| Chain sequence(s) |
C: SSELTQDPVVSVALGQTVRITCQGDSLRTYHASWYQQKPRQAPVLVIYDENNRPSGIPDRFSGSTSGNTASLTITGAQAEDEADYYCNSRDSSGNRLVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
B: QVQLQQWGAGLLKPSETLSLTCAVYGGSFSGYYWSWIRQPPGKGLEWIGEINHSGSTNYNPSLRSRVTISVDTSKNQFSLKLRSVTAADTAVYYCARGFMVRGIMWNYYYMDVWGKGTTVTVSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT input PDB |
| Selected Chain(s) | C,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] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[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 (00:04:12)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/de689051e8ea467/tmp/folded.pdb (00:04:12)
[INFO] Main: Simulation completed successfully. (00:06:20)
|
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 | B | -1.4659 | |
| 2 | V | B | -1.1186 | |
| 3 | Q | B | -1.7484 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -1.6297 | |
| 6 | Q | B | -0.9420 | |
| 7 | W | B | -0.0244 | |
| 8 | G | B | 0.0730 | |
| 9 | A | B | 0.1667 | |
| 10 | G | B | 0.2595 | |
| 11 | L | B | 0.2794 | |
| 12 | L | B | 0.0000 | |
| 13 | K | B | -1.9411 | |
| 14 | P | B | -1.4905 | |
| 15 | S | B | -1.4148 | |
| 16 | E | B | -1.6593 | |
| 17 | T | B | -1.6206 | |
| 18 | L | B | 0.0000 | |
| 19 | S | B | -0.7649 | |
| 20 | L | B | 0.0000 | |
| 21 | T | B | -0.3005 | |
| 22 | C | B | 0.0000 | |
| 23 | A | B | 0.0000 | |
| 24 | V | B | 0.0000 | |
| 25 | Y | B | -0.5361 | |
| 26 | G | B | -0.7971 | |
| 27 | G | B | -0.7497 | |
| 28 | S | B | -0.4543 | |
| 29 | F | B | 0.0000 | |
| 30 | S | B | -0.6834 | |
| 31 | G | B | -0.4602 | |
| 32 | Y | B | 0.0650 | |
| 33 | Y | B | 0.1328 | |
| 34 | W | B | 0.0000 | |
| 35 | S | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | I | B | 0.0000 | |
| 38 | R | B | 0.0000 | |
| 39 | Q | B | -0.7904 | |
| 40 | P | B | -0.9019 | |
| 41 | P | B | -1.0228 | |
| 42 | G | B | -1.4855 | |
| 43 | K | B | -2.2471 | |
| 44 | G | B | -1.4383 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -0.7580 | |
| 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 | N | B | -0.6216 | |
| 53 | H | B | -1.0656 | |
| 54 | S | B | -0.8108 | |
| 55 | G | B | -0.7068 | |
| 56 | S | B | -0.5285 | |
| 57 | T | B | -0.4603 | |
| 58 | N | B | -0.8100 | |
| 59 | Y | B | -0.8424 | |
| 60 | N | B | -1.0118 | |
| 61 | P | B | -1.0118 | |
| 62 | S | B | -0.8784 | |
| 63 | L | B | 0.0000 | |
| 64 | R | B | -2.1340 | |
| 65 | S | B | -1.5390 | |
| 66 | R | B | -1.8096 | |
| 67 | V | B | 0.0000 | |
| 68 | T | B | -1.0860 | |
| 69 | I | B | 0.0000 | |
| 70 | S | B | -0.5575 | |
| 71 | V | B | -0.7552 | |
| 72 | D | B | -1.4693 | |
| 73 | T | B | -1.3929 | |
| 74 | S | B | -1.4014 | |
