 | G | A | -0.7283 | |
| 107 | G | A | 0.0000 | |
| 108 | T | A | 0.0000 | |
| 109 | K | A | -1.0152 | |
| 110 | L | A | 0.0000 | |
| 111 | E | A | -1.2084 | |
| 112 | I | A | 0.0000 | |
| 113 | K | A | -1.5888 | |
| 114 | V | A | -0.1916 | |
| 115 | A | A | -0.4003 | |
| 116 | A | A | -0.4737 | |
| 117 | P | A | 0.0000 | |
| 118 | S | A | -0.1933 | |
| 119 | V | A | 0.0000 | |
| 120 | F | A | 0.0000 | |
| 121 | I | A | 0.0000 | |
| 122 | F | A | 0.0000 | |
| 123 | P | A | -0.7066 | |
| 124 | P | A | 0.0000 | |
| 125 | S | A | 0.0000 | |
| 126 | D | A | -2.8543 | |
| 127 | E | A | -3.0223 | |
| 128 | Q | A | 0.0000 | |
| 129 | L | A | -2.2783 | |
| 130 | K | A | -2.8735 | |
| 131 | S | A | -1.8242 | |
| 132 | G | A | -1.3174 | |
| 133 | T | A | -1.0567 | |
| 134 | A | A | 0.0000 | |
| 135 | S | A | 0.0000 | |
| 136 | V | A | 0.0000 | |
| 137 | V | A | 0.0000 | |
| 138 | C | A | 0.0000 | |
| 139 | L | A | 0.0000 | |
| 140 | L | A | 0.0000 | |
| 141 | N | A | 0.0000 | |
| 142 | N | A | -0.7424 | |
| 143 | F | A | 0.0000 | |
| 144 | Y | A | -1.2619 | |
| 145 | P | A | -1.8644 | |
| 146 | R | A | -3.2323 | |
| 147 | E | A | -3.2356 | |
| 148 | A | A | -2.3614 | |
| 149 | K | A | -2.3537 | |
| 150 | V | A | -0.8992 | |
| 151 | Q | A | -0.5557 | |
| 152 | W | A | 0.0000 | |
| 153 | K | A | -0.9278 | |
| 154 | V | A | 0.0000 | |
| 155 | D | A | -2.0151 | |
| 156 | N | A | -1.5483 | |
| 157 | A | A | -0.5704 | |
| 158 | L | A | 0.1879 | |
| 159 | Q | A | -0.5881 | |
| 160 | S | A | -0.8002 | |
| 161 | G | A | -1.3031 | |
| 162 | N | A | -1.6566 | |
| 163 | S | A | -1.5110 | |
| 164 | Q | A | -1.5297 | |
| 165 | E | A | -1.9211 | |
| 166 | S | A | -0.9919 | |
| 167 | V | A | -0.9771 | |
| 168 | T | A | 0.0000 | |
| 169 | E | A | -1.8721 | |
| 170 | Q | A | 0.0000 | |
| 171 | D | A | -1.9977 | |
| 172 | S | A | -2.3441 | |
| 173 | K | A | -2.7277 | |
| 174 | D | A | -1.8738 | |
| 175 | S | A | 0.0000 | |
| 176 | T | A | 0.0000 | |
| 177 | Y | A | 0.0000 | |
| 178 | S | A | 0.0000 | |
| 179 | L | A | 0.0000 | |
| 180 | S | A | 0.0000 | |
| 181 | S | A | 0.0000 | |
| 182 | T | A | -0.8393 | |
| 183 | L | A | 0.0000 | |
| 184 | T | A | -0.6455 | |
| 185 | L | A | -0.7955 | |
| 186 | S | A | -1.0035 | |
| 187 | K | A | -1.9926 | |
| 188 | A | A | -1.7702 | |
| 189 | D | A | -2.3790 | |
| 190 | Y | A | 0.0000 | |
| 191 | E | A | -3.2877 | |
| 192 | K | A | -3.5004 | |
| 193 | H | A | -2.9503 | |
| 194 | K | A | -3.0749 | |
| 195 | V | A | -1.3899 | |
| 196 | Y | A | 0.0000 | |
| 197 | A | A | 0.0000 | |
| 198 | C | A | 0.0000 | |
| 199 | E | A | -0.6923 | |
| 200 | V | A | 0.0000 | |
| 201 | T | A | -1.1987 | |
| 202 | H | A | 0.0000 | |
| 203 | Q | A | -2.0777 | |
| 204 | G | A | -0.8610 | |
| 205 | L | A | -0.4525 | |
| 206 | S | A | -0.4978 | |
| 207 | S | A | -0.4872 | |
| 208 | P | A | -0.5969 | |
| 209 | V | A | -0.0239 | |
| 210 | T | A | -0.3910 | |
| 211 | K | A | -0.7429 | |
| 212 | S | A | -0.6310 | |
| 213 | F | A | 0.0000 | |
| 214 | N | A | -1.7072 | |
| 215 | R | A | -2.2563 | |
| 216 | G | A | -1.9749 | |
| 217 | E | A | -2.3307 | |
| 218 | C | A | -1.0829 | |
| 1 | Q | B | -1.5517 | |
| 2 | V | B | -1.2160 | |
