| Chain sequence(s) |
A: APSVFPISSCCGSTQQQPVVGCLATGYIPGPATFSWSGASGATSVTVPETHGVGPHKRASFLRPPHAGSGDFFTCSVNHQATRTSLTQNVEGCVAGGEPTPPEVQVLHSSVCSTLGDDSVELLCVITGFSPPPVEVEWLVDGAPAHLVATMTRPQREAGSKTYMATSQTNVSREDWKAGKAFTCRVKHPATGGTAQGHARFCPEF
B: APSVFPISSCCGSTQQQPVVGCLATGYIPGPATFSWSGASGATSVTVPETHGVGPHKRASFLRPPHAGSGDFFTCSVNHQATRTSLTQNVEGCVAGGEPTPPEVQVLHSSVCSTLGDDSVELLCVITGFSPPPVEVEWLVDGAPAHLVATMTRPQREAGSKTYMATSQTNVSREDWKAGKAFTCRVKHPATGGTAQGHARFCPEF 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. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:03:14)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/c9f26e1e15554fd/tmp/folded.pdb (00:03:14)
[INFO] Main: Simulation completed successfully. (00:06:06)
|
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 | A | A | -0.2916 | |
| 2 | P | A | 0.0000 | |
| 3 | S | A | -0.1159 | |
| 4 | V | A | 0.1726 | |
| 5 | F | A | 0.4099 | |
| 6 | P | A | 0.3110 | |
| 7 | I | A | 0.8314 | |
| 8 | S | A | 0.5537 | |
| 9 | S | A | 0.0959 | |
| 10 | C | A | 0.1808 | |
| 11 | C | A | -0.0611 | |
| 12 | G | A | -0.5777 | |
| 13 | S | A | -0.8689 | |
| 14 | T | A | -1.1677 | |
| 15 | Q | A | -1.9800 | |
| 16 | Q | A | -2.0482 | |
| 17 | Q | A | -1.8259 | |
| 18 | P | A | -1.2082 | |
| 19 | V | A | -0.3662 | |
| 20 | V | A | 0.0000 | |
| 21 | G | A | 0.0000 | |
| 22 | C | A | 0.0000 | |
| 23 | L | A | 0.3730 | |
| 24 | A | A | 0.0000 | |
| 25 | T | A | -0.6231 | |
| 26 | G | A | -0.6657 | |
| 27 | Y | A | 0.0000 | |
| 28 | I | A | 0.8060 | |
| 29 | P | A | 0.0889 | |
| 30 | G | A | -0.6030 | |
| 31 | P | A | -0.7803 | |
| 32 | A | A | 0.0000 | |
| 33 | T | A | -0.6426 | |
| 34 | F | A | 0.0418 | |
| 35 | S | A | -0.2632 | |
| 36 | W | A | -0.1976 | |
| 37 | S | A | -0.4621 | |
| 38 | G | A | -0.7064 | |
| 39 | A | A | -0.8393 | |
| 40 | S | A | -0.7159 | |
| 41 | G | A | -0.9440 | |
| 42 | A | A | -0.9465 | |
| 43 | T | A | -0.3258 | |
| 44 | S | A | 0.2724 | |
| 45 | V | A | 1.0966 | |
| 46 | T | A | 0.7422 | |
| 47 | V | A | 0.4780 | |
| 48 | P | A | -0.4452 | |
| 49 | E | A | -1.2340 | |
| 50 | T | A | -1.1843 | |
| 51 | H | A | -1.3727 | |
| 52 | G | A | -0.4542 | |
| 53 | V | A | 1.1245 | |
| 54 | G | A | 0.1635 | |
| 55 | P | A | -0.3972 | |
| 56 | H | A | -1.0630 | |
| 57 | K | A | -1.7982 | |
| 58 | R | A | -1.1006 | |
| 59 | A | A | 0.1992 | |
| 60 | S | A | 0.0000 | |
| 61 | F | A | 0.9378 | |
| 62 | L | A | 0.0000 | |
| 63 | R | A | -1.0811 | |
| 64 | P | A | 0.0000 | |
| 65 | P | A | -1.3228 | |
| 66 | H | A | -1.5844 | |