| 75 | K | B | -2.1653 | |
| 76 | N | B | -1.5334 | |
| 77 | Q | B | -1.3304 | |
| 78 | F | B | 0.0000 | |
| 79 | S | B | -0.4121 | |
| 80 | L | B | 0.0000 | |
| 81 | K | B | -1.6073 | |
| 82 | L | B | 0.0000 | |
| 83 | R | B | -2.2130 | |
| 84 | S | B | -1.6418 | |
| 85 | V | B | 0.0000 | |
| 86 | T | B | -0.7405 | |
| 87 | A | B | -0.2861 | |
| 88 | A | B | 0.0250 | |
| 89 | D | B | 0.0000 | |
| 90 | T | B | 0.0768 | |
| 91 | A | B | 0.0000 | |
| 92 | V | B | -0.2281 | |
| 93 | Y | B | 0.0000 | |
| 94 | Y | B | 0.0000 | |
| 95 | C | B | 0.0000 | |
| 96 | A | B | 0.0000 | |
| 97 | R | B | -0.1836 | |
| 98 | G | B | 0.0000 | |
| 99 | F | B | 0.5952 | |
| 100 | M | B | 0.3070 | |
| 101 | V | B | -0.0889 | |
| 102 | R | B | -0.9823 | |
| 103 | G | B | 0.3750 | |
| 104 | I | B | 2.1221 | |
| 105 | M | B | 1.8622 | |
| 106 | W | B | 0.6162 | |
| 107 | N | B | -0.2151 | |
| 108 | Y | B | -0.1349 | |
| 109 | Y | B | 0.0000 | |
| 110 | Y | B | 0.3130 | |
| 111 | M | B | 0.0000 | |
| 112 | D | B | -0.2814 | |
| 113 | V | B | 0.0000 | |
| 114 | W | B | -0.6251 | |
| 115 | G | B | 0.0000 | |
| 116 | K | B | -2.4717 | |
| 117 | G | B | -1.3587 | |
| 118 | T | B | -0.4204 | |
| 119 | T | B | -0.0564 | |
| 120 | V | B | 0.0000 | |
| 121 | T | B | -0.1077 | |
| 122 | V | B | 0.0000 | |
| 123 | S | B | -0.6262 | |
| 124 | P | B | -0.8631 | |
| 125 | A | B | -0.6896 | |
| 126 | S | B | -0.7607 | |
| 127 | T | B | -0.8655 | |
| 128 | K | B | -1.1768 | |
| 129 | G | B | -1.3517 | |
| 130 | P | B | 0.0000 | |
| 131 | S | B | -0.1981 | |
| 132 | V | B | 0.0000 | |
| 133 | F | B | 0.0000 | |
| 134 | P | B | -0.9987 | |
| 135 | L | B | 0.0000 | |
| 136 | A | B | -0.9098 | |
| 137 | P | B | 0.0000 | |
| 138 | S | B | -1.0249 | |
| 139 | S | B | -1.3686 | |
| 140 | K | B | -1.9925 | |
| 141 | S | B | -1.1303 | |
| 142 | T | B | -1.0607 | |
| 143 | S | B | -0.9916 | |
| 144 | G | B | -0.8306 | |
| 145 | G | B | -0.8583 | |
| 146 | T | B | -0.6171 | |
| 147 | A | B | 0.0000 | |
| 148 | A | B | 0.0000 | |
| 149 | L | B | 0.0000 | |
| 150 | G | B | 0.0000 | |
| 151 | C | B | 0.0000 | |
| 152 | L | B | 0.0000 | |
| 153 | V | B | 0.0000 | |
| 154 | K | B | 0.0000 | |
| 155 | D | B | -0.2655 | |
| 156 | Y | B | 0.0000 | |
| 157 | F | B | 0.0000 | |
| 158 | P | B | -0.7543 | |
| 159 | E | B | -0.9327 | |
| 160 | P | B | -0.9802 | |
| 161 | V | B | -0.8115 | |
| 162 | T | B | -0.6623 | |
| 163 | V | B | -0.3530 | |
| 164 | S | B | -0.3454 | |
| 165 | W | B | 0.0000 | |
| 166 | N | B | -0.6739 | |
| 167 | S | B | -0.5882 | |
| 168 | G | B | -0.3941 | |
| 169 | A | B | -0.1722 | |
| 170 | L | B | 0.0503 | |
| 171 | T | B | -0.1856 | |
| 172 | S | B | -0.2845 | |
