| Chain sequence(s) |
A: QVQLVQPAAEVKKPGESLKISCQASGYTVTNYWIAWVRQEPGKGLEWMGMIYPGDSDRRYSPSLQGHITFSADKSSGTAYLQWSSLKASDTAMYYCARLGKYSSSWPYYYYGMDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV
B: EIVMTQSPATLSVSPGERATLSCRASQSVSSNLAWYQQKPGQAPRLLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQFHHWPITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC input PDB |
| Selected Chain(s) | A,B |
| Distance of aggregation | 5 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage | Used: no changes made |
| 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: Running AlphaCutter (00:00:01)
[INFO] PDB: AlphaCutter did not cut any residues. The original structure will be used
for analysis. (00:00:10)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:11)
[INFO] FoldX: Starting FoldX energy minimization (00:00:11)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:04:15)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/cd180446187c524/tmp/folded.pdb (00:04:15)
[INFO] Main: Simulation completed successfully. (00:06:25)
|
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 | Q | A | -1.1326 | |
| 2 | V | A | -0.0269 | |
| 3 | Q | A | -0.4935 | |
| 4 | L | A | 0.0000 | |
| 5 | V | A | 1.2767 | |
| 6 | Q | A | 0.0000 | |
| 7 | P | A | -0.0645 | |
| 8 | A | A | 0.0534 | |
| 9 | A | A | 0.0377 | |
| 10 | E | A | -0.3061 | |
| 11 | V | A | 0.5677 | |
| 12 | K | A | -0.5824 | |
| 13 | K | A | -1.7162 | |
| 14 | P | A | -0.7352 | |
| 15 | G | A | -0.6159 | |
| 16 | E | A | -0.6091 | |
| 17 | S | A | -0.3490 | |
| 18 | L | A | 0.0000 | |
| 19 | K | A | -1.7023 | |
| 20 | I | A | 0.0000 | |
| 21 | S | A | -0.0473 | |
| 22 | C | A | 0.0000 | |
| 23 | Q | A | -0.4476 | |
| 24 | A | A | 0.0000 | |
| 25 | S | A | -0.2256 | |
| 26 | G | A | -0.3993 | |
| 27 | Y | A | 0.1096 | |
| 28 | T | A | -0.0316 | |
| 29 | V | A | 0.0000 | |
| 30 | T | A | -0.2526 | |
| 31 | N | A | -1.0972 | |
| 32 | Y | A | 0.0417 | |
| 33 | W | A | 0.2484 | |
| 34 | I | A | 0.0000 | |
| 35 | A | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | V | A | 0.0000 | |
| 38 | R | A | -0.2573 | |
| 39 | Q | A | 0.0000 | |
| 40 | E | A | -0.6332 | |
| 41 | P | A | -0.4553 | |
| 42 | G | A | -0.8382 | |
| 43 | K | A | -1.8133 | |
| 44 | G | A | -0.4545 | |
| 45 | L | A | 0.0000 | |
| 46 | E | A | -0.6487 | |
| 47 | W | A | 0.0000 | |
| 48 | M | A | 0.0000 | |
| 49 | G | A | 0.0000 | |
| 50 | M | A | 0.0000 | |
| 51 | I | A | 0.0000 | |
| 52 | Y | A | 0.2450 | |
| 53 | P | A | 0.0000 | |
| 54 | G | A | -0.4537 | |
| 55 | D | A | -1.8279 | |
| 56 | S | A | -0.4960 | |
| 57 | D | A | -0.6515 | |
| 58 | R | A | -1.2947 | |
| 59 | R | A | -1.2479 | |
