| Chain sequence(s) |
A: DIQMTQSPSSLSASVGDRVTITCHASQNINVWLSWYQQKPGKVPKLLIYKASDLHTGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCQQGQSYPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
B: EVQLVESGGGLVKPGGSLRLSCAASGFTFSDSGMHWIRQAPGKGLEWVSYISSGSSTIHYADTVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCASPLYYYGRSYNAVAYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT 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. (00:00:03)
[INFO] FoldX: Starting FoldX energy minimization (00:00:03)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:04:57)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/5a1c3e6a15bfb77/tmp/folded.pdb (00:04:57)
[INFO] Main: Simulation completed successfully. (00:06:58)
|
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 | -2.3677 | |
| 2 | I | A | -1.8264 | |
| 3 | Q | A | -1.9669 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.9917 | |
| 6 | Q | A | -0.8781 | |
| 7 | S | A | -0.6986 | |
| 8 | P | A | -0.6552 | |
| 9 | S | A | -0.8941 | |
| 10 | S | A | -0.9968 | |
| 11 | L | A | -0.6950 | |
| 12 | S | A | -1.0216 | |
| 13 | A | A | -0.9823 | |
| 14 | S | A | -0.8819 | |
| 15 | V | A | -0.0385 | |
| 16 | G | A | -0.8508 | |
| 17 | D | A | -1.7244 | |
| 18 | R | A | -2.3111 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.6375 | |
| 21 | I | A | 0.0000 | |
| 22 | T | A | -0.7376 | |
| 23 | C | A | 0.0000 | |
| 24 | H | A | -1.9704 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -1.9404 | |
| 27 | Q | A | -2.7374 | |
| 28 | N | A | -2.4944 | |
| 29 | I | A | 0.0000 | |
| 30 | N | A | -1.6860 | |
| 31 | V | A | -0.5810 | |
| 32 | W | A | -0.3611 | |
| 33 | L | A | 0.0000 | |
| 34 | S | A | 0.0000 | |
| 35 | W | A | 0.0000 | |
| 36 | Y | A | 0.0000 | |
| 37 | Q | A | 0.0000 | |
| 38 | Q | A | -1.1557 | |
| 39 | K | A | -1.7457 | |
| 40 | P | A | -1.5261 | |
| 41 | G | A | -1.5588 | |
| 42 | K | A | -2.1102 | |
| 43 | V | A | -0.7973 | |
| 44 | P | A | 0.0000 | |
| 45 | K | A | -0.9735 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | 0.0000 | |
| 50 | K | A | -0.9549 | |
| 51 | A | A | 0.0000 | |
| 52 | S | A | -0.8443 | |
| 53 | D | A | -1.0684 | |
| 54 | L | A | -0.2908 | |
| 55 | H | A | -0.4855 | |
| 56 | T | A | -0.3454 | |
| 57 | G | A | -0.5060 | |
| 58 | V | A | 0.0000 | |
| 59 | P | A | -0.3884 | |
| 60 | S | A | -0.4530 | |
| 61 | R | A | -0.8347 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.4906 | |
| 64 | G | A | -0.6065 | |
| 65 | S | A | -0.9190 | |
| 66 | G | A | -1.2596 | |
| 67 | S | A | -1.3079 | |
| 68 | G | A | -1.7650 | |
| 69 | T | A | -2.1236 | |