| 173 | G | B | -0.3708 | |
| 174 | V | B | 0.1140 | |
| 175 | H | B | -0.1444 | |
| 176 | T | B | -0.0385 | |
| 177 | F | B | 0.0000 | |
| 178 | P | B | -0.0133 | |
| 179 | A | B | 0.1585 | |
| 180 | V | B | 0.0000 | |
| 181 | L | B | 0.8900 | |
| 182 | Q | B | 0.1709 | |
| 183 | S | B | -0.1716 | |
| 184 | S | B | -0.1999 | |
| 185 | G | B | 0.0148 | |
| 186 | L | B | 0.0027 | |
| 187 | Y | B | 0.2280 | |
| 188 | S | B | 0.0000 | |
| 189 | L | B | 0.0000 | |
| 190 | S | B | 0.0000 | |
| 191 | S | B | 0.0000 | |
| 192 | V | B | 0.1453 | |
| 193 | V | B | 0.0000 | |
| 194 | T | B | -0.2285 | |
| 195 | V | B | 0.0000 | |
| 196 | P | B | -0.6197 | |
| 197 | S | B | -0.5702 | |
| 198 | S | B | -0.5602 | |
| 199 | S | B | -0.5374 | |
| 200 | L | B | -0.7491 | |
| 201 | G | B | -0.9406 | |
| 202 | T | B | -0.6582 | |
| 203 | Q | B | -1.0871 | |
| 204 | T | B | -1.0473 | |
| 205 | Y | B | 0.0000 | |
| 206 | I | B | -1.1503 | |
| 207 | C | B | 0.0000 | |
| 208 | N | B | -1.3948 | |
| 209 | V | B | 0.0000 | |
| 210 | N | B | -1.9963 | |
| 211 | H | B | 0.0000 | |
| 212 | K | B | -2.8098 | |
| 213 | P | B | -1.7067 | |
| 214 | S | B | -1.8681 | |
| 215 | N | B | -2.6077 | |
| 216 | T | B | -2.0924 | |
| 217 | K | B | -2.6691 | |
| 218 | V | B | -1.5155 | |
| 219 | D | B | -2.3362 | |
| 220 | K | B | -2.0170 | |
| 221 | K | B | -2.4308 | |
| 222 | V | B | 0.0000 | |
| 223 | E | B | -2.4804 | |
| 224 | P | B | -1.1457 | |
| 225 | K | B | -1.1286 | |
| 226 | S | B | -1.0018 | |
| 227 | C | B | -0.8587 | |
| 228 | D | B | -2.4221 | |
| 229 | K | B | -2.6848 | |
| 230 | T | B | -1.9364 | |
| 231 | H | B | -1.9343 | |
| 232 | T | B | -1.2240 | |
| 1 | S | C | -0.9480 | |
| 2 | S | C | -1.6310 | |
| 3 | E | C | -2.3201 | |
| 4 | L | C | 0.0000 | |
| 5 | T | C | -1.4295 | |
| 6 | Q | C | -1.5464 | |
| 7 | D | C | -1.8183 | |
| 8 | P | C | -0.9074 | |
| 9 | V | C | 0.4857 | |
| 10 | V | C | -0.0529 | |
| 11 | S | C | 0.1485 | |
| 12 | V | C | 0.0000 | |
| 13 | A | C | -0.0199 | |
| 14 | L | C | 0.1754 | |
| 15 | G | C | -0.6097 | |
| 16 | Q | C | -1.0867 | |
| 17 | T | C | -1.1304 | |
| 18 | V | C | 0.0000 | |
| 19 | R | C | -1.8552 | |
| 20 | I | C | 0.0000 | |
| 21 | T | C | -1.1055 | |
| 22 | C | C | 0.0000 | |
| 23 | Q | C | -2.1962 | |
| 24 | G | C | -2.3857 | |
| 25 | D | C | -3.0684 | |
| 26 | S | C | 0.0000 | |
| 27 | L | C | 0.0000 | |
| 28 | R | C | -2.8146 | |
| 29 | T | C | -1.1323 | |
| 30 | Y | C | -0.9088 | |
| 31 | H | C | 0.0000 | |
| 32 | A | C | 0.0000 | |
| 33 | S | C | 0.0000 | |
| 34 | W | C | 0.0000 | |
| 35 | Y | C | 0.0000 | |
| 36 | Q | C | -0.2558 | |
| 37 | Q | C | 0.0000 | |
| 38 | K | C | -1.7882 | |
| 39 | P | C | -2.0601 | |
