| Chain sequence(s) |
A: DVLMTQTPLSLPVTLGDQASISCRSSQSIVHSNGYTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLRISGVEAEDLGVYYCFQGSHVPWTFGGGTKLEIKASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS
B: QVQLQQSGAELARPGASVKLSCKASGYTFTNYGITWVKQRTGQGLEWIGEIYPRSGNTYYNEKFKGKATLTADKSSSTASMELRSLTSEDSAVYFCATKGLWYFDVWGTGTTVTVSSVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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 (00:12:15)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/7301074cabd45d2/tmp/folded.pdb (00:12:15)
[INFO] Main: Simulation completed successfully. (00:19:33)
|
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 | -1.4211 | |
| 2 | V | A | 0.0000 | |
| 3 | L | A | 0.4588 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.4006 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | -0.1028 | |
| 8 | P | A | 0.3712 | |
| 9 | L | A | 1.1012 | |
| 10 | S | A | 0.0165 | |
| 11 | L | A | -0.2832 | |
| 12 | P | A | -0.8387 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.1381 | |
| 15 | L | A | -0.5594 | |
| 16 | G | A | -1.4929 | |
| 17 | D | A | -2.5505 | |
| 18 | Q | A | -2.7647 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -1.2645 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.9185 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.2491 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -0.9727 | |
| 27 | Q | A | -1.3227 | |
| 28 | S | A | -0.8260 | |
| 29 | I | A | 0.0000 | |
| 30 | V | A | 0.5628 | |
| 31 | H | A | -0.1682 | |
| 32 | S | A | -0.6802 | |
| 33 | N | A | -1.1411 | |
| 34 | G | A | -0.4104 | |
| 35 | Y | A | 0.6131 | |
| 36 | T | A | 0.3976 | |
| 37 | Y | A | 0.4503 | |
| 38 | L | A | 0.0000 | |
| 39 | E | A | 0.0000 | |
| 40 | W | A | 0.0000 | |
| 41 | Y | A | 0.0000 | |
| 42 | L | A | 0.0000 | |
| 43 | Q | A | 0.0000 | |
| 44 | K | A | -1.6996 | |
| 45 | P | A | -1.0764 | |
| 46 | G | A | -1.3540 | |
| 47 | Q | A | -1.9376 | |
| 48 | S | A | -1.2128 | |
| 49 | P | A | 0.0000 | |
| 50 | K | A | -1.6396 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | -0.0975 | |
| 55 | K | A | -0.3175 | |
| 56 | V | A | -0.3471 | |
| 57 | S | A | -0.8190 | |
| 58 | N | A | -1.1572 | |
| 59 | R | A | -1.6368 | |
| 60 | F | A | -0.5879 | |
| 61 | S | A | -0.5759 | |
| 62 | G | A | -0.8035 | |
| 63 | V | A | -0.9604 | |
| 64 | P | A | -1.2907 | |
| 65 | D | A | -2.2677 | |
| 66 | R | A | -2.1164 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.5562 | |
| 69 | G | A | 0.0000 | |
| 70 | S | A | -0.9086 | |
| 71 | G | A | -0.9684 | |
| 72 | S | A | -0.7412 | |
| 73 | G | A | -0.7417 | |
| 74 | T | A | -1.4205 | |
| 75 | D | A | -1.9786 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -1.1806 | |
| 78 | L | A | 0.0000 | |
| 79 | R | A | -2.3673 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.2590 | |
| 82 | G | A | -1.8614 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -1.8604 | |
| 85 | A | A | -1.1958 | |
| 86 | E | A | -2.1418 | |
| 87 | D | A | 0.0000 | |
| 88 | L | A | -0.9523 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | -0.3844 | |
| 91 | Y | A | 0.0000 | |
| 92 | Y | A | 0.0000 | |
| 93 | C | A | 0.0000 | |
| 94 | F | A | 0.0000 | |
| 95 | Q | A | 0.0000 | |
| 96 | G | A | 0.0000 | |