| 70 | D | A | -2.6150 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.7819 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.6256 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.3645 | |
| 77 | S | A | -1.2227 | |
| 78 | L | A | 0.0000 | |
| 79 | Q | A | -0.9000 | |
| 80 | P | A | -1.3920 | |
| 81 | E | A | -1.5070 | |
| 82 | D | A | 0.0000 | |
| 83 | V | A | 0.0000 | |
| 84 | A | A | 0.0000 | |
| 85 | T | A | -1.0815 | |
| 86 | Y | A | 0.0000 | |
| 87 | Y | A | 0.0000 | |
| 88 | C | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | Q | A | 0.0000 | |
| 91 | G | A | 0.0000 | |
| 92 | Q | A | -0.8268 | |
| 93 | S | A | -0.5078 | |
| 94 | Y | A | -0.1992 | |
| 95 | P | A | -0.6775 | |
| 96 | L | A | 0.0000 | |
| 97 | T | A | -0.6729 | |
| 98 | F | A | -0.2865 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -1.2148 | |
| 101 | G | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -2.0171 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | -1.4746 | |
| 106 | I | A | 0.0000 | |
| 107 | K | A | -1.3175 | |
| 108 | R | A | -0.8565 | |
| 109 | T | A | -0.1235 | |
| 110 | V | A | 0.3477 | |
| 111 | A | A | -0.0010 | |
| 112 | A | A | -0.1326 | |
| 113 | P | A | 0.0000 | |
| 114 | S | A | -0.2263 | |
| 115 | V | A | 0.0000 | |
| 116 | F | A | 0.0000 | |
| 117 | I | A | 0.0000 | |
| 118 | F | A | 0.0000 | |
| 119 | P | A | -0.4809 | |
| 120 | P | A | 0.0000 | |
| 121 | S | A | -1.8705 | |
| 122 | D | A | -3.1900 | |
| 123 | E | A | -3.1618 | |
| 124 | Q | A | 0.0000 | |
| 125 | L | A | -2.3117 | |
| 126 | K | A | -2.9016 | |
| 127 | S | A | -1.7919 | |
| 128 | G | A | -1.2515 | |
| 129 | T | A | -0.9720 | |
| 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 | L | A | 0.0000 | |
| 136 | L | A | 0.0000 | |
| 137 | N | A | 0.0000 | |
| 138 | N | A | -0.8383 | |
| 139 | F | A | 0.0000 | |
| 140 | Y | A | 0.0000 | |
| 141 | P | A | -1.4116 | |
| 142 | R | A | -2.3074 | |
| 143 | E | A | -2.8821 | |
| 144 | A | A | -2.1661 | |
| 145 | K | A | -2.4154 | |
| 146 | V | A | -1.1175 | |
| 147 | Q | A | -0.6987 | |
| 148 | W | A | 0.0000 | |
| 149 | K | A | -0.5876 | |
| 150 | V | A | 0.0000 | |
| 151 | D | A | -1.9129 | |
| 152 | N | A | -1.5310 | |
| 153 | A | A | -0.2629 | |
| 154 | L | A | 0.6836 | |
| 155 | Q | A | -0.3132 | |
| 156 | S | A | -0.6643 | |
| 157 | G | A | -1.2674 | |
| 158 | N | A | -1.5803 | |
| 159 | S | A | -1.3690 | |
| 160 | Q | A | -1.2289 | |
| 161 | E | A | -1.3400 | |
| 162 | S | A | -0.7377 | |
| 163 | V | A | -0.6261 | |
| 164 | T | A | 0.0000 | |
| 165 | E | A | -2.2256 | |
| 166 | Q | A | 0.0000 | |
| 167 | D | A | -2.0406 | |
| 168 | S | A | -2.0914 | |
| 169 | K | A | -2.4330 | |
| 170 | D | A | -1.7177 | |
| 171 | S | A | 0.0000 | |
| 172 | T | A | 0.0000 | |