| 67 | A | A | -1.0625 | |
| 68 | G | A | -0.9503 | |
| 69 | S | A | -0.9328 | |
| 70 | G | A | -1.0973 | |
| 71 | D | A | -1.2482 | |
| 72 | F | A | -0.4973 | |
| 73 | F | A | 0.0000 | |
| 74 | T | A | -0.4588 | |
| 75 | C | A | 0.0000 | |
| 76 | S | A | -0.3502 | |
| 77 | V | A | 0.0000 | |
| 78 | N | A | -1.5533 | |
| 79 | H | A | 0.0000 | |
| 80 | Q | A | -2.2712 | |
| 81 | A | A | -1.0812 | |
| 82 | T | A | -1.2405 | |
| 83 | R | A | -2.5160 | |
| 84 | T | A | -1.4544 | |
| 85 | S | A | -1.0148 | |
| 86 | L | A | -0.0171 | |
| 87 | T | A | -0.2623 | |
| 88 | Q | A | -0.3906 | |
| 89 | N | A | -0.7126 | |
| 90 | V | A | 0.0000 | |
| 91 | E | A | -0.5205 | |
| 92 | G | A | 0.0000 | |
| 93 | C | A | 0.0265 | |
| 94 | V | A | -0.4338 | |
| 95 | A | A | -1.1018 | |
| 96 | G | A | -1.0294 | |
| 97 | G | A | -1.8855 | |
| 98 | E | A | -2.4579 | |
| 99 | P | A | -1.5858 | |
| 100 | T | A | -1.2531 | |
| 101 | P | A | -1.1753 | |
| 102 | P | A | 0.0000 | |
| 103 | E | A | -2.0953 | |
| 104 | V | A | 0.0000 | |
| 105 | Q | A | -1.3262 | |
| 106 | V | A | 0.0000 | |
| 107 | L | A | 0.0000 | |
| 108 | H | A | 0.0000 | |
| 109 | S | A | -0.5719 | |
| 110 | S | A | -0.4484 | |
| 111 | V | A | -0.6548 | |
| 112 | C | A | 0.0694 | |
| 113 | S | A | 0.0788 | |
| 114 | T | A | -0.0065 | |
| 115 | L | A | 0.7067 | |
| 116 | G | A | -0.8505 | |
| 117 | D | A | -2.5685 | |
| 118 | D | A | -3.0475 | |
| 119 | S | A | -2.5029 | |
| 120 | V | A | 0.0000 | |
| 121 | E | A | -1.2442 | |
| 122 | L | A | 0.0000 | |
| 123 | L | A | 0.0000 | |
| 124 | C | A | 0.0000 | |
| 125 | V | A | -0.3418 | |
| 126 | I | A | 0.0000 | |
| 127 | T | A | -1.0113 | |
| 128 | G | A | -1.2074 | |
| 129 | F | A | 0.0000 | |
| 130 | S | A | 0.0000 | |
| 131 | P | A | -0.8716 | |
| 132 | P | A | 0.0000 | |
| 133 | P | A | -0.1056 | |
| 134 | V | A | -0.2407 | |
| 135 | E | A | -0.9848 | |
| 136 | V | A | -0.9314 | |
| 137 | E | A | -1.9508 | |
| 138 | W | A | 0.0000 | |
| 139 | L | A | 0.0000 | |
| 140 | V | A | -1.2055 | |
| 141 | D | A | -2.2330 | |
| 142 | G | A | -1.4463 | |
| 143 | A | A | -0.8662 | |
| 144 | P | A | -1.0818 | |
| 145 | A | A | -0.6838 | |
| 146 | H | A | -0.5657 | |
| 147 | L | A | 0.2917 | |
| 148 | V | A | 1.4252 | |
| 149 | A | A | 0.3700 | |
| 150 | T | A | 0.1272 | |
| 151 | M | A | 0.2852 | |
| 152 | T | A | -0.3769 | |
| 153 | R | A | -1.0685 | |
| 154 | P | A | -0.9773 | |
| 155 | Q | A | -1.7232 | |
| 156 | R | A | -2.8078 | |
| 157 | E | A | -1.9923 | |