| 60 | Y | A | -0.0608 | |
| 61 | S | A | 0.0000 | |
| 62 | P | A | -0.2153 | |
| 63 | S | A | -0.2453 | |
| 64 | L | A | 0.0000 | |
| 65 | Q | A | -1.2826 | |
| 66 | G | A | -0.8720 | |
| 67 | H | A | -1.0792 | |
| 68 | I | A | 0.0000 | |
| 69 | T | A | -0.0395 | |
| 70 | F | A | 0.0000 | |
| 71 | S | A | -0.0434 | |
| 72 | A | A | -0.1586 | |
| 73 | D | A | -1.1596 | |
| 74 | K | A | -1.9003 | |
| 75 | S | A | -0.5662 | |
| 76 | S | A | -0.2255 | |
| 77 | G | A | -0.2582 | |
| 78 | T | A | 0.0000 | |
| 79 | A | A | 0.0000 | |
| 80 | Y | A | 0.1762 | |
| 81 | L | A | 0.0000 | |
| 82 | Q | A | -0.6121 | |
| 83 | W | A | 0.0000 | |
| 84 | S | A | -0.2788 | |
| 85 | S | A | -0.3313 | |
| 86 | L | A | 0.0000 | |
| 87 | K | A | -1.7072 | |
| 88 | A | A | -0.2927 | |
| 89 | S | A | -0.2020 | |
| 90 | D | A | 0.0000 | |
| 91 | T | A | -0.0112 | |
| 92 | A | A | 0.0000 | |
| 93 | M | A | 0.2851 | |
| 94 | Y | A | 0.0000 | |
| 95 | Y | A | 0.0000 | |
| 96 | C | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | R | A | -0.1882 | |
| 99 | L | A | 0.0000 | |
| 100 | G | A | 0.0000 | |
| 101 | K | A | -0.3098 | |
| 102 | Y | A | 1.1665 | |
| 103 | S | A | 0.0230 | |
| 104 | S | A | -0.1492 | |
| 105 | S | A | -0.0008 | |
| 106 | W | A | 1.1022 | |
| 107 | P | A | 0.1929 | |
| 108 | Y | A | 1.4544 | |
| 109 | Y | A | 1.3233 | |
| 110 | Y | A | 0.5776 | |
| 111 | Y | A | 0.2140 | |
| 112 | G | A | 0.0000 | |
| 113 | M | A | 0.0000 | |
| 114 | D | A | -0.4221 | |
| 115 | V | A | 0.1654 | |
| 116 | W | A | 0.0000 | |
| 117 | G | A | 0.0000 | |
| 118 | Q | A | -1.0439 | |
| 119 | G | A | -0.2343 | |
| 120 | T | A | 0.0000 | |
| 121 | L | A | 0.5224 | |
| 122 | V | A | 0.0000 | |
| 123 | T | A | 0.0000 | |
| 124 | V | A | 0.0000 | |
| 125 | S | A | -0.0696 | |
| 126 | S | A | -0.2162 | |
| 127 | A | A | -0.0676 | |
| 128 | S | A | -0.2242 | |
| 129 | T | A | -0.3101 | |
| 130 | K | A | -1.0588 | |
| 131 | G | A | -0.2950 | |
| 132 | P | A | 0.0000 | |
| 133 | S | A | -0.0883 | |
| 134 | V | A | 0.0000 | |
| 135 | F | A | 0.0000 | |
| 136 | P | A | -0.0454 | |
| 137 | L | A | 0.0000 | |
| 138 | A | A | 0.0364 | |
| 139 | P | A | -0.0678 | |
| 140 | S | A | -0.1541 | |
| 141 | S | A | -0.3773 | |
| 142 | K | A | -0.8294 | |
| 143 | S | A | 0.0000 | |
| 144 | T | A | -0.0439 | |
| 145 | S | A | -0.1885 | |
| 146 | G | A | -0.5705 | |
| 147 | G | A | -0.5571 | |
| 148 | T | A | -0.1434 | |
| 149 | A | A | 0.0000 | |
| 150 | A | A | 0.0000 | |
| 151 | L | A | 0.0000 | |
| 152 | G | A | 0.0000 | |
| 153 | C | A | 0.0000 | |
| 154 | L | A | 0.0000 | |
| 155 | V | A | 0.0000 | |
| 156 | K | A | 0.0000 | |
| 157 | D | A | -0.3568 | |
