| Chain sequence(s) |
A: EVQLVESGGGLVKPGGSLRLSCAASGFTFSGYGMHWVRQAPGKGLEWVAFISSGSGTIYYADTVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARRGVDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC
B: DVVMTQSPLSLPVTLGQPASISCKSSQSLLYSDGKTYLNWLLQRPGQSPRRLIYLVSKLDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCWQSTHFPFTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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 (00:04:55)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/9583d75514502e7/tmp/folded.pdb (00:04:55)
[INFO] Main: Simulation completed successfully. (00:06:40)
|
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 | -2.2086 | |
| 2 | V | A | -1.3771 | |
| 3 | Q | A | -1.5443 | |
| 4 | L | A | 0.0000 | |
| 5 | V | A | 0.2308 | |
| 6 | E | A | 0.0000 | |
| 7 | S | A | -0.4798 | |
| 8 | G | A | -0.7642 | |
| 9 | G | A | -0.3186 | |
| 10 | G | A | -0.2205 | |
| 11 | L | A | -0.1129 | |
| 12 | V | A | -0.8165 | |
| 13 | K | A | -2.0627 | |
| 14 | P | A | -1.8972 | |
| 15 | G | A | -1.5477 | |
| 16 | G | A | -1.3222 | |
| 17 | S | A | -1.3307 | |
| 18 | L | A | -1.0578 | |
| 19 | R | A | -1.7913 | |
| 20 | L | A | 0.0000 | |
| 21 | S | A | -0.4438 | |
| 22 | C | A | 0.0000 | |
| 23 | A | A | -0.3560 | |
| 24 | A | A | 0.0000 | |
| 25 | S | A | -1.0571 | |
| 26 | G | A | -1.3635 | |
| 27 | F | A | -0.5843 | |
| 28 | T | A | -0.2734 | |
| 29 | F | A | 0.0000 | |
| 30 | S | A | -0.8478 | |
| 31 | G | A | -0.5944 | |
| 32 | Y | A | -0.3150 | |
| 33 | G | A | 0.0000 | |
| 34 | M | A | 0.0000 | |
| 35 | H | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | V | A | 0.0000 | |
| 38 | R | A | 0.0000 | |
| 39 | Q | A | -0.7516 | |
| 40 | A | A | -1.1601 | |
| 41 | P | A | -0.9544 | |
| 42 | G | A | -1.4525 | |
| 43 | K | A | -2.3157 | |
| 44 | G | A | -1.4884 | |
| 45 | L | A | 0.0000 | |
| 46 | E | A | -0.9468 | |
| 47 | W | A | 0.0000 | |
| 48 | V | A | 0.0000 | |
| 49 | A | A | 0.0000 | |
| 50 | F | A | 0.4789 | |
| 51 | I | A | 0.0000 | |
| 52 | S | A | -0.3069 | |
| 53 | S | A | -0.7248 | |
| 54 | G | A | -0.8020 | |
| 55 | S | A | -0.5623 | |
| 56 | G | A | -0.4919 | |
| 57 | T | A | 0.2419 | |
| 58 | I | A | 1.1799 | |
| 59 | Y | A | 0.9831 | |
| 60 | Y | A | -0.1792 | |
| 61 | A | A | -1.2828 | |
| 62 | D | A | -2.5733 | |
| 63 | T | A | -1.7016 | |
| 64 | V | A | 0.0000 | |
| 65 | K | A | -2.4991 | |
| 66 | G | A | -1.7324 | |
| 67 | R | A | -1.4647 | |
| 68 | F | A | 0.0000 | |
| 69 | T | A | -0.5784 | |
| 70 | I | A | 0.0000 | |
| 71 | S | A | -0.2021 | |
| 72 | R | A | -0.9999 | |
| 73 | D | A | -1.5168 | |
| 74 | N | A | -1.7261 | |