| 158 | A | A | -1.2245 | |
| 159 | G | A | -1.1878 | |
| 160 | S | A | -1.6745 | |
| 161 | K | A | -2.7862 | |
| 162 | T | A | -2.0293 | |
| 163 | Y | A | 0.0000 | |
| 164 | M | A | -0.9088 | |
| 165 | A | A | 0.0000 | |
| 166 | T | A | 0.0000 | |
| 167 | S | A | 0.0000 | |
| 168 | Q | A | -0.6145 | |
| 169 | T | A | 0.0000 | |
| 170 | N | A | -1.4280 | |
| 171 | V | A | 0.0000 | |
| 172 | S | A | -2.1993 | |
| 173 | R | A | -2.6921 | |
| 174 | E | A | -2.9560 | |
| 175 | D | A | -2.2175 | |
| 176 | W | A | 0.0000 | |
| 177 | K | A | -1.9389 | |
| 178 | A | A | -1.4965 | |
| 179 | G | A | -1.5771 | |
| 180 | K | A | -2.0140 | |
| 181 | A | A | -1.7372 | |
| 182 | F | A | 0.0000 | |
| 183 | T | A | 0.0000 | |
| 184 | C | A | 0.0000 | |
| 185 | R | A | -2.2314 | |
| 186 | V | A | 0.0000 | |
| 187 | K | A | -1.8168 | |
| 188 | H | A | 0.0000 | |
| 189 | P | A | -0.6732 | |
| 190 | A | A | -0.6074 | |
| 191 | T | A | -0.8096 | |
| 192 | G | A | -0.8625 | |
| 193 | G | A | -0.7538 | |
| 194 | T | A | -1.2895 | |
| 195 | A | A | -1.4419 | |
| 196 | Q | A | -2.0439 | |
| 197 | G | A | 0.0000 | |
| 198 | H | A | -1.6863 | |
| 199 | A | A | 0.0000 | |
| 200 | R | A | -1.9903 | |
| 201 | F | A | -0.9357 | |
| 202 | C | A | -0.7017 | |
| 203 | P | A | -1.2950 | |
| 204 | E | A | -1.8320 | |
| 205 | F | A | -0.6660 | |
| 1 | A | B | -0.2776 | |
| 2 | P | B | 0.0000 | |
| 3 | S | B | -0.1478 | |
| 4 | V | B | 0.1769 | |
| 5 | F | B | 0.4336 | |
| 6 | P | B | 0.4263 | |
| 7 | I | B | 0.9987 | |
| 8 | S | B | 0.6257 | |
| 9 | S | B | 0.1165 | |
| 10 | C | B | 0.2023 | |
| 11 | C | B | -0.0643 | |
| 12 | G | B | -0.5772 | |
| 13 | S | B | -0.8786 | |
| 14 | T | B | -1.1728 | |
| 15 | Q | B | -1.9704 | |
| 16 | Q | B | -2.0446 | |
| 17 | Q | B | -1.8386 | |
| 18 | P | B | -1.2018 | |
| 19 | V | B | -0.2623 | |
| 20 | V | B | 0.0000 | |
| 21 | G | B | 0.0000 | |
| 22 | C | B | 0.0000 | |
| 23 | L | B | 0.4654 | |
| 24 | A | B | 0.0000 | |
| 25 | T | B | -0.6150 | |
| 26 | G | B | -0.6323 | |
| 27 | Y | B | 0.0000 | |
| 28 | I | B | 0.9352 | |
| 29 | P | B | 0.1631 | |
| 30 | G | B | -0.6028 | |
| 31 | P | B | -0.7998 | |
| 32 | A | B | 0.0000 | |
| 33 | T | B | -0.6662 | |
| 34 | F | B | 0.0559 | |
| 35 | S | B | -0.2639 | |
| 36 | W | B | -0.1804 | |
| 37 | S | B | -0.4153 | |
| 38 | G | B | -0.5820 | |
| 39 | A | B | -0.7652 | |
| 40 | S | B | -0.7160 | |
| 41 | G | B | -0.9596 | |
| 42 | A | B | -0.9851 | |
| 43 | T | B | -0.3525 | |
| 44 | S | B | 0.3123 | |