| 158 | Y | A | 0.0000 | |
| 159 | F | A | 0.0000 | |
| 160 | P | A | 0.0000 | |
| 161 | E | A | -0.5156 | |
| 162 | P | A | -0.3451 | |
| 163 | V | A | 0.1302 | |
| 164 | T | A | 0.0047 | |
| 165 | V | A | 0.1817 | |
| 166 | S | A | -0.0200 | |
| 167 | W | A | 0.0000 | |
| 168 | N | A | -0.2835 | |
| 169 | S | A | -0.3398 | |
| 170 | G | A | -0.4629 | |
| 171 | A | A | 0.0278 | |
| 172 | L | A | 0.2588 | |
| 173 | T | A | -0.0642 | |
| 174 | S | A | -0.2721 | |
| 175 | G | A | -0.2171 | |
| 176 | V | A | 0.3026 | |
| 177 | H | A | -0.0401 | |
| 178 | T | A | -0.0566 | |
| 179 | F | A | 0.0000 | |
| 180 | P | A | -0.2003 | |
| 181 | A | A | 0.0317 | |
| 182 | V | A | 0.5550 | |
| 183 | L | A | 1.3998 | |
| 184 | Q | A | 0.0667 | |
| 185 | S | A | -0.2791 | |
| 186 | S | A | -0.2688 | |
| 187 | G | A | -0.1005 | |
| 188 | L | A | 0.1386 | |
| 189 | Y | A | 0.0000 | |
| 190 | S | A | 0.0000 | |
| 191 | L | A | 0.0000 | |
| 192 | S | A | 0.0000 | |
| 193 | S | A | 0.0000 | |
| 194 | V | A | 0.0000 | |
| 195 | V | A | 0.0000 | |
| 196 | T | A | -0.0117 | |
| 197 | V | A | 0.0000 | |
| 198 | P | A | -0.2716 | |
| 199 | S | A | -0.1609 | |
| 200 | S | A | -0.2311 | |
| 201 | S | A | 0.0187 | |
| 202 | L | A | 0.3746 | |
| 203 | G | A | -0.3946 | |
| 204 | T | A | -0.3008 | |
| 205 | Q | A | -0.7797 | |
| 206 | T | A | -0.1888 | |
| 207 | Y | A | 0.0000 | |
| 208 | I | A | 0.2058 | |
| 209 | C | A | 0.0000 | |
| 210 | N | A | 0.0000 | |
| 211 | V | A | 0.0000 | |
| 212 | N | A | -0.9698 | |
| 213 | H | A | 0.0000 | |
| 214 | K | A | -1.8665 | |
| 215 | P | A | -0.4050 | |
| 216 | S | A | -0.2974 | |
| 217 | N | A | -1.4878 | |
| 218 | T | A | -0.5654 | |
| 219 | K | A | -1.7255 | |
| 220 | V | A | -0.1760 | |
| 221 | D | A | -1.2978 | |
| 222 | K | A | -1.0468 | |
| 223 | K | A | -1.6392 | |
| 224 | V | A | 0.1713 | |
| 1 | E | B | -1.8199 | |
| 2 | I | B | 0.0000 | |
| 3 | V | B | 1.7728 | |
| 4 | M | B | 0.0000 | |
| 5 | T | B | -0.0430 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.1913 | |
| 8 | P | B | -0.1497 | |
| 9 | A | B | 0.0282 | |
| 10 | T | B | -0.0428 | |
| 11 | L | B | 0.2418 | |
| 12 | S | B | -0.1254 | |
| 13 | V | B | 0.0000 | |
| 14 | S | B | -0.2312 | |
| 15 | P | B | -0.3530 | |
| 16 | G | B | -0.7707 | |
| 17 | E | B | -1.7346 | |
| 18 | R | B | -2.1092 | |
| 19 | A | B | 0.0000 | |
| 20 | T | B | -0.0222 | |
| 21 | L | B | 0.0000 | |
| 22 | S | B | -0.0791 | |
| 23 | C | B | 0.0000 | |
| 24 | R | B | -2.0286 | |
| 25 | A | B | 0.0000 | |
| 26 | S | B | -0.3292 | |
| 27 | Q | B | -0.7202 | |
| 28 | S | B | -0.3189 | |
| 29 | V | B | 0.0000 | |
| 30 | S | B | -0.1547 | |
| 31 | S | B | -0.1943 | |