| 75 | A | A | -1.3544 | |
| 76 | K | A | -2.2825 | |
| 77 | N | A | -1.7468 | |
| 78 | S | A | -1.0999 | |
| 79 | L | A | 0.0000 | |
| 80 | Y | A | -0.4716 | |
| 81 | L | A | 0.0000 | |
| 82 | Q | A | -1.0591 | |
| 83 | M | A | 0.0000 | |
| 84 | N | A | -1.4789 | |
| 85 | S | A | -1.3665 | |
| 86 | L | A | 0.0000 | |
| 87 | R | A | -2.3369 | |
| 88 | A | A | -1.7292 | |
| 89 | E | A | -2.2031 | |
| 90 | D | A | 0.0000 | |
| 91 | T | A | -0.6937 | |
| 92 | A | A | 0.0000 | |
| 93 | V | A | 0.2709 | |
| 94 | Y | A | 0.0000 | |
| 95 | Y | A | 0.0000 | |
| 96 | C | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | R | A | -0.8066 | |
| 99 | R | A | -1.8415 | |
| 100 | G | A | -0.9338 | |
| 101 | V | A | 0.0000 | |
| 102 | D | A | -0.7215 | |
| 103 | Y | A | -0.3109 | |
| 104 | W | A | -0.3012 | |
| 105 | G | A | 0.0000 | |
| 106 | Q | A | -1.3941 | |
| 107 | G | A | -0.4953 | |
| 108 | T | A | -0.0951 | |
| 109 | L | A | 0.2029 | |
| 110 | V | A | 0.0000 | |
| 111 | T | A | -0.4784 | |
| 112 | V | A | 0.0000 | |
| 113 | S | A | -0.9076 | |
| 114 | S | A | -0.8024 | |
| 115 | A | A | -0.5175 | |
| 116 | S | A | -0.5950 | |
| 117 | T | A | -0.5970 | |
| 118 | K | A | -1.1665 | |
| 119 | G | A | -1.4146 | |
| 120 | P | A | -0.6385 | |
| 121 | S | A | -0.3502 | |
| 122 | V | A | 0.0000 | |
| 123 | F | A | 0.0000 | |
| 124 | P | A | -0.9605 | |
| 125 | L | A | 0.0000 | |
| 126 | A | A | -1.2106 | |
| 127 | P | A | 0.0000 | |
| 128 | S | A | -1.1624 | |
| 129 | S | A | -1.1467 | |
| 130 | K | A | -1.8158 | |
| 131 | S | A | 0.0000 | |
| 132 | T | A | -0.9798 | |
| 133 | S | A | -0.8270 | |
| 134 | G | A | -0.8104 | |
| 135 | G | A | -0.8758 | |
| 136 | T | A | -0.6066 | |
| 137 | A | A | 0.0000 | |
| 138 | A | A | 0.0000 | |
| 139 | L | A | 0.0000 | |
| 140 | G | A | 0.0000 | |
| 141 | C | A | 0.0000 | |
| 142 | L | A | 0.0000 | |
| 143 | V | A | 0.0000 | |
| 144 | K | A | 0.0000 | |
| 145 | D | A | -0.3625 | |
| 146 | Y | A | 0.0000 | |
| 147 | F | A | 0.0000 | |
| 148 | P | A | 0.0000 | |
| 149 | E | A | -0.4364 | |
| 150 | P | A | -0.7266 | |
| 151 | V | A | -0.8032 | |
| 152 | T | A | -0.7579 | |
| 153 | V | A | -0.3115 | |
| 154 | S | A | -0.4460 | |
| 155 | W | A | 0.0000 | |
| 156 | N | A | -0.6735 | |
| 157 | S | A | -0.6412 | |
| 158 | G | A | -0.4822 | |
| 159 | A | A | -0.2186 | |
| 160 | L | A | 0.0369 | |
| 161 | T | A | -0.1572 | |
| 162 | S | A | -0.1755 | |
| 163 | G | A | -0.2095 | |
| 164 | V | A | 0.1758 | |
| 165 | H | A | -0.3017 | |
| 166 | T | A | 0.0335 | |
| 167 | F | A | 0.0000 | |
| 168 | P | A | -0.2711 | |
| 169 | A | A | 0.3034 | |
