| Chain sequence(s) |
A: DIELTQSPATLSVTPGDSVSLSCRASQSISNNLHWYQQKSHESPRLLIKYVSQSSSGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
B: QVQLQESGAEVMKPGASVKISCKATGYTFSTYWIEWVKQRPGHGLEWIGEILPGSGSTYYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARGDGNYGYWGQGTTLTVSSASTTPPSVFPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC 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 |
| Mutated residues | ST30B,GC104B,VA51A,SA55A,SL54A,SP40A |
| Energy difference between WT (input) and mutated protein (by FoldX) | -1.31617 kcal/mol |
| 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 (00:00:03)
[INFO] FoldX: Building mutant model (00:02:32)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:03:27)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/825e495c678c510/tmp/folded.pdb (00:03:27)
[INFO] Main: Simulation completed successfully. (00:05:38)
|
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 | -2.3096 | |
| 2 | I | A | 0.0000 | |
| 3 | E | A | -2.9309 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -1.4826 | |
| 6 | Q | A | -1.1409 | |
| 7 | S | A | -0.8206 | |
| 8 | P | A | -0.5219 | |
| 9 | A | A | -0.5319 | |
| 10 | T | A | -0.6270 | |
| 11 | L | A | -0.4820 | |
| 12 | S | A | -0.8845 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.5864 | |
| 15 | P | A | -1.8863 | |
| 16 | G | A | -1.9948 | |
| 17 | D | A | -2.5083 | |
| 18 | S | A | -1.8433 | |
| 19 | V | A | -0.7779 | |
| 20 | S | A | -0.4582 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.9171 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.9082 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -2.2128 | |
| 27 | Q | A | -2.1906 | |
| 28 | S | A | -1.5219 | |
| 29 | I | A | 0.0000 | |
| 30 | S | A | -1.1595 | |
| 31 | N | A | -1.2911 | |
| 32 | N | A | -0.8841 | |
| 33 | L | A | 0.0000 | |
| 34 | H | A | 0.0000 | |
| 35 | W | A | 0.0000 | |
| 36 | Y | A | 0.0000 | |
| 37 | Q | A | 0.0000 | |
| 38 | Q | A | 0.0000 | |
| 39 | K | A | -2.8370 | |
| 40 | P | A | -2.2753 | mutated: SP40A |
| 41 | H | A | -2.5553 | |
| 42 | E | A | -3.2579 | |
| 43 | S | A | -1.9259 | |
| 44 | P | A | 0.0000 | |
| 45 | R | A | -1.2472 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | K | A | -0.3958 | |
| 50 | Y | A | -0.2708 | |
| 51 | A | A | 0.0000 | mutated: VA51A |
| 52 | S | A | -0.7277 | |
| 53 | Q | A | -0.6814 | |
| 54 | L | A | 0.5902 | mutated: SL54A |
| 55 | A | A | 0.1438 | mutated: SA55A |
| 56 | S | A | -0.1570 | |
| 57 | G | A | -0.3045 | |
| 58 | I | A | -0.0446 | |
| 59 | P | A | -0.1817 | |
| 60 | S | A | -0.4376 | |
| 61 | R | A | -1.1237 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.6201 | |