| 32 | N | B | -0.3565 | |
| 33 | L | B | 0.0000 | |
| 34 | A | B | 0.0000 | |
| 35 | W | B | 0.0000 | |
| 36 | Y | B | 0.0000 | |
| 37 | Q | B | 0.0000 | |
| 38 | Q | B | 0.0000 | |
| 39 | K | B | -0.5506 | |
| 40 | P | B | -0.2878 | |
| 41 | G | B | -0.7094 | |
| 42 | Q | B | -1.2834 | |
| 43 | A | B | -0.2186 | |
| 44 | P | B | 0.0000 | |
| 45 | R | B | -1.0671 | |
| 46 | L | B | 0.0000 | |
| 47 | L | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | Y | B | 0.2095 | |
| 50 | G | B | -0.1032 | |
| 51 | A | B | 0.0000 | |
| 52 | S | B | -0.2211 | |
| 53 | T | B | -0.2236 | |
| 54 | R | B | -0.7521 | |
| 55 | A | B | -0.1500 | |
| 56 | T | B | -0.1565 | |
| 57 | G | B | -0.4795 | |
| 58 | I | B | 0.0000 | |
| 59 | P | B | -0.0682 | |
| 60 | A | B | -0.0201 | |
| 61 | R | B | -0.3263 | |
| 62 | F | B | 0.0000 | |
| 63 | S | B | -0.1367 | |
| 64 | G | B | 0.0000 | |
| 65 | S | B | -0.2497 | |
| 66 | G | B | -0.2730 | |
| 67 | S | B | -0.2757 | |
| 68 | G | B | -0.1848 | |
| 69 | T | B | -0.3897 | |
| 70 | E | B | -1.9728 | |
| 71 | F | B | 0.0000 | |
| 72 | T | B | -0.0261 | |
| 73 | L | B | 0.0000 | |
| 74 | T | B | -0.0161 | |
| 75 | I | B | 0.0000 | |
| 76 | S | B | -0.4286 | |
| 77 | S | B | -0.1841 | |
| 78 | L | B | 0.0000 | |
| 79 | Q | B | -0.5386 | |
| 80 | S | B | -0.5882 | |
| 81 | E | B | -1.5486 | |
| 82 | D | B | 0.0000 | |
| 83 | F | B | 0.3102 | |
| 84 | A | B | 0.0000 | |
| 85 | V | B | 0.1865 | |
| 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 | F | B | 0.0000 | |
| 92 | H | B | -0.4545 | |
| 93 | H | B | -0.5706 | |
| 94 | W | B | 1.0538 | |
| 95 | P | B | 0.0000 | |
| 96 | I | B | 0.0000 | |
| 97 | T | B | 0.0263 | |
| 98 | F | B | 0.1875 | |
| 99 | G | B | 0.0000 | |
| 100 | Q | B | -1.1494 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | R | B | -0.4020 | |
| 104 | L | B | 0.0000 | |
| 105 | E | B | 0.0000 | |
| 106 | I | B | -0.0153 | |
| 107 | K | B | -1.2405 | |
| 108 | R | B | -0.8308 | |
| 109 | T | B | 0.0344 | |
| 110 | V | B | 1.1691 | |
| 111 | A | B | 0.2284 | |
| 112 | A | B | 0.0091 | |
| 113 | P | B | 0.0000 | |
| 114 | S | B | -0.0730 | |
| 115 | V | B | 0.0000 | |
| 116 | F | B | 0.0000 | |
| 117 | I | B | 0.0000 | |
| 118 | F | B | 0.0000 | |
| 119 | P | B | -0.0452 | |
| 120 | P | B | 0.0000 | |
| 121 | S | B | -0.3608 | |
| 122 | D | B | -2.0727 | |
| 123 | E | B | -1.8033 | |
| 124 | Q | B | 0.0000 | |
| 125 | L | B | -0.1148 | |
| 126 | K | B | -1.7009 | |
| 127 | S | B | -0.5845 | |
| 128 | G | B | -0.3876 | |
| 129 | T | B | -0.1516 | |
| 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 | -0.2229 | |
| 138 | N | B | -0.5186 | |
| 139 | F | B | 0.0000 | |