| 3 | Q | B | -2.0538 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -2.2189 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -1.0132 | |
| 8 | G | B | -1.0449 | |
| 9 | A | B | -0.8196 | |
| 10 | E | B | -0.9188 | |
| 11 | L | B | -0.7491 | |
| 12 | A | B | -1.0499 | |
| 13 | R | B | -2.1129 | |
| 14 | P | B | -1.5824 | |
| 15 | G | B | -1.4665 | |
| 16 | A | B | -1.3419 | |
| 17 | S | B | -1.7439 | |
| 18 | V | B | 0.0000 | |
| 19 | K | B | -1.9979 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -0.9007 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -1.8136 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.3302 | |
| 26 | G | B | -1.0985 | |
| 27 | Y | B | -0.3957 | |
| 28 | T | B | -0.2042 | |
| 29 | F | B | 0.0000 | |
| 30 | T | B | -1.2137 | |
| 31 | S | B | -0.3636 | |
| 32 | Y | B | 0.0298 | |
| 33 | G | B | 0.0000 | |
| 34 | I | B | 0.0000 | |
| 35 | S | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | K | B | -0.7201 | |
| 39 | Q | B | -1.1200 | |
| 40 | R | B | -1.7497 | |
| 41 | T | B | -1.0862 | |
| 42 | G | B | -1.3787 | |
| 43 | Q | B | -2.0077 | |
| 44 | G | B | -1.3408 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -1.1901 | |
| 47 | W | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | G | B | 0.0000 | |
| 50 | E | B | 0.0000 | |
| 51 | I | B | 0.0000 | |
| 52 | Y | B | 0.0000 | |
| 53 | P | B | 0.0000 | |
| 54 | R | B | -2.6320 | |
| 55 | S | B | -1.7066 | |
| 56 | G | B | -1.9196 | |
| 57 | N | B | -1.6226 | |
| 58 | T | B | -0.4986 | |
| 59 | Y | B | -0.0479 | |
| 60 | Y | B | -0.7702 | |
| 61 | N | B | 0.0000 | |
| 62 | E | B | -3.3281 | |
| 63 | K | B | -3.2116 | |
| 64 | F | B | 0.0000 | |
| 65 | K | B | -3.0156 | |
| 66 | G | B | -2.1974 | |
| 67 | K | B | -2.2123 | |
| 68 | A | B | 0.0000 | |
| 69 | T | B | -1.1186 | |
| 70 | L | B | 0.0000 | |
| 71 | T | B | -0.6789 | |
| 72 | A | B | -1.3987 | |
| 73 | D | B | -2.0137 | |
| 74 | K | B | -2.6058 | |
| 75 | S | B | -1.3221 | |
| 76 | S | B | -1.1660 | |
| 77 | S | B | -1.3167 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.5887 | |
| 81 | M | B | 0.0000 | |
| 82 | E | B | -1.8446 | |
| 83 | L | B | 0.0000 | |
| 84 | R | B | -2.2873 | |
| 85 | S | B | -1.5237 | |
| 86 | L | B | 0.0000 | |
| 87 | T | B | -1.4775 | |
| 88 | S | B | -1.4341 | |
| 89 | E | B | -2.0592 | |
| 90 | D | B | 0.0000 | |
| 91 | S | B | -0.9222 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | -0.1782 | |
| 94 | Y | B | 0.0000 | |
| 95 | F | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | R | B | 0.0000 | |
| 99 | R | B | 0.0000 | |
| 100 | A | B | 0.5521 | |
| 101 | S | B | 0.1551 | |
| 102 | T | B | 0.8804 | |
| 103 | V | B | 1.4805 | |
| 104 | V | B | 2.0843 | |
| 105 | A | B | 1.1007 | |
| 106 | P | B | 0.0000 | |
| 107 | Y | B | 1.1405 | |
| 108 | A | B | 0.0000 | |
| 109 | M | B | 0.0000 | |
| 110 | D | B | -0.4556 | |
| 111 | Y | B | -0.3316 | |
| 112 | W | B | 0.0000 | |
| 113 | G | B | 0.0000 | |
| 114 | Q | B | -1.8256 | |
| 115 | G | B | -1.0062 | |
| 116 | T | B | 0.0000 | |
| 117 | S | B | -0.3926 | |
| 118 | V | B | 0.0000 | |
| 119 | T | B | 0.0000 | |
| 120 | V | B | 0.0000 | |
| 121 | A | B | -0.7148 | |
| 122 | S | B | -0.7506 | |
| 123 | T | B | -1.1086 | |
| 124 | K | B | -1.3239 | |
| 125 | G | B | -1.3660 | |
| 126 | P | B | -0.5768 | |