| 40 | R | C | -2.7906 | |
| 41 | Q | C | -2.4418 | |
| 42 | A | C | -1.2262 | |
| 43 | P | C | 0.0000 | |
| 44 | V | C | 1.0338 | |
| 45 | L | C | 0.0000 | |
| 46 | V | C | 0.0000 | |
| 47 | I | C | 0.0000 | |
| 48 | Y | C | -0.9205 | |
| 49 | D | C | -1.0836 | |
| 50 | E | C | -1.7334 | |
| 51 | N | C | -1.9667 | |
| 52 | N | C | -1.7318 | |
| 53 | R | C | -1.7313 | |
| 54 | P | C | -0.7112 | |
| 55 | S | C | -0.6326 | |
| 56 | G | C | -0.8092 | |
| 57 | I | C | -0.5833 | |
| 58 | P | C | -1.2152 | |
| 59 | D | C | -2.1135 | |
| 60 | R | C | -1.3128 | |
| 61 | F | C | 0.0000 | |
| 62 | S | C | -1.3826 | |
| 63 | G | C | 0.0000 | |
| 64 | S | C | -0.9366 | |
| 65 | T | C | -1.2387 | |
| 66 | S | C | -1.1551 | |
| 67 | G | C | -1.8598 | |
| 68 | N | C | -2.4295 | |
| 69 | T | C | -1.4961 | |
| 70 | A | C | 0.0000 | |
| 71 | S | C | 0.0000 | |
| 72 | L | C | 0.0000 | |
| 73 | T | C | -1.0162 | |
| 74 | I | C | 0.0000 | |
| 75 | T | C | -1.1429 | |
| 76 | G | C | -0.7891 | |
| 77 | A | C | 0.0000 | |
| 78 | Q | C | -1.1656 | |
| 79 | A | C | -1.2224 | |
| 80 | E | C | -2.1050 | |
| 81 | D | C | 0.0000 | |
| 82 | E | C | -1.4277 | |
| 83 | A | C | 0.0000 | |
| 84 | D | C | -1.3430 | |
| 85 | Y | C | 0.0000 | |
| 86 | Y | C | 0.0000 | |
| 87 | C | C | 0.0000 | |
| 88 | N | C | 0.0000 | |
| 89 | S | C | 0.0000 | |
| 90 | R | C | 0.0000 | |
| 91 | D | C | 0.0000 | |
| 92 | S | C | -1.1574 | |
| 93 | S | C | -0.8695 | |
| 94 | G | C | -1.0097 | |
| 95 | N | C | -1.6086 | |
| 96 | R | C | -1.0907 | |
| 97 | L | C | 0.0000 | |
| 98 | V | C | -0.5201 | |
| 99 | F | C | -0.3328 | |
| 100 | G | C | 0.0000 | |
| 101 | G | C | -1.6634 | |
| 102 | G | C | -1.2839 | |
| 103 | T | C | 0.0000 | |
| 104 | K | C | -1.7161 | |
| 105 | L | C | 0.0000 | |
| 106 | T | C | -0.2494 | |
| 107 | V | C | 0.0000 | |
| 108 | L | C | -0.0423 | |
| 109 | G | C | -0.6244 | |
| 110 | Q | C | -1.6946 | |
| 111 | P | C | -1.6027 | |
| 112 | K | C | -2.3514 | |
| 113 | A | C | -1.4730 | |
| 114 | A | C | -0.7634 | |
| 115 | P | C | -0.3878 | |
| 116 | S | C | -0.2294 | |
| 117 | V | C | -0.3208 | |
| 118 | T | C | -0.5217 | |
| 119 | L | C | 0.0000 | |
| 120 | F | C | 0.0000 | |
| 121 | P | C | -0.3118 | |
| 122 | P | C | 0.0000 | |
| 123 | S | C | 0.0000 | |
| 124 | S | C | -1.4734 | |
| 125 | E | C | -2.2037 | |
| 126 | E | C | 0.0000 | |
| 127 | L | C | -1.9113 | |
| 128 | Q | C | -2.2585 | |
| 129 | A | C | -1.8086 | |
| 130 | N | C | -2.4936 | |
| 131 | K | C | -2.1712 | |
| 132 | A | C | 0.0000 | |
| 133 | T | C | 0.0000 | |
| 134 | L | C | 0.0000 | |
| 135 | V | C | 0.0000 | |
| 136 | C | C | 0.0000 | |
| 137 | L | C | 0.0000 | |
| 138 | I | C | 0.0000 | |