| 140 | Y | B | 0.0000 | |
| 141 | P | B | -0.2402 | |
| 142 | R | B | -1.4743 | |
| 143 | E | B | -2.0262 | |
| 144 | A | B | -0.6231 | |
| 145 | K | B | -1.6103 | |
| 146 | V | B | 0.0000 | |
| 147 | Q | B | -0.3769 | |
| 148 | W | B | 0.0000 | |
| 149 | K | B | -0.0813 | |
| 150 | V | B | 0.0000 | |
| 151 | D | B | -1.0607 | |
| 152 | N | B | -1.4300 | |
| 153 | A | B | 0.0681 | |
| 154 | L | B | 1.4495 | |
| 155 | Q | B | -0.1296 | |
| 156 | S | B | -0.3642 | |
| 157 | G | B | -0.7314 | |
| 158 | N | B | -1.3680 | |
| 159 | S | B | -0.4001 | |
| 160 | Q | B | -0.7503 | |
| 161 | E | B | -1.2480 | |
| 162 | S | B | -0.1830 | |
| 163 | V | B | 0.2719 | |
| 164 | T | B | -0.1576 | |
| 165 | E | B | -1.0437 | |
| 166 | Q | B | 0.0000 | |
| 167 | D | B | -0.4833 | |
| 168 | S | B | -0.6071 | |
| 169 | K | B | -1.8251 | |
| 170 | D | B | -0.7788 | |
| 171 | S | B | -0.1620 | |
| 172 | T | B | 0.0000 | |
| 173 | Y | B | 0.0000 | |
| 174 | S | B | 0.0000 | |
| 175 | L | B | 0.0000 | |
| 176 | S | B | 0.0000 | |
| 177 | S | B | 0.0000 | |
| 178 | T | B | -0.0107 | |
| 179 | L | B | 0.0000 | |
| 180 | T | B | 0.0123 | |
| 181 | L | B | 0.1369 | |
| 182 | S | B | -0.2126 | |
| 183 | K | B | -0.6744 | |
| 184 | A | B | -0.2993 | |
| 185 | D | B | -1.1957 | |
| 186 | Y | B | 0.0000 | |
| 187 | E | B | -1.7781 | |
| 188 | K | B | -2.0310 | |
| 189 | H | B | -0.8712 | |
| 190 | K | B | -1.1948 | |
| 191 | V | B | 0.2729 | |
| 192 | Y | B | 0.0000 | |
| 193 | A | B | 0.0000 | |
| 194 | C | B | 0.0000 | |
| 195 | E | B | -0.2700 | |
| 196 | V | B | 0.0000 | |
| 197 | T | B | -0.0664 | |
| 198 | H | B | 0.0000 | |
| 199 | Q | B | -1.2274 | |
| 200 | G | B | -0.3303 | |
| 201 | L | B | 0.1672 | |
| 202 | S | B | -0.2100 | |
| 203 | S | B | -0.2954 | |
| 204 | P | B | -0.1809 | |
| 205 | V | B | 0.4185 | |
| 206 | T | B | -0.0835 | |
| 207 | K | B | -0.5247 | |
| 208 | S | B | -0.1630 | |
| 209 | F | B | 0.0000 | |
| 210 | N | B | -0.2368 | |
| 211 | R | B | -0.5161 | |
| 212 | G | B | -0.8680 | |
| 213 | E | B | -1.7642 | |
| 214 | C | B | 0.3811 |
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 | -0.277 | 3.5728 | View | CSV | PDB |
| 4.5 | -0.291 | 3.5728 | View | CSV | PDB |
| 5.0 | -0.3069 | 3.5728 | View | CSV | PDB |
| 5.5 | -0.3214 | 3.5728 | View | CSV | PDB |
| 6.0 | -0.3304 | 3.5728 | View | CSV | PDB |
| 6.5 | -0.3305 | 3.5728 | View | CSV | PDB |
| 7.0 | -0.3219 | 3.5728 | View | CSV | PDB |
| 7.5 | -0.3073 | 3.5728 | View | CSV | PDB |
| 8.0 | -0.2894 | 3.5728 | View | CSV | PDB |
| 8.5 | -0.2692 | 3.5728 | View | CSV | PDB |
| 9.0 | -0.2473 | 3.5728 | 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