| 170 | V | A | 0.6021 | |
| 171 | L | A | 1.2476 | |
| 172 | Q | A | 0.3249 | |
| 173 | S | A | -0.0491 | |
| 174 | S | A | -0.1984 | |
| 175 | G | A | 0.0552 | |
| 176 | L | A | 0.1673 | |
| 177 | Y | A | 0.5072 | |
| 178 | S | A | 0.0000 | |
| 179 | L | A | 0.0000 | |
| 180 | S | A | 0.0000 | |
| 181 | S | A | 0.0000 | |
| 182 | V | A | 0.0000 | |
| 183 | V | A | 0.0000 | |
| 184 | T | A | -0.1374 | |
| 185 | V | A | 0.0000 | |
| 186 | P | A | -0.6022 | |
| 187 | S | A | -0.5553 | |
| 188 | S | A | -0.5621 | |
| 189 | S | A | -0.5384 | |
| 190 | L | A | -0.7424 | |
| 191 | G | A | -0.9260 | |
| 192 | T | A | -0.6597 | |
| 193 | Q | A | -1.1039 | |
| 194 | T | A | -0.9720 | |
| 195 | Y | A | 0.0000 | |
| 196 | I | A | -1.0183 | |
| 197 | C | A | 0.0000 | |
| 198 | N | A | -1.5247 | |
| 199 | V | A | 0.0000 | |
| 200 | N | A | -2.4396 | |
| 201 | H | A | 0.0000 | |
| 202 | K | A | -2.8564 | |
| 203 | P | A | -1.5875 | |
| 204 | S | A | -1.8767 | |
| 205 | N | A | -2.6532 | |
| 206 | T | A | -2.1834 | |
| 207 | K | A | -2.8837 | |
| 208 | V | A | -1.6034 | |
| 209 | D | A | -2.4019 | |
| 210 | K | A | -1.8828 | |
| 211 | K | A | -2.0697 | |
| 212 | V | A | 0.0000 | |
| 213 | E | A | -2.7487 | |
| 214 | P | A | -1.7879 | |
| 215 | K | A | -2.0119 | |
| 216 | S | A | -0.8543 | |
| 217 | C | A | 0.0823 | |
| 1 | D | B | -1.6061 | |
| 2 | V | B | 0.0000 | |
| 3 | V | B | 0.6837 | |
| 4 | M | B | 0.0000 | |
| 5 | T | B | -0.4178 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.1819 | |
| 8 | P | B | 0.2442 | |
| 9 | L | B | 0.8583 | |
| 10 | S | B | 0.0342 | |
| 11 | L | B | -0.2018 | |
| 12 | P | B | -0.7581 | |
| 13 | V | B | 0.0000 | |
| 14 | T | B | -1.0014 | |
| 15 | L | B | -0.8225 | |
| 16 | G | B | -1.2674 | |
| 17 | Q | B | -1.6200 | |
| 18 | P | B | -1.8518 | |
| 19 | A | B | 0.0000 | |
| 20 | S | B | -0.8875 | |
| 21 | I | B | 0.0000 | |
| 22 | S | B | -0.9516 | |
| 23 | C | B | 0.0000 | |
| 24 | K | B | -2.2287 | |
| 25 | S | B | 0.0000 | |
| 26 | S | B | -0.9868 | |
| 27 | Q | B | -1.5323 | |
| 28 | S | B | -0.6404 | |
| 29 | L | B | 0.0000 | |
| 30 | L | B | 0.8601 | |
| 31 | Y | B | 0.6825 | |
| 32 | S | B | -0.4805 | |
| 33 | D | B | -1.6765 | |
| 34 | G | B | -1.1103 | |
| 35 | K | B | -0.9383 | |
| 36 | T | B | 0.1278 | |
| 37 | Y | B | 0.5483 | |
| 38 | L | B | 0.0000 | |
| 39 | N | B | 0.0000 | |
| 40 | W | B | 0.0000 | |
| 41 | L | B | 0.0000 | |
| 42 | L | B | 0.0000 | |
| 43 | Q | B | -0.9767 | |
| 44 | R | B | -1.5432 | |
| 45 | P | B | -1.3396 | |
| 46 | G | B | -1.5750 | |
| 47 | Q | B | -1.9610 | |
| 48 | S | B | -1.2937 | |
| 49 | P | B | 0.0000 | |