| 64 | G | A | -0.4841 | |
| 65 | S | A | -0.8972 | |
| 66 | G | A | -1.2746 | |
| 67 | S | A | -1.2725 | |
| 68 | G | A | -1.4063 | |
| 69 | T | A | -1.8420 | |
| 70 | D | A | -2.0830 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.8322 | |
| 73 | L | A | 0.0000 | |
| 74 | S | A | -0.6800 | |
| 75 | I | A | 0.0000 | |
| 76 | N | A | -2.1926 | |
| 77 | S | A | -2.0537 | |
| 78 | V | A | 0.0000 | |
| 79 | E | A | -2.4987 | |
| 80 | T | A | -1.7916 | |
| 81 | E | A | -2.4258 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | -1.1447 | |
| 84 | G | A | -1.2126 | |
| 85 | M | A | -0.8739 | |
| 86 | Y | A | 0.0000 | |
| 87 | F | A | 0.0000 | |
| 88 | C | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | Q | A | 0.0000 | |
| 91 | S | A | -0.4226 | |
| 92 | N | A | -0.7997 | |
| 93 | S | A | -0.3412 | |
| 94 | W | A | 0.3317 | |
| 95 | P | A | -0.5277 | |
| 96 | R | A | 0.0000 | |
| 97 | T | A | -0.9293 | |
| 98 | F | A | 0.0000 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -1.2241 | |
| 101 | G | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -1.3836 | |
| 104 | L | A | 0.0000 | |
| 105 | E | A | -1.0630 | |
| 106 | I | A | -1.3866 | |
| 107 | K | A | -2.0363 | |
| 108 | R | A | -1.8174 | |
| 109 | A | A | -1.3714 | |
| 110 | D | A | -2.4928 | |
| 111 | A | A | -1.3483 | |
| 112 | A | A | -0.7347 | |
| 113 | P | A | 0.0000 | |
| 114 | T | A | -0.1350 | |
| 115 | V | A | 0.0000 | |
| 116 | S | A | 0.0346 | |
| 117 | I | A | 0.1680 | |
| 118 | F | A | 0.0000 | |
| 119 | P | A | 0.0000 | |
| 120 | P | A | 0.0000 | |
| 121 | S | A | 0.0000 | |
| 122 | S | A | -0.6330 | |
| 123 | E | A | -0.9944 | |
| 124 | Q | A | 0.0000 | |
| 125 | L | A | -0.8528 | |
| 126 | T | A | -0.5903 | |
| 127 | S | A | -0.6205 | |
| 128 | G | A | -1.1660 | |
| 129 | G | A | -1.0191 | |
| 130 | A | A | 0.0000 | |
| 131 | S | A | 0.0000 | |
| 132 | V | A | 0.0000 | |
| 133 | V | A | 0.0000 | |
| 134 | C | A | 0.0000 | |
| 135 | F | A | 0.0000 | |
| 136 | L | A | 0.0000 | |
| 137 | N | A | 0.0000 | |
| 138 | N | A | -1.0523 | |
| 139 | F | A | 0.0000 | |
| 140 | Y | A | 0.0000 | |
| 141 | P | A | -2.3324 | |
| 142 | K | A | -2.7628 | |
| 143 | D | A | -2.9191 | |
| 144 | I | A | 0.0000 | |
| 145 | N | A | -2.1569 | |
| 146 | V | A | -0.8211 | |
| 147 | K | A | -1.8669 | |
| 148 | W | A | 0.0000 | |
| 149 | K | A | -2.4012 | |
| 150 | I | A | 0.0000 | |
| 151 | D | A | -2.2403 | |
| 152 | G | A | -1.7927 | |
| 153 | S | A | -2.0246 | |
| 154 | E | A | -3.2265 | |
| 155 | R | A | -2.6506 | |
| 156 | Q | A | -2.5273 | |
| 157 | N | A | -2.0309 | |
| 158 | G | A | -0.8588 | |
| 159 | V | A | -0.4214 | |