| 139 | S | C | -0.6272 | |
| 140 | D | C | -1.3317 | |
| 141 | F | C | 0.0000 | |
| 142 | Y | C | 0.0000 | |
| 143 | P | C | -1.3091 | |
| 144 | G | C | -1.0348 | |
| 145 | A | C | -0.2102 | |
| 146 | V | C | -0.1011 | |
| 147 | T | C | -0.0708 | |
| 148 | V | C | 0.2319 | |
| 149 | A | C | -0.3701 | |
| 150 | W | C | 0.0000 | |
| 151 | K | C | -0.8941 | |
| 152 | A | C | 0.0000 | |
| 153 | D | C | -1.2663 | |
| 154 | S | C | -0.8540 | |
| 155 | S | C | -0.7298 | |
| 156 | P | C | -0.8380 | |
| 157 | V | C | -0.8404 | |
| 158 | K | C | -1.6876 | |
| 159 | A | C | -0.8228 | |
| 160 | G | C | -0.6436 | |
| 161 | V | C | -0.5159 | |
| 162 | E | C | -0.4686 | |
| 163 | T | C | -0.0163 | |
| 164 | T | C | 0.0000 | |
| 165 | T | C | -0.3446 | |
| 166 | P | C | -0.5374 | |
| 167 | S | C | -1.2733 | |
| 168 | K | C | -2.6167 | |
| 169 | Q | C | -2.0784 | |
| 170 | S | C | -1.6909 | |
| 171 | N | C | -2.2554 | |
| 172 | N | C | -2.8161 | |
| 173 | K | C | -2.4957 | |
| 174 | Y | C | -1.5339 | |
| 175 | A | C | 0.0000 | |
| 176 | A | C | 0.0000 | |
| 177 | S | C | 0.0000 | |
| 178 | S | C | 0.0000 | |
| 179 | Y | C | 0.0000 | |
| 180 | L | C | 0.0000 | |
| 181 | S | C | -0.3734 | |
| 182 | L | C | -0.9675 | |
| 183 | T | C | -1.6830 | |
| 184 | P | C | -2.3492 | |
| 185 | E | C | -3.1240 | |
| 186 | Q | C | -2.3334 | |
| 187 | W | C | 0.0000 | |
| 188 | K | C | -3.1019 | |
| 189 | S | C | -2.3834 | |
| 190 | H | C | -2.3485 | |
| 191 | R | C | -2.6954 | |
| 192 | S | C | -1.7765 | |
| 193 | Y | C | 0.0000 | |
| 194 | S | C | 0.0000 | |
| 195 | C | C | 0.0000 | |
| 196 | Q | C | -0.7341 | |
| 197 | V | C | 0.0000 | |
| 198 | T | C | -0.6262 | |
| 199 | H | C | 0.0000 | |
| 200 | E | C | -2.3162 | |
| 201 | G | C | -1.4365 | |
| 202 | S | C | -0.8568 | |
| 203 | T | C | -0.6695 | |
| 204 | V | C | -0.5288 | |
| 205 | E | C | -1.4584 | |
| 206 | K | C | -1.5017 | |
| 207 | T | C | -1.0243 | |
| 208 | V | C | 0.0000 | |
| 209 | A | C | 0.0000 | |
| 210 | P | C | -1.5796 | |
| 211 | T | C | -1.3989 | |
| 212 | E | C | -1.7382 | |
| 213 | C | C | -0.6482 | |
| 214 | S | C | -0.5921 |
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 | -0.7333 | 3.0513 | View | CSV | PDB |
| 4.5 | -0.7688 | 3.0513 | View | CSV | PDB |
| 5.0 | -0.8096 | 3.0513 | View | CSV | PDB |
| 5.5 | -0.8464 | 3.0513 | View | CSV | PDB |
| 6.0 | -0.869 | 3.0513 | View | CSV | PDB |
| 6.5 | -0.8696 | 3.0513 | View | CSV | PDB |
| 7.0 | -0.8485 | 3.0513 | View | CSV | PDB |
| 7.5 | -0.8131 | 3.0513 | View | CSV | PDB |
| 8.0 | -0.7699 | 3.0513 | View | CSV | PDB |
| 8.5 | -0.7211 | 3.0513 | View | CSV | PDB |
| 9.0 | -0.6672 | 3.0513 | 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