| 50 | R | B | -1.1624 | |
| 51 | R | B | -0.5583 | |
| 52 | L | B | 0.0000 | |
| 53 | I | B | 0.0000 | |
| 54 | Y | B | -0.1603 | |
| 55 | L | B | -0.1471 | |
| 56 | V | B | 0.0000 | |
| 57 | S | B | -0.9391 | |
| 58 | K | B | -1.5044 | |
| 59 | L | B | -0.8581 | |
| 60 | D | B | -0.8956 | |
| 61 | S | B | -0.6220 | |
| 62 | G | B | -0.7269 | |
| 63 | V | B | -0.7288 | |
| 64 | P | B | -1.1211 | |
| 65 | D | B | -2.0262 | |
| 66 | R | B | -2.2247 | |
| 67 | F | B | 0.0000 | |
| 68 | S | B | -1.5172 | |
| 69 | G | B | -0.9873 | |
| 70 | S | B | -1.1355 | |
| 71 | G | B | -1.1762 | |
| 72 | S | B | -0.7793 | |
| 73 | G | B | -0.5726 | |
| 74 | T | B | -1.5232 | |
| 75 | D | B | -2.2636 | |
| 76 | F | B | 0.0000 | |
| 77 | T | B | -1.2327 | |
| 78 | L | B | 0.0000 | |
| 79 | K | B | -2.1326 | |
| 80 | I | B | 0.0000 | |
| 81 | S | B | -2.3235 | |
| 82 | R | B | -2.8051 | |
| 83 | V | B | 0.0000 | |
| 84 | E | B | -2.4141 | |
| 85 | A | B | -2.1869 | |
| 86 | E | B | -2.6565 | |
| 87 | D | B | 0.0000 | |
| 88 | V | B | 0.0000 | |
| 89 | G | B | 0.0000 | |
| 90 | V | B | -0.2536 | |
| 91 | Y | B | 0.0000 | |
| 92 | Y | B | 0.0000 | |
| 93 | C | B | 0.0000 | |
| 94 | W | B | 0.0000 | |
| 95 | Q | B | 0.0000 | |
| 96 | S | B | 0.0677 | |
| 97 | T | B | 0.0000 | |
| 98 | H | B | -0.1282 | |
| 99 | F | B | 0.3243 | |
| 100 | P | B | -0.2532 | |
| 101 | F | B | 0.0000 | |
| 102 | T | B | -0.0217 | |
| 103 | F | B | 0.0881 | |
| 104 | G | B | 0.0000 | |
| 105 | Q | B | -0.8475 | |
| 106 | G | B | 0.0000 | |
| 107 | T | B | 0.0000 | |
| 108 | K | B | -0.8502 | |
| 109 | L | B | 0.0000 | |
| 110 | E | B | -1.0886 | |
| 111 | I | B | 0.0000 | |
| 112 | K | B | -1.0123 | |
| 113 | R | B | -0.8333 | |
| 114 | T | B | 0.0024 | |
| 115 | V | B | 0.3366 | |
| 116 | A | B | -0.0520 | |
| 117 | A | B | -0.0929 | |
| 118 | P | B | 0.0000 | |
| 119 | S | B | -0.2011 | |
| 120 | V | B | 0.0000 | |
| 121 | F | B | 0.0000 | |
| 122 | I | B | 0.0000 | |
| 123 | F | B | 0.0000 | |
| 124 | P | B | -0.4601 | |
| 125 | P | B | 0.0000 | |
| 126 | S | B | -1.6227 | |
| 127 | D | B | -2.6813 | |
| 128 | E | B | -2.4599 | |
| 129 | Q | B | 0.0000 | |
| 130 | L | B | -2.1501 | |
| 131 | K | B | -2.7057 | |
| 132 | S | B | -1.6783 | |
| 133 | G | B | -1.2542 | |
| 134 | T | B | -0.9779 | |
| 135 | A | B | 0.0000 | |
| 136 | S | B | 0.0000 | |
| 137 | V | B | 0.0000 | |
| 138 | V | B | 0.0000 | |
| 139 | C | B | 0.0000 | |
| 140 | L | B | 0.0000 | |
| 141 | L | B | 0.0000 | |
| 142 | N | B | -0.3533 | |
| 143 | N | B | -0.8147 | |
| 144 | F | B | 0.0000 | |
| 145 | Y | B | 0.0000 | |
| 146 | P | B | -1.7260 | |