| 160 | L | A | 0.1840 | |
| 161 | N | A | -0.0823 | |
| 162 | S | A | -0.1702 | |
| 163 | W | A | -0.3925 | |
| 164 | T | A | -1.1917 | |
| 165 | D | A | -2.2768 | |
| 166 | Q | A | -2.1853 | |
| 167 | D | A | -2.5357 | |
| 168 | S | A | -2.2893 | |
| 169 | K | A | -2.6561 | |
| 170 | D | A | -2.4319 | |
| 171 | S | A | 0.0000 | |
| 172 | T | A | 0.0000 | |
| 173 | Y | A | 0.0000 | |
| 174 | S | A | 0.0000 | |
| 175 | M | A | 0.0000 | |
| 176 | S | A | 0.0000 | |
| 177 | S | A | 0.0000 | |
| 178 | T | A | 0.0000 | |
| 179 | L | A | 0.0000 | |
| 180 | T | A | -0.1865 | |
| 181 | L | A | 0.0000 | |
| 182 | T | A | -1.4558 | |
| 183 | K | A | -2.3903 | |
| 184 | D | A | -3.2222 | |
| 185 | E | A | -2.7696 | |
| 186 | Y | A | 0.0000 | |
| 187 | E | A | -2.9054 | |
| 188 | R | A | -3.3396 | |
| 189 | H | A | -2.5714 | |
| 190 | N | A | -2.3319 | |
| 191 | S | A | -1.6820 | |
| 192 | Y | A | 0.0000 | |
| 193 | T | A | -0.8067 | |
| 194 | C | A | 0.0000 | |
| 195 | E | A | -0.6316 | |
| 196 | A | A | 0.0000 | |
| 197 | T | A | -1.1076 | |
| 198 | H | A | 0.0000 | |
| 199 | K | A | -2.6903 | |
| 200 | T | A | -1.3222 | |
| 201 | S | A | -0.7387 | |
| 202 | T | A | -0.5633 | |
| 203 | S | A | -0.4024 | |
| 204 | P | A | -0.3924 | |
| 205 | I | A | 0.6413 | |
| 206 | V | A | 0.7412 | |
| 207 | K | A | -0.0350 | |
| 208 | S | A | -0.2099 | |
| 209 | F | A | -0.5957 | |
| 210 | N | A | -1.6612 | |
| 211 | R | A | -2.1685 | |
| 212 | N | A | -2.4684 | |
| 213 | E | A | -2.2595 | |
| 214 | C | A | -0.5547 | |
| 1 | Q | B | -1.3496 | |
| 2 | V | B | -0.6233 | |
| 3 | Q | B | -1.4537 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -2.0455 | |
| 6 | E | B | 0.0000 | |
| 7 | S | B | -1.0222 | |
| 8 | G | B | -0.9053 | |
| 9 | A | B | -0.1903 | |
| 10 | E | B | -0.2429 | |
| 11 | V | B | 0.3644 | |
| 12 | M | B | -0.4576 | |
| 13 | K | B | -1.7226 | |
| 14 | P | B | -1.3777 | |
| 15 | G | B | -1.1333 | |
| 16 | A | B | -0.8571 | |
| 17 | S | B | -0.9581 | |
| 18 | V | B | 0.0000 | |
| 19 | K | B | -1.2656 | |
| 20 | I | B | 0.0000 | |
| 21 | S | B | -0.8048 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -1.6081 | |
| 24 | A | B | 0.0000 | |
| 25 | T | B | -1.0197 | |
| 26 | G | B | -0.8094 | |
| 27 | Y | B | -0.2526 | |
| 28 | T | B | -0.0588 | |
| 29 | F | B | 0.0000 | |
| 30 | T | B | -0.0432 | mutated: ST30B |
| 31 | T | B | 0.2125 | |
| 32 | Y | B | 0.6416 | |
| 33 | W | B | 0.6105 | |
| 34 | I | B | 0.0000 | |
| 35 | E | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | K | B | 0.0000 | |
| 39 | Q | B | -0.7789 | |
| 40 | R | B | -1.4004 | |
| 41 | P | B | -1.0057 | |
| 42 | G | B | -1.2909 | |