| 45 | V | B | 1.1886 | |
| 46 | T | B | 0.8910 | |
| 47 | V | B | 0.7517 | |
| 48 | P | B | -0.3970 | |
| 49 | E | B | -1.3489 | |
| 50 | T | B | -1.2082 | |
| 51 | H | B | -1.3853 | |
| 52 | G | B | -0.3995 | |
| 53 | V | B | 1.1607 | |
| 54 | G | B | 0.2068 | |
| 55 | P | B | -0.3295 | |
| 56 | H | B | -1.0315 | |
| 57 | K | B | -1.7467 | |
| 58 | R | B | -1.0755 | |
| 59 | A | B | 0.3151 | |
| 60 | S | B | 0.0000 | |
| 61 | F | B | 1.1036 | |
| 62 | L | B | 0.0000 | |
| 63 | R | B | -1.1409 | |
| 64 | P | B | 0.0000 | |
| 65 | P | B | -1.3390 | |
| 66 | H | B | -1.5273 | |
| 67 | A | B | -0.9307 | |
| 68 | G | B | -0.8163 | |
| 69 | S | B | -0.8498 | |
| 70 | G | B | -0.8692 | |
| 71 | D | B | -0.7613 | |
| 72 | F | B | -0.0393 | |
| 73 | F | B | 0.0000 | |
| 74 | T | B | -0.3762 | |
| 75 | C | B | 0.0000 | |
| 76 | S | B | -0.3335 | |
| 77 | V | B | 0.0000 | |
| 78 | N | B | -1.5453 | |
| 79 | H | B | 0.0000 | |
| 80 | Q | B | -2.2727 | |
| 81 | A | B | -1.0641 | |
| 82 | T | B | -1.2244 | |
| 83 | R | B | -2.5156 | |
| 84 | T | B | -1.4491 | |
| 85 | S | B | -1.0029 | |
| 86 | L | B | -0.0031 | |
| 87 | T | B | -0.2382 | |
| 88 | Q | B | -0.2788 | |
| 89 | N | B | -0.5774 | |
| 90 | V | B | 0.0000 | |
| 91 | E | B | -0.4123 | |
| 92 | G | B | 0.0000 | |
| 93 | C | B | 0.0000 | |
| 94 | V | B | -0.4277 | |
| 95 | A | B | -1.1293 | |
| 96 | G | B | -1.0270 | |
| 97 | G | B | -1.8916 | |
| 98 | E | B | -2.4634 | |
| 99 | P | B | -1.5869 | |
| 100 | T | B | -1.2582 | |
| 101 | P | B | -1.1608 | |
| 102 | P | B | 0.0000 | |
| 103 | E | B | -2.0878 | |
| 104 | V | B | 0.0000 | |
| 105 | Q | B | -1.2028 | |
| 106 | V | B | 0.0000 | |
| 107 | L | B | 0.0000 | |
| 108 | H | B | 0.0000 | |
| 109 | S | B | -0.5729 | |
| 110 | S | B | -0.4690 | |
| 111 | V | B | -0.5053 | |
| 112 | C | B | 0.0457 | |
| 113 | S | B | 0.0925 | |
| 114 | T | B | 0.0110 | |
| 115 | L | B | 0.7656 | |
| 116 | G | B | -0.7530 | |
| 117 | D | B | -2.4994 | |
| 118 | D | B | -2.9527 | |
| 119 | S | B | -2.3466 | |
| 120 | V | B | 0.0000 | |
| 121 | E | B | -1.0746 | |
| 122 | L | B | 0.0000 | |
| 123 | L | B | 0.0000 | |
| 124 | C | B | 0.0000 | |
| 125 | V | B | 0.0000 | |
| 126 | I | B | 0.0000 | |
| 127 | T | B | -1.0101 | |
| 128 | G | B | -1.2103 | |
| 129 | F | B | 0.0000 | |
| 130 | S | B | 0.0000 | |
| 131 | P | B | -0.8679 | |
| 132 | P | B | -0.3639 | |
| 133 | P | B | -0.0922 | |
| 134 | V | B | -0.2289 | |
| 135 | E | B | -0.9830 | |
| 136 | V | B | -0.9310 | |