| 97 | S | A | 0.0000 | |
| 98 | H | A | 0.3938 | |
| 99 | V | A | 1.2322 | |
| 100 | P | A | 0.0492 | |
| 101 | W | A | 0.0000 | |
| 102 | T | A | 0.0680 | |
| 103 | F | A | 0.0000 | |
| 104 | G | A | 0.0000 | |
| 105 | G | A | -0.4339 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.8872 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -1.2351 | |
| 111 | I | A | -0.6561 | |
| 112 | K | A | -1.6569 | |
| 113 | A | A | -0.9587 | |
| 114 | S | A | -0.7513 | |
| 115 | T | A | -1.2498 | |
| 116 | K | A | -1.4041 | |
| 117 | G | A | -1.5443 | |
| 118 | P | A | 0.0000 | |
| 119 | S | A | -0.4640 | |
| 120 | V | A | 0.0000 | |
| 121 | F | A | -0.6159 | |
| 122 | P | A | -0.9841 | |
| 123 | L | A | 0.0000 | |
| 124 | A | A | -1.2233 | |
| 125 | P | A | 0.0000 | |
| 126 | S | A | -1.0884 | |
| 127 | S | A | -0.8798 | |
| 128 | K | A | -1.2545 | |
| 129 | S | A | 0.0000 | |
| 130 | T | A | -0.7094 | |
| 131 | S | A | -0.6965 | |
| 132 | G | A | -0.7877 | |
| 133 | G | A | -0.8581 | |
| 134 | T | A | -0.5761 | |
| 135 | A | A | 0.0000 | |
| 136 | A | A | 0.0000 | |
| 137 | L | A | 0.0000 | |
| 138 | G | A | 0.0000 | |
| 139 | C | A | 0.0000 | |
| 140 | L | A | 0.0000 | |
| 141 | V | A | 0.0000 | |
| 142 | K | A | 0.0000 | |
| 143 | D | A | -0.5954 | |
| 144 | Y | A | 0.0000 | |
| 145 | F | A | -0.2363 | |
| 146 | P | A | -0.7693 | |
| 147 | E | A | -0.9925 | |
| 148 | P | A | -0.9229 | |
| 149 | V | A | -0.8529 | |
| 150 | T | A | -0.7635 | |
| 151 | V | A | -0.4047 | |
| 152 | S | A | -0.4109 | |
| 153 | W | A | 0.0000 | |
| 154 | N | A | -0.8500 | |
| 155 | S | A | -0.6833 | |
| 156 | G | A | -0.5746 | |
| 157 | A | A | -0.3121 | |
| 158 | L | A | -0.0725 | |
| 159 | T | A | -0.2231 | |
| 160 | S | A | -0.2261 | |
| 161 | G | A | -0.3007 | |
| 162 | V | A | 0.1404 | |
| 163 | H | A | -0.3245 | |
| 164 | T | A | -0.1550 | |
| 165 | F | A | 0.0000 | |
| 166 | P | A | -0.3869 | |
| 167 | A | A | 0.1780 | |
| 168 | V | A | 0.5323 | |
| 169 | L | A | 1.0187 | |
| 170 | Q | A | 0.1802 | |
| 171 | S | A | -0.2334 | |
| 172 | S | A | -0.2898 | |
| 173 | G | A | 0.0158 | |
| 174 | L | A | 0.0781 | |
| 175 | Y | A | 0.3511 | |
| 176 | S | A | 0.0000 | |
| 177 | L | A | 0.0000 | |
| 178 | S | A | 0.0000 | |
| 179 | S | A | 0.0000 | |
| 180 | V | A | 0.0000 | |
| 181 | V | A | 0.0000 | |
| 182 | T | A | -0.1562 | |
| 183 | V | A | 0.0000 | |
| 184 | P | A | -0.6426 | |
| 185 | S | A | -0.5665 | |
| 186 | S | A | -0.6201 | |
| 187 | S | A | -0.6704 | |
| 188 | L | A | -0.8926 | |
| 189 | G | A | -1.0458 | |
| 190 | T | A | -0.8721 | |
| 191 | Q | A | -1.5217 | |
| 192 | T | A | -1.2974 | |
| 193 | Y | A | 0.0000 | |
| 194 | I | A | -1.2044 | |
| 195 | C | A | 0.0000 | |
| 196 | N | A | -1.3999 | |
| 197 | V | A | 0.0000 | |
| 198 | N | A | -2.2818 | |
| 199 | H | A | 0.0000 | |
| 200 | K | A | -2.8903 | |
| 201 | P | A | -1.9576 | |
| 202 | S | A | -1.9336 | |
| 203 | N | A | -2.7160 | |
| 204 | T | A | -2.2549 | |
| 205 | K | A | -2.7610 | |
| 206 | V | A | -1.5174 | |
| 207 | D | A | -2.1371 | |
| 208 | K | A | -1.9373 | |
| 209 | K | A | -2.4052 | |
| 210 | V | A | 0.0000 | |
| 211 | E | A | -2.8077 | |
| 212 | P | A | -1.8076 | |
| 213 | K | A | -2.0188 | |
| 214 | S | A | -1.1255 | |
| 1 | Q | B | -1.2514 | |