| 43 | H | B | -1.6865 | |
| 44 | G | B | -1.1296 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -0.8065 | |
| 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 | L | B | 0.3184 | |
| 53 | P | B | 0.0000 | |
| 54 | G | B | -0.9112 | |
| 55 | S | B | -0.6587 | |
| 56 | G | B | -0.7171 | |
| 57 | S | B | -0.1513 | |
| 58 | T | B | 0.4549 | |
| 59 | Y | B | 0.7184 | |
| 60 | Y | B | -0.8262 | |
| 61 | N | B | -1.8875 | |
| 62 | E | B | -3.1996 | |
| 63 | K | B | -3.2327 | |
| 64 | F | B | 0.0000 | |
| 65 | K | B | -2.9859 | |
| 66 | G | B | -2.0524 | |
| 67 | K | B | -1.7745 | |
| 68 | A | B | 0.0000 | |
| 69 | T | B | -0.6917 | |
| 70 | F | B | 0.0000 | |
| 71 | T | B | -0.3299 | |
| 72 | A | B | -0.6851 | |
| 73 | D | B | -1.1705 | |
| 74 | T | B | -0.8557 | |
| 75 | S | B | -0.7085 | |
| 76 | S | B | -0.8182 | |
| 77 | N | B | -1.0260 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.4008 | |
| 81 | M | B | 0.0000 | |
| 82 | Q | B | -1.0600 | |
| 83 | L | B | 0.0000 | |
| 84 | S | B | -0.8656 | |
| 85 | S | B | -0.8323 | |
| 86 | L | B | 0.0000 | |
| 87 | T | B | -1.2438 | |
| 88 | S | B | -1.4269 | |
| 89 | E | B | -2.0356 | |
| 90 | D | B | 0.0000 | |
| 91 | S | B | -0.6736 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | -0.1579 | |
| 94 | Y | B | 0.0000 | |
| 95 | Y | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | R | B | 0.0000 | |
| 99 | G | B | 0.1434 | |
| 100 | D | B | -0.1957 | |
| 101 | G | B | -0.3725 | |
| 102 | N | B | 0.0000 | |
| 103 | Y | B | 0.0000 | |
| 104 | C | B | 0.2342 | mutated: GC104B |
| 105 | Y | B | 0.2660 | |
| 106 | W | B | -0.4749 | |
| 107 | G | B | 0.0000 | |
| 108 | Q | B | -2.1007 | |
| 109 | G | B | -1.2688 | |
| 110 | T | B | 0.0000 | |
| 111 | T | B | -0.1897 | |
| 112 | L | B | 0.0000 | |
| 113 | T | B | -0.2942 | |
| 114 | V | B | 0.0000 | |
| 115 | S | B | -0.9607 | |
| 116 | S | B | -1.0892 | |
| 117 | A | B | -0.8507 | |
| 118 | S | B | -0.5977 | |
| 119 | T | B | -0.3310 | |
| 120 | T | B | -0.1907 | |
| 121 | P | B | -0.5362 | |
| 122 | P | B | 0.0000 | |
| 123 | S | B | -0.1848 | |
| 124 | V | B | 0.0000 | |
| 125 | F | B | -0.2964 | |
| 126 | P | B | -0.3906 | |
| 127 | L | B | 0.0000 | |
| 128 | A | B | 0.0000 | |
| 129 | P | B | 0.0000 | |
| 130 | G | B | -0.1819 | |
| 131 | S | B | -0.2940 | |
| 132 | A | B | -0.3681 | |
| 133 | A | B | -0.4137 | |
| 134 | Q | B | -0.7167 | |
| 135 | T | B | -0.8079 | |
| 136 | N | B | -1.3126 | |
| 137 | S | B | -0.6240 | |
| 138 | M | B | 0.1227 | |
| 139 | V | B | 0.0000 | |
| 140 | T | B | 0.1430 | |
| 141 | L | B | 0.0000 | |
| 142 | G | B | 0.0000 | |
| 143 | C | B | 0.0000 | |