| 127 | S | B | -0.4714 | |
| 128 | V | B | 0.0000 | |
| 129 | F | B | 0.0000 | |
| 130 | P | B | -1.0756 | |
| 131 | L | B | 0.0000 | |
| 132 | A | B | -1.1700 | |
| 133 | P | B | 0.0000 | |
| 134 | S | B | -1.0947 | |
| 135 | S | B | -0.9870 | |
| 136 | K | B | -1.2689 | |
| 137 | S | B | 0.0000 | |
| 138 | T | B | -0.7753 | |
| 139 | S | B | -0.8079 | |
| 140 | G | B | -0.8377 | |
| 141 | G | B | -0.8968 | |
| 142 | T | B | -0.6355 | |
| 143 | A | B | 0.0000 | |
| 144 | A | B | 0.0000 | |
| 145 | L | B | 0.0000 | |
| 146 | G | B | 0.0000 | |
| 147 | C | B | 0.0000 | |
| 148 | L | B | 0.0000 | |
| 149 | V | B | 0.0000 | |
| 150 | K | B | 0.0000 | |
| 151 | D | B | -0.3944 | |
| 152 | Y | B | 0.0000 | |
| 153 | F | B | -0.1960 | |
| 154 | P | B | 0.0000 | |
| 155 | E | B | -0.8292 | |
| 156 | P | B | -0.7226 | |
| 157 | V | B | -0.6034 | |
| 158 | T | B | -0.5096 | |
| 159 | V | B | -0.2579 | |
| 160 | S | B | -0.3376 | |
| 161 | W | B | 0.0000 | |
| 162 | N | B | -0.7283 | |
| 163 | S | B | -0.6710 | |
| 164 | G | B | -0.5179 | |
| 165 | A | B | -0.2522 | |
| 166 | L | B | 0.0144 | |
| 167 | T | B | -0.1687 | |
| 168 | S | B | -0.1695 | |
| 169 | G | B | -0.1856 | |
| 170 | V | B | 0.1856 | |
| 171 | H | B | -0.2568 | |
| 172 | T | B | 0.0301 | |
| 173 | F | B | 0.0000 | |
| 174 | P | B | -0.2935 | |
| 175 | A | B | 0.1607 | |
| 176 | V | B | 0.5503 | |
| 177 | L | B | 1.1541 | |
| 178 | Q | B | 0.2665 | |
| 179 | S | B | -0.2018 | |
| 180 | S | B | -0.2312 | |
| 181 | G | B | 0.0910 | |
| 182 | L | B | 0.1843 | |
| 183 | Y | B | 0.4339 | |
| 184 | S | B | 0.0000 | |
| 185 | L | B | 0.0000 | |
| 186 | S | B | 0.0000 | |
| 187 | S | B | 0.0000 | |
| 188 | V | B | 0.0000 | |
| 189 | V | B | 0.0000 | |
| 190 | T | B | -0.1167 | |
| 191 | V | B | 0.0000 | |
| 192 | P | B | -0.5387 | |
| 193 | S | B | -0.5902 | |
| 194 | S | B | -0.6048 | |
| 195 | S | B | -0.6157 | |
| 196 | L | B | -0.8301 | |
| 197 | G | B | -0.9936 | |
| 198 | T | B | -0.7746 | |
| 199 | Q | B | -1.2926 | |
| 200 | T | B | -1.0849 | |
| 201 | Y | B | 0.0000 | |
| 202 | I | B | -1.1010 | |
| 203 | C | B | 0.0000 | |
| 204 | N | B | -1.3794 | |
| 205 | V | B | 0.0000 | |
| 206 | N | B | -1.7362 | |
| 207 | H | B | 0.0000 | |
| 208 | K | B | -2.7593 | |
| 209 | P | B | -1.5999 | |
| 210 | S | B | -1.7714 | |
| 211 | N | B | -2.5565 | |
| 212 | T | B | -2.0334 | |
| 213 | K | B | -2.6301 | |
| 214 | V | B | -1.5384 | |
| 215 | D | B | -2.4328 | |
| 216 | K | B | -2.0438 | |
| 217 | K | B | -2.2074 | |
| 218 | V | B | 0.0000 | |
| 219 | E | B | -2.7206 | |
| 220 | P | B | -1.8252 | |
| 221 | K | B | -2.0505 | |
| 222 | S | B | -1.2499 |
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 | -0.8664 | 1.6898 | View | CSV | PDB |
| 4.5 | -0.9089 | 1.6902 | View | CSV | PDB |
| 5.0 | -0.9592 | 1.6912 | View | CSV | PDB |
| 5.5 | -1.0063 | 1.6936 | View | CSV | PDB |
| 6.0 | -1.0373 | 1.6982 | View | CSV | PDB |
| 6.5 | -1.041 | 1.7038 | View | CSV | PDB |
| 7.0 | -1.0169 | 1.708 | View | CSV | PDB |
| 7.5 | -0.9744 | 1.7101 | View | CSV | PDB |
| 8.0 | -0.922 | 1.711 | View | CSV | PDB |
| 8.5 | -0.8632 | 1.7112 | View | CSV | PDB |
| 9.0 | -0.7986 | 1.7111 | 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