| 147 | R | B | -3.0870 | |
| 148 | E | B | -3.2230 | |
| 149 | A | B | -2.2424 | |
| 150 | K | B | -2.1733 | |
| 151 | V | B | -0.9016 | |
| 152 | Q | B | -0.4476 | |
| 153 | W | B | 0.0000 | |
| 154 | K | B | -0.5330 | |
| 155 | V | B | 0.0000 | |
| 156 | D | B | -1.9034 | |
| 157 | N | B | -1.5163 | |
| 158 | A | B | -0.2404 | |
| 159 | L | B | 0.8079 | |
| 160 | Q | B | -0.0170 | |
| 161 | S | B | -0.3507 | |
| 162 | G | B | -0.8682 | |
| 163 | N | B | -0.7598 | |
| 164 | S | B | -0.9637 | |
| 165 | Q | B | -1.1205 | |
| 166 | E | B | -1.3845 | |
| 167 | S | B | -0.7258 | |
| 168 | V | B | -0.6767 | |
| 169 | T | B | -1.1433 | |
| 170 | E | B | -2.2852 | |
| 171 | Q | B | 0.0000 | |
| 172 | D | B | -2.0585 | |
| 173 | S | B | -2.4045 | |
| 174 | K | B | -2.7257 | |
| 175 | D | B | -1.8521 | |
| 176 | S | B | 0.0000 | |
| 177 | T | B | 0.0000 | |
| 178 | Y | B | 0.0000 | |
| 179 | S | B | 0.0000 | |
| 180 | L | B | 0.0000 | |
| 181 | S | B | 0.0000 | |
| 182 | S | B | 0.0000 | |
| 183 | T | B | -0.5485 | |
| 184 | L | B | 0.0000 | |
| 185 | T | B | -0.3885 | |
| 186 | L | B | -0.5859 | |
| 187 | S | B | -0.9963 | |
| 188 | K | B | -2.0882 | |
| 189 | A | B | -1.7765 | |
| 190 | D | B | -2.2574 | |
| 191 | Y | B | 0.0000 | |
| 192 | E | B | -3.3577 | |
| 193 | K | B | -3.4725 | |
| 194 | H | B | -2.8261 | |
| 195 | K | B | -3.0940 | |
| 196 | V | B | -1.3198 | |
| 197 | Y | B | 0.0000 | |
| 198 | A | B | 0.0000 | |
| 199 | C | B | 0.0000 | |
| 200 | E | B | -0.7765 | |
| 201 | V | B | 0.0000 | |
| 202 | T | B | -1.1125 | |
| 203 | H | B | 0.0000 | |
| 204 | Q | B | -1.7413 | |
| 205 | G | B | -0.4226 | |
| 206 | L | B | -0.2298 | |
| 207 | S | B | -0.4506 | |
| 208 | S | B | -0.4083 | |
| 209 | P | B | -0.5138 | |
| 210 | V | B | 0.0935 | |
| 211 | T | B | -0.3865 | |
| 212 | K | B | -0.7826 | |
| 213 | S | B | -0.6646 | |
| 214 | F | B | -0.9239 | |
| 215 | N | B | -1.6049 | |
| 216 | R | B | -2.2370 | |
| 217 | G | B | -1.8577 | |
| 218 | E | B | -1.9608 | |
| 219 | C | B | -0.7409 |
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 | -0.7318 | 1.7277 | View | CSV | PDB |
| 4.5 | -0.7751 | 1.7277 | View | CSV | PDB |
| 5.0 | -0.8245 | 1.7277 | View | CSV | PDB |
| 5.5 | -0.8703 | 1.7277 | View | CSV | PDB |
| 6.0 | -0.9006 | 1.7277 | View | CSV | PDB |
| 6.5 | -0.9057 | 1.7277 | View | CSV | PDB |
| 7.0 | -0.8849 | 1.7277 | View | CSV | PDB |
| 7.5 | -0.8468 | 1.7276 | View | CSV | PDB |
| 8.0 | -0.7987 | 1.7276 | View | CSV | PDB |
| 8.5 | -0.7434 | 1.7273 | View | CSV | PDB |
| 9.0 | -0.6814 | 1.7266 | 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