| 144 | L | B | 0.0000 | |
| 145 | V | B | 0.0000 | |
| 146 | K | B | 0.0000 | |
| 147 | G | B | -0.1505 | |
| 148 | Y | B | 0.0000 | |
| 149 | F | B | 0.0000 | |
| 150 | P | B | -0.6288 | |
| 151 | E | B | -1.0004 | |
| 152 | P | B | -0.8614 | |
| 153 | V | B | 0.0000 | |
| 154 | T | B | -0.4370 | |
| 155 | V | B | -0.2823 | |
| 156 | T | B | -0.4039 | |
| 157 | W | B | 0.0000 | |
| 158 | N | B | -0.9683 | |
| 159 | S | B | -0.7940 | |
| 160 | G | B | -0.6194 | |
| 161 | S | B | -0.4752 | |
| 162 | L | B | -0.1855 | |
| 163 | S | B | -0.3436 | |
| 164 | S | B | -0.2742 | |
| 165 | G | B | -0.1179 | |
| 166 | V | B | 0.2627 | |
| 167 | H | B | -0.1293 | |
| 168 | T | B | 0.0706 | |
| 169 | F | B | 0.0000 | |
| 170 | P | B | -0.1124 | |
| 171 | A | B | 0.2967 | |
| 172 | V | B | 0.9254 | |
| 173 | L | B | 1.2282 | |
| 174 | Q | B | 0.0827 | |
| 175 | S | B | -0.7468 | |
| 176 | D | B | -1.4504 | |
| 177 | L | B | -0.3610 | |
| 178 | Y | B | 0.2496 | |
| 179 | T | B | 0.0000 | |
| 180 | L | B | 0.0000 | |
| 181 | S | B | 0.0000 | |
| 182 | S | B | 0.0000 | |
| 183 | S | B | 0.0000 | |
| 184 | V | B | 0.0000 | |
| 185 | T | B | 0.1296 | |
| 186 | V | B | 0.0000 | |
| 187 | P | B | -0.2580 | |
| 188 | S | B | -0.7222 | |
| 189 | S | B | -0.8019 | |
| 190 | P | B | -0.9298 | |
| 191 | R | B | 0.0000 | |
| 192 | P | B | -0.7329 | |
| 193 | S | B | -1.3102 | |
| 194 | E | B | -2.0833 | |
| 195 | T | B | -1.1896 | |
| 196 | V | B | 0.0000 | |
| 197 | T | B | -1.4445 | |
| 198 | C | B | 0.0000 | |
| 199 | N | B | -1.6271 | |
| 200 | V | B | 0.0000 | |
| 201 | A | B | -1.0395 | |
| 202 | H | B | 0.0000 | |
| 203 | P | B | -0.8301 | |
| 204 | A | B | -0.4631 | |
| 205 | S | B | -0.5275 | |
| 206 | S | B | -0.7543 | |
| 207 | T | B | -0.9503 | |
| 208 | K | B | -2.0218 | |
| 209 | V | B | -1.3912 | |
| 210 | D | B | -2.6455 | |
| 211 | K | B | -1.7002 | |
| 212 | K | B | -1.8890 | |
| 213 | I | B | 0.0000 | |
| 214 | V | B | 0.8458 | |
| 215 | P | B | 0.0969 | |
| 216 | R | B | -0.6976 | |
| 217 | D | B | -1.3503 | |
| 218 | C | B | -0.2958 |
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 | -0.5827 | 2.286 | View | CSV | PDB |
| 4.5 | -0.6341 | 2.229 | View | CSV | PDB |
| 5.0 | -0.6948 | 2.1541 | View | CSV | PDB |
| 5.5 | -0.7539 | 2.0708 | View | CSV | PDB |
| 6.0 | -0.7997 | 1.9842 | View | CSV | PDB |
| 6.5 | -0.8246 | 1.8967 | View | CSV | PDB |
| 7.0 | -0.8297 | 1.809 | View | CSV | PDB |
| 7.5 | -0.8221 | 1.7217 | View | CSV | PDB |
| 8.0 | -0.8073 | 1.6358 | View | CSV | PDB |
| 8.5 | -0.7862 | 1.6291 | View | CSV | PDB |
| 9.0 | -0.7574 | 1.709 | 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