| 173 | Y | A | 0.0000 | |
| 174 | S | A | 0.0000 | |
| 175 | L | A | 0.0000 | |
| 176 | S | A | 0.0000 | |
| 177 | S | A | 0.0000 | |
| 178 | T | A | -0.6198 | |
| 179 | L | A | 0.0000 | |
| 180 | T | A | -0.5980 | |
| 181 | L | A | -0.7170 | |
| 182 | S | A | -0.9122 | |
| 183 | K | A | -1.9164 | |
| 184 | A | A | -1.7059 | |
| 185 | D | A | -2.2181 | |
| 186 | Y | A | 0.0000 | |
| 187 | E | A | -3.3897 | |
| 188 | K | A | -3.5022 | |
| 189 | H | A | -2.8892 | |
| 190 | K | A | -3.1637 | |
| 191 | V | A | -1.3914 | |
| 192 | Y | A | 0.0000 | |
| 193 | A | A | 0.0000 | |
| 194 | C | A | 0.0000 | |
| 195 | E | A | -0.6952 | |
| 196 | V | A | 0.0000 | |
| 197 | T | A | -1.2389 | |
| 198 | H | A | 0.0000 | |
| 199 | Q | A | -1.6902 | |
| 200 | G | A | -0.4413 | |
| 201 | L | A | -0.2327 | |
| 202 | S | A | -0.4486 | |
| 203 | S | A | -0.4082 | |
| 204 | P | A | -0.5562 | |
| 205 | V | A | 0.1083 | |
| 206 | T | A | -0.4031 | |
| 207 | K | A | -0.7826 | |
| 208 | S | A | -0.6498 | |
| 209 | F | A | 0.0000 | |
| 210 | N | A | -1.6989 | |
| 211 | R | A | -2.3212 | |
| 212 | G | A | -1.8797 | |
| 213 | E | A | -2.0868 | |
| 214 | C | A | -1.2514 | |
| 1 | E | B | -2.1409 | |
| 2 | V | B | -1.2407 | |
| 3 | Q | B | -1.3074 | |
| 4 | L | B | 0.0000 | |
| 5 | V | B | 1.0150 | |
| 6 | E | B | 0.0000 | |
| 7 | S | B | -0.3971 | |
| 8 | G | B | -0.9459 | |
| 9 | G | B | -0.7704 | |
| 10 | G | B | -0.6011 | |
| 11 | L | B | -0.2255 | |
| 12 | V | B | -0.9108 | |
| 13 | K | B | -2.1438 | |
| 14 | P | B | -2.0835 | |
| 15 | G | B | -1.6480 | |
| 16 | G | B | -1.3405 | |
| 17 | S | B | -1.4369 | |
| 18 | L | B | -1.2181 | |
| 19 | R | B | -2.1373 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -0.4094 | |
| 22 | C | B | 0.0000 | |
| 23 | A | B | -0.1221 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -0.8809 | |
| 26 | G | B | -1.2649 | |
| 27 | F | B | -0.6852 | |
| 28 | T | B | -0.6950 | |
| 29 | F | B | 0.0000 | |
| 30 | S | B | -1.6044 | |
| 31 | D | B | -1.9924 | |
| 32 | S | B | 0.0000 | |
| 33 | G | B | 0.0000 | |
| 34 | M | B | 0.0000 | |
| 35 | H | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | I | B | 0.0000 | |
| 38 | R | B | 0.0000 | |
| 39 | Q | B | -0.7634 | |
| 40 | A | B | -1.1932 | |
| 41 | P | B | -0.9805 | |
| 42 | G | B | -1.4481 | |
| 43 | K | B | -2.2494 | |
| 44 | G | B | -1.3890 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -0.8836 | |
| 47 | W | B | 0.0000 | |
| 48 | V | B | 0.0000 | |
| 49 | S | B | 0.0000 | |
| 50 | Y | B | 0.3311 | |
| 51 | I | B | 0.0000 | |
| 52 | S | B | -0.4246 | |
| 53 | S | B | -1.1692 | |
| 54 | G | B | -1.0353 | |
| 55 | S | B | -0.4649 | |
| 56 | S | B | -0.2561 | |