| 2 | V | B | -0.4839 | |
| 3 | Q | B | -1.6878 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -2.1099 | |
| 6 | Q | B | -1.3257 | |
| 7 | S | B | -1.1581 | |
| 8 | G | B | -0.6850 | |
| 9 | A | B | -0.1598 | |
| 10 | E | B | -0.1930 | |
| 11 | L | B | 0.7511 | |
| 12 | A | B | -0.4590 | |
| 13 | R | B | -1.5870 | |
| 14 | P | B | -1.3956 | |
| 15 | G | B | -1.4334 | |
| 16 | A | B | -1.1517 | |
| 17 | S | B | -1.7306 | |
| 18 | V | B | 0.0000 | |
| 19 | K | B | -2.3053 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -1.1295 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -2.1289 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.2044 | |
| 26 | G | B | -0.7201 | |
| 27 | Y | B | -0.3371 | |
| 28 | T | B | -0.4393 | |
| 29 | F | B | 0.0000 | |
| 30 | T | B | -1.7491 | |
| 31 | N | B | -1.3821 | |
| 32 | Y | B | -0.2152 | |
| 33 | G | B | 0.0000 | |
| 34 | I | B | 0.0000 | |
| 35 | T | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | K | B | -0.5489 | |
| 39 | Q | B | -0.7688 | |
| 40 | R | B | -1.3680 | |
| 41 | T | B | -1.3078 | |
| 42 | G | B | -1.4652 | |
| 43 | Q | B | -1.6689 | |
| 44 | G | B | -1.1689 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -1.1342 | |
| 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 | -0.8156 | |
| 53 | P | B | 0.0000 | |
| 54 | R | B | -2.8060 | |
| 55 | S | B | -1.7303 | |
| 56 | G | B | -1.8866 | |
| 57 | N | B | -1.5034 | |
| 58 | T | B | -0.2418 | |
| 59 | Y | B | 0.4977 | |
| 60 | Y | B | -0.4051 | |
| 61 | N | B | 0.0000 | |
| 62 | E | B | -3.1282 | |
| 63 | K | B | -3.2154 | |
| 64 | F | B | 0.0000 | |
| 65 | K | B | -2.9796 | |
| 66 | G | B | -2.2435 | |
| 67 | K | B | -2.2243 | |
| 68 | A | B | 0.0000 | |
| 69 | T | B | -1.1567 | |
| 70 | L | B | 0.0000 | |
| 71 | T | B | -0.8446 | |
| 72 | A | B | -1.7969 | |
| 73 | D | B | -2.8060 | |
| 74 | K | B | -2.9827 | |
| 75 | S | B | -1.6046 | |
| 76 | S | B | -1.5503 | |
| 77 | S | B | -1.6335 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | S | B | 0.0000 | |
| 81 | M | B | 0.0000 | |
| 82 | E | B | -1.8248 | |
| 83 | L | B | 0.0000 | |
| 84 | R | B | -2.4765 | |
| 85 | S | B | -1.5909 | |
| 86 | L | B | 0.0000 | |
| 87 | T | B | -1.7350 | |
| 88 | S | B | -2.0671 | |
| 89 | E | B | -2.4242 | |
| 90 | D | B | 0.0000 | |
| 91 | S | B | 0.0000 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | 0.1329 | |
| 94 | Y | B | 0.0000 | |
| 95 | F | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | T | B | 0.0000 | |
| 99 | K | B | 0.1823 | |
| 100 | G | B | 0.6066 | |
| 101 | L | B | 1.6226 | |
| 102 | W | B | 0.9063 | |
| 103 | Y | B | 0.4583 | |
| 104 | F | B | 0.0000 | |
| 105 | D | B | -0.0378 | |
| 106 | V | B | -0.1782 | |
| 107 | W | B | -0.5643 | |
| 108 | G | B | 0.0000 | |
| 109 | T | B | -0.7925 | |
| 110 | G | B | -0.4859 | |
| 111 | T | B | 0.0000 | |
| 112 | T | B | 0.0239 | |
| 113 | V | B | 0.0000 | |
| 114 | T | B | 0.0000 | |
| 115 | V | B | 0.0000 | |
| 116 | S | B | -0.3617 | |
| 117 | S | B | 0.0857 | |
| 118 | V | B | 0.9533 | |
| 119 | A | B | 0.2463 | |
| 120 | A | B | 0.0240 | |
| 121 | P | B | 0.0000 | |
| 122 | S | B | -0.2461 | |
| 123 | V | B | 0.0000 | |
| 124 | F | B | 0.0000 | |
| 125 | I | B | 0.0000 | |
| 126 | F | B | 0.0000 | |