| 137 | E | B | -1.9373 | |
| 138 | W | B | 0.0000 | |
| 139 | L | B | 0.0000 | |
| 140 | V | B | -1.1963 | |
| 141 | D | B | -2.2327 | |
| 142 | G | B | -1.4583 | |
| 143 | A | B | -0.8739 | |
| 144 | P | B | -1.0899 | |
| 145 | A | B | -0.6840 | |
| 146 | H | B | -0.5621 | |
| 147 | L | B | 0.3777 | |
| 148 | V | B | 1.5246 | |
| 149 | A | B | 0.5506 | |
| 150 | T | B | 0.2920 | |
| 151 | M | B | 0.3931 | |
| 152 | T | B | -0.2992 | |
| 153 | R | B | -1.0417 | |
| 154 | P | B | -0.9195 | |
| 155 | Q | B | -1.5790 | |
| 156 | R | B | -2.7235 | |
| 157 | E | B | -1.9406 | |
| 158 | A | B | -1.2378 | |
| 159 | G | B | -1.1869 | |
| 160 | S | B | -1.6783 | |
| 161 | K | B | -2.7901 | |
| 162 | T | B | -2.0112 | |
| 163 | Y | B | 0.0000 | |
| 164 | M | B | -0.8945 | |
| 165 | A | B | 0.0000 | |
| 166 | T | B | 0.0000 | |
| 167 | S | B | 0.0000 | |
| 168 | Q | B | -0.1631 | |
| 169 | T | B | 0.0000 | |
| 170 | N | B | -1.1056 | |
| 171 | V | B | 0.0000 | |
| 172 | S | B | -2.0038 | |
| 173 | R | B | 0.0000 | |
| 174 | E | B | -2.7934 | |
| 175 | D | B | -1.9830 | |
| 176 | W | B | 0.0000 | |
| 177 | K | B | -1.9088 | |
| 178 | A | B | -1.4224 | |
| 179 | G | B | -1.5116 | |
| 180 | K | B | -1.9389 | |
| 181 | A | B | -1.6984 | |
| 182 | F | B | 0.0000 | |
| 183 | T | B | 0.0000 | |
| 184 | C | B | 0.0000 | |
| 185 | R | B | -2.2707 | |
| 186 | V | B | 0.0000 | |
| 187 | K | B | -1.7588 | |
| 188 | H | B | 0.0000 | |
| 189 | P | B | -0.6234 | |
| 190 | A | B | -0.5853 | |
| 191 | T | B | -0.7886 | |
| 192 | G | B | -0.8346 | |
| 193 | G | B | -0.7290 | |
| 194 | T | B | -1.2775 | |
| 195 | A | B | -1.4285 | |
| 196 | Q | B | -2.0249 | |
| 197 | G | B | 0.0000 | |
| 198 | H | B | -1.6552 | |
| 199 | A | B | 0.0000 | |
| 200 | R | B | -1.9505 | |
| 201 | F | B | -0.9533 | |
| 202 | C | B | -0.6670 | |
| 203 | P | B | -1.2623 | |
| 204 | E | B | -1.7348 | |
| 205 | F | B | -0.5136 |
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 | -0.3318 | 4.0025 | View | CSV | PDB |
| 4.5 | -0.3731 | 4.005 | View | CSV | PDB |
| 5.0 | -0.4239 | 4.0107 | View | CSV | PDB |
| 5.5 | -0.4743 | 4.0206 | View | CSV | PDB |
| 6.0 | -0.5145 | 4.0353 | View | CSV | PDB |
| 6.5 | -0.5375 | 4.0575 | View | CSV | PDB |
| 7.0 | -0.5436 | 4.0891 | View | CSV | PDB |
| 7.5 | -0.5399 | 4.127 | View | CSV | PDB |
| 8.0 | -0.5321 | 4.1677 | View | CSV | PDB |
| 8.5 | -0.521 | 4.2094 | View | CSV | PDB |
| 9.0 | -0.5049 | 4.2513 | 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