| 57 | T | B | 0.0973 | |
| 58 | I | B | 0.6620 | |
| 59 | H | B | -0.1643 | |
| 60 | Y | B | -0.7881 | |
| 61 | A | B | 0.0000 | |
| 62 | D | B | -2.7293 | |
| 63 | T | B | -1.7361 | |
| 64 | V | B | 0.0000 | |
| 65 | K | B | -2.6721 | |
| 66 | G | B | -1.7872 | |
| 67 | R | B | -1.5873 | |
| 68 | F | B | 0.0000 | |
| 69 | T | B | -0.7991 | |
| 70 | I | B | 0.0000 | |
| 71 | S | B | -0.2397 | |
| 72 | R | B | -0.9885 | |
| 73 | D | B | -1.4938 | |
| 74 | N | B | -1.8791 | |
| 75 | A | B | -1.3462 | |
| 76 | K | B | -2.2727 | |
| 77 | N | B | -1.7271 | |
| 78 | S | B | 0.0000 | |
| 79 | L | B | 0.0000 | |
| 80 | Y | B | -0.5457 | |
| 81 | L | B | 0.0000 | |
| 82 | Q | B | -1.2770 | |
| 83 | M | B | 0.0000 | |
| 84 | N | B | -1.6177 | |
| 85 | S | B | -1.4643 | |
| 86 | L | B | 0.0000 | |
| 87 | R | B | -2.8470 | |
| 88 | A | B | -1.9873 | |
| 89 | E | B | -2.3820 | |
| 90 | D | B | 0.0000 | |
| 91 | T | B | -0.8374 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | 0.1869 | |
| 94 | Y | B | 0.0000 | |
| 95 | Y | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | S | B | 0.0000 | |
| 99 | P | B | 0.0000 | |
| 100 | L | B | 0.0000 | |
| 101 | Y | B | 0.1185 | |
| 102 | Y | B | 0.6053 | |
| 103 | Y | B | 0.8447 | |
| 104 | G | B | -0.6666 | |
| 105 | R | B | -1.3538 | |
| 106 | S | B | -0.5185 | |
| 107 | Y | B | -0.3101 | |
| 108 | N | B | -0.3800 | |
| 109 | A | B | 0.0000 | |
| 110 | V | B | 0.0000 | |
| 111 | A | B | 0.1894 | |
| 112 | Y | B | 0.3736 | |
| 113 | W | B | 0.1640 | |
| 114 | G | B | 0.0000 | |
| 115 | Q | B | -0.9700 | |
| 116 | G | B | 0.0000 | |
| 117 | T | B | -0.1045 | |
| 118 | T | B | -0.2188 | |
| 119 | V | B | 0.0000 | |
| 120 | T | B | -0.6625 | |
| 121 | V | B | 0.0000 | |
| 122 | S | B | -1.0026 | |
| 123 | S | B | -0.8265 | |
| 124 | A | B | -0.5404 | |
| 125 | S | B | -0.6324 | |
| 126 | T | B | -0.7784 | |
| 127 | K | B | -1.2772 | |
| 128 | G | B | -1.3636 | |
| 129 | P | B | 0.0000 | |
| 130 | S | B | -0.4268 | |
| 131 | V | B | 0.0000 | |
| 132 | F | B | 0.0000 | |
| 133 | P | B | -1.3277 | |
| 134 | L | B | 0.0000 | |
| 135 | A | B | -1.3022 | |
| 136 | P | B | 0.0000 | |
| 137 | S | B | -0.8568 | |
| 138 | S | B | -0.4681 | |
| 139 | K | B | -0.8331 | |
| 140 | S | B | 0.0000 | |
| 141 | T | B | -0.6232 | |
| 142 | S | B | -0.6691 | |
| 143 | G | B | -0.8001 | |
| 144 | G | B | -0.8693 | |
| 145 | T | B | -0.6080 | |
| 146 | A | B | 0.0000 | |
| 147 | A | B | 0.0000 | |
| 148 | L | B | 0.0000 | |
| 149 | G | B | 0.0000 | |
| 150 | C | B | 0.0000 | |
| 151 | L | B | 0.0000 | |
| 152 | V | B | 0.0000 | |
| 153 | K | B | 0.0000 | |
| 154 | D | B | -0.3586 | |
| 155 | Y | B | 0.0000 | |