| 127 | P | B | -0.8231 | |
| 128 | P | B | 0.0000 | |
| 129 | S | B | 0.0000 | |
| 130 | D | B | -2.7774 | |
| 131 | E | B | -2.6757 | |
| 132 | Q | B | 0.0000 | |
| 133 | L | B | -2.1908 | |
| 134 | K | B | -2.7884 | |
| 135 | S | B | -1.7544 | |
| 136 | G | B | -1.2871 | |
| 137 | T | B | -1.0995 | |
| 138 | A | B | 0.0000 | |
| 139 | S | B | 0.0000 | |
| 140 | V | B | 0.0000 | |
| 141 | V | B | 0.0000 | |
| 142 | C | B | 0.0000 | |
| 143 | L | B | 0.0000 | |
| 144 | L | B | 0.0000 | |
| 145 | N | B | 0.0000 | |
| 146 | N | B | -0.9955 | |
| 147 | F | B | 0.0000 | |
| 148 | Y | B | 0.0000 | |
| 149 | P | B | -1.0835 | |
| 150 | R | B | -2.8782 | |
| 151 | E | B | -3.1478 | |
| 152 | A | B | -2.3298 | |
| 153 | K | B | -2.5054 | |
| 154 | V | B | -1.2003 | |
| 155 | Q | B | -0.8718 | |
| 156 | W | B | 0.0000 | |
| 157 | K | B | -0.7355 | |
| 158 | V | B | 0.0000 | |
| 159 | D | B | -1.8766 | |
| 160 | N | B | -1.5946 | |
| 161 | A | B | -0.4404 | |
| 162 | L | B | 0.2963 | |
| 163 | Q | B | -0.5080 | |
| 164 | S | B | -0.8373 | |
| 165 | G | B | -1.2938 | |
| 166 | N | B | -1.6469 | |
| 167 | S | B | -1.3907 | |
| 168 | Q | B | -1.2499 | |
| 169 | E | B | -1.3552 | |
| 170 | S | B | -0.7484 | |
| 171 | V | B | -0.8957 | |
| 172 | T | B | 0.0000 | |
| 173 | E | B | -2.3116 | |
| 174 | Q | B | -2.0397 | |
| 175 | D | B | -2.3060 | |
| 176 | S | B | -2.3532 | |
| 177 | K | B | -2.7821 | |
| 178 | D | B | -2.3144 | |
| 179 | S | B | 0.0000 | |
| 180 | T | B | 0.0000 | |
| 181 | Y | B | -1.4388 | |
| 182 | S | B | 0.0000 | |
| 183 | L | B | 0.0000 | |
| 184 | S | B | 0.0000 | |
| 185 | S | B | 0.0000 | |
| 186 | T | B | -0.6520 | |
| 187 | L | B | 0.0000 | |
| 188 | T | B | -0.6871 | |
| 189 | L | B | -0.9406 | |
| 190 | S | B | -1.1922 | |
| 191 | K | B | -2.1928 | |
| 192 | A | B | -2.0077 | |
| 193 | D | B | -2.8325 | |
| 194 | Y | B | 0.0000 | |
| 195 | E | B | -3.3594 | |
| 196 | K | B | -3.5240 | |
| 197 | H | B | -2.6677 | |
| 198 | K | B | -2.7792 | |
| 199 | V | B | -1.1545 | |
| 200 | Y | B | 0.0000 | |
| 201 | A | B | 0.0000 | |
| 202 | C | B | 0.0000 | |
| 203 | E | B | -0.7882 | |
| 204 | V | B | 0.0000 | |
| 205 | T | B | -1.2825 | |
| 206 | H | B | 0.0000 | |
| 207 | Q | B | -1.6206 | |
| 208 | G | B | -0.2702 | |
| 209 | L | B | -0.3320 | |
| 210 | S | B | -0.4624 | |
| 211 | S | B | -0.4413 | |
| 212 | P | B | -0.6013 | |
| 213 | V | B | -0.0175 | |
| 214 | T | B | -0.3775 | |
| 215 | K | B | -0.6095 | |
| 216 | S | B | -0.5788 | |
| 217 | F | B | 0.0000 | |
| 218 | N | B | -1.6673 | |
| 219 | R | B | -2.1540 | |
| 220 | G | B | -1.8364 | |
| 221 | E | B | -2.3020 | |
| 222 | C | B | -0.8340 |
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 | -0.7727 | 2.1731 | View | CSV | PDB |
| 4.5 | -0.8185 | 2.1622 | View | CSV | PDB |
| 5.0 | -0.8722 | 2.1505 | View | CSV | PDB |
| 5.5 | -0.9235 | 2.1399 | View | CSV | PDB |
| 6.0 | -0.96 | 2.1326 | View | CSV | PDB |
| 6.5 | -0.9712 | 2.1306 | View | CSV | PDB |
| 7.0 | -0.9561 | 2.1332 | View | CSV | PDB |
| 7.5 | -0.9231 | 2.1386 | View | CSV | PDB |
| 8.0 | -0.8801 | 2.1455 | View | CSV | PDB |
| 8.5 | -0.8297 | 2.1544 | View | CSV | PDB |
| 9.0 | -0.7725 | 2.1662 | 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