| 156 | F | B | 0.0000 | |
| 157 | P | B | 0.0000 | |
| 158 | E | B | -0.6111 | |
| 159 | P | B | -0.7958 | |
| 160 | V | B | 0.0000 | |
| 161 | T | B | -0.6123 | |
| 162 | V | B | -0.1627 | |
| 163 | S | B | -0.3526 | |
| 164 | W | B | 0.0000 | |
| 165 | N | B | -0.7296 | |
| 166 | S | B | -0.6423 | |
| 167 | G | B | -0.4687 | |
| 168 | A | B | -0.2149 | |
| 169 | L | B | 0.0371 | |
| 170 | T | B | -0.1509 | |
| 171 | S | B | -0.1623 | |
| 172 | G | B | -0.1877 | |
| 173 | V | B | 0.1926 | |
| 174 | H | B | -0.3140 | |
| 175 | T | B | 0.0348 | |
| 176 | F | B | 0.0000 | |
| 177 | P | B | -0.3045 | |
| 178 | A | B | 0.2654 | |
| 179 | V | B | 0.6214 | |
| 180 | L | B | 1.2650 | |
| 181 | Q | B | 0.3454 | |
| 182 | S | B | -0.0425 | |
| 183 | S | B | -0.1918 | |
| 184 | G | B | 0.0636 | |
| 185 | L | B | 0.1432 | |
| 186 | Y | B | 0.4732 | |
| 187 | S | B | 0.0000 | |
| 188 | L | B | 0.0000 | |
| 189 | S | B | 0.0000 | |
| 190 | S | B | 0.0000 | |
| 191 | V | B | 0.0000 | |
| 192 | V | B | 0.0000 | |
| 193 | T | B | -0.1238 | |
| 194 | V | B | 0.0000 | |
| 195 | P | B | -0.6147 | |
| 196 | S | B | -0.5735 | |
| 197 | S | B | -0.5836 | |
| 198 | S | B | -0.5677 | |
| 199 | L | B | -0.7680 | |
| 200 | G | B | -0.9407 | |
| 201 | T | B | -0.6830 | |
| 202 | Q | B | -1.1475 | |
| 203 | T | B | -1.0798 | |
| 204 | Y | B | 0.0000 | |
| 205 | I | B | -1.2348 | |
| 206 | C | B | 0.0000 | |
| 207 | N | B | -1.4310 | |
| 208 | V | B | 0.0000 | |
| 209 | N | B | -1.8376 | |
| 210 | H | B | 0.0000 | |
| 211 | K | B | -2.7519 | |
| 212 | P | B | -1.6078 | |
| 213 | S | B | -1.8035 | |
| 214 | N | B | -2.5610 | |
| 215 | T | B | -2.0402 | |
| 216 | K | B | -2.6559 | |
| 217 | V | B | -1.5453 | |
| 218 | D | B | -2.4744 | |
| 219 | K | B | -2.0931 | |
| 220 | K | B | -2.4910 | |
| 221 | V | B | 0.0000 | |
| 222 | E | B | -2.8683 | |
| 223 | P | B | -1.8571 | |
| 224 | K | B | -2.5866 | |
| 225 | S | B | -1.9353 | |
| 226 | C | B | -1.8584 | |
| 227 | D | B | -2.8925 | |
| 228 | K | B | -2.8325 | |
| 229 | T | B | -1.9524 | |
| 230 | H | B | -1.8853 | |
| 231 | T | B | -0.8431 |
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 | -0.7928 | 1.5047 | View | CSV | PDB |
| 4.5 | -0.8356 | 1.4848 | View | CSV | PDB |
| 5.0 | -0.8833 | 1.4615 | View | CSV | PDB |
| 5.5 | -0.9253 | 1.4374 | View | CSV | PDB |
| 6.0 | -0.9502 | 1.4148 | View | CSV | PDB |
| 6.5 | -0.9508 | 1.3957 | View | CSV | PDB |
| 7.0 | -0.9296 | 1.3805 | View | CSV | PDB |
| 7.5 | -0.895 | 1.3682 | View | CSV | PDB |
| 8.0 | -0.8531 | 1.3577 | View | CSV | PDB |
| 8.5 | -0.8051 | 1.4694 | View | CSV | PDB |
| 9.0 | -0.7504 | 1.6274 | 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