| Chain sequence(s) |
A: EVQLLESGGGLVQPGGSLRLSCAASGFTFSIYSMNWVRQAPGKGLEWVSSIGSSGGTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAGSQWLYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH
B: DIQMTQSPSSLSASVGDRVTITCRSSQRIMTYLNWYQQKPGKAPKLLIFVASHSQSGVPSRFRGSGSETDFTLTISGLQPEDSATYYCQQSFWTPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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 | LQ8A,WY104A,AG51B,FY49B,WF93B |
| Energy difference between WT (input) and mutated protein (by FoldX) | 0.870624 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. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] FoldX: Building mutant model (00:01:58)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:02:28)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/41f769a199c4e6a/tmp/folded.pdb (00:02:28)
[INFO] Main: Simulation completed successfully. (00:04:34)
|
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 |
|---|---|---|---|---|
| 4 | E | A | -1.3855 | |
| 5 | V | A | 0.1669 | |
| 6 | Q | A | -0.9099 | |
| 7 | L | A | 0.0000 | |
| 8 | Q | A | -1.3347 | mutated: LQ8A |
| 9 | E | A | 0.0000 | |
| 10 | S | A | -0.8063 | |
| 11 | G | A | -0.7270 | |
| 12 | G | A | -0.7051 | |
| 13 | G | A | -0.5765 | |
| 14 | L | A | -0.3829 | |
| 15 | V | A | 0.0000 | |
| 16 | Q | A | -1.7479 | |
| 17 | P | A | -1.9196 | |
| 18 | G | A | -1.6060 | |
| 19 | G | A | -1.1303 | |
| 20 | S | A | -0.8914 | |
| 21 | L | A | -0.7091 | |
| 22 | R | A | -1.2940 | |
| 23 | L | A | 0.0000 | |
| 24 | S | A | -0.5925 | |
| 25 | C | A | 0.0000 | |
| 26 | A | A | -0.9269 | |
| 27 | A | A | -0.6726 | |
| 28 | S | A | -0.6110 | |
| 29 | G | A | -0.5069 | |
| 30 | F | A | 0.2188 | |
| 31 | T | A | 0.4278 | |
| 32 | F | A | 0.0000 | |
| 33 | S | A | 0.1244 | |
| 34 | I | A | 1.3321 | |
| 35 | Y | A | 0.7917 | |
| 36 | S | A | 0.4007 | |
| 37 | M | A | 0.0000 | |
| 38 | N | A | 0.0000 | |
| 39 | W | A | 0.0000 | |
| 40 | V | A | 0.0000 | |
| 41 | R | A | 0.0000 | |
| 42 | Q | A | -0.9277 | |
| 43 | A | A | -1.3470 | |
| 44 | P | A | -1.2853 | |
| 45 | G | A | -1.4733 | |
| 46 | K | A | -2.3034 | |
| 47 | G | A | -1.5149 | |
| 48 | L | A | 0.0000 | |
| 49 | E | A | -1.1745 | |
| 50 | W | A | 0.0000 | |
| 51 | V | A | 0.0000 | |
| 52 | S | A | 0.0000 | |
| 53 | S | A | 0.0000 | |
| 54 | I | A | 0.0000 | |
| 55 | G | A | 0.0458 | |
| 56 | S | A | 0.1359 | |
| 57 | S | A | -0.2907 | |
| 58 | G | A | -0.7507 | |
| 59 | G | A | -0.5845 | |
| 60 | T | A | -0.2596 | |
| 61 | T | A | 0.1437 | |
| 62 | Y | A | 0.2715 | |
| 63 | Y | A | -0.5338 | |
| 64 | A | A | -1.4747 | |
| 65 | D | A | -2.6178 | |
| 66 | S | A | -1.8872 | |
| 67 | V | A | 0.0000 | |
| 68 | K | A | -2.5505 | |
| 69 | G | A | -1.7785 | |
| 70 | R | A | -1.3270 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.6454 | |
| 73 | I | A | 0.0000 | |
| 74 | S | A | -0.4950 | |
| 75 | R | A | -1.1563 | |
| 76 | D | A | -1.7611 | |
| 77 | N | A | -1.7914 | |
| 78 | S | A | -1.7344 | |
| 79 | K | A | -2.4845 | |
| 80 | N | A | -1.9568 | |
| 81 | T | A | -1.3643 | |
| 82 | L | A | 0.0000 | |
| 83 | Y | A | -0.4053 | |
| 84 | L | A | 0.0000 | |
| 85 | Q | A | -0.8254 | |
| 86 | M | A | 0.0000 | |
| 87 | N | A | -1.3147 | |
| 88 | S | A | -1.3884 | |
| 89 | L | A | 0.0000 | |
| 90 | R | A | -2.8661 | |
| 91 | A | A | -2.0407 | |
| 92 | E | A | -2.4434 | |
| 93 | D | A | 0.0000 | |
| 94 | T | A | -0.9599 | |
| 95 | A | A | 0.0000 | |
| 96 | V | A | -0.0116 | |
| 97 | Y | A | 0.0000 | |
| 98 | Y | A | 0.0000 | |
| 99 | C | A | 0.0000 | |
| 100 | A | A | 0.0000 | |
| 101 | G | A | 0.0000 | |
| 102 | S | A | 0.0000 | |
| 103 | Q | A | 0.7256 | |
| 104 | Y | A | 1.7422 | mutated: WY104A |
| 105 | L | A | 1.9252 | |
| 106 | Y | A | 1.3901 | |
| 107 | G | A | 0.0000 | |
| 108 | M | A | 0.0000 | |
| 109 | D | A | -0.8248 | |
| 110 | V | A | 0.0000 | |
| 111 | W | A | -0.5402 | |
| 112 | G | A | 0.0000 | |
| 113 | Q | A | -1.8639 | |
| 114 | G | A | -1.0612 | |
| 115 | T | A | -0.4740 | |
| 116 | T | A | -0.1254 | |
| 117 | V | A | 0.0000 | |
| 118 | T | A | 0.0000 | |
| 119 | V | A | 0.0000 | |
| 120 | S | A | -0.8909 | |
| 121 | S | A | -0.7763 | |
| 122 | A | A | -0.5465 | |
| 123 | S | A | -0.6761 | |
| 124 | T | A | -0.9553 | |
| 125 | K | A | -1.5967 | |
| 126 | G | A | -1.5862 | |
| 127 | P | A | 0.0000 | |
| 128 | S | A | -0.4659 | |
| 129 | V | A | 0.0000 | |
| 130 | F | A | 0.0000 | |
| 131 | P | A | -1.1717 | |
| 132 | L | A | 0.0000 | |
| 133 | A | A | -1.0989 | |
| 134 | P | A | 0.0000 | |
| 135 | S | A | -1.1309 | |
| 136 | S | A | -1.5943 | |
| 137 | K | A | -1.9501 | |
| 138 | S | A | -1.1434 | |
| 139 | T | A | -1.0728 | |
| 140 | S | A | -0.7964 | |
| 141 | G | A | -0.9635 | |
| 142 | G | A | -0.8917 | |
| 143 | T | A | -0.6112 | |
| 144 | A | A | 0.0000 | |
| 145 | A | A | 0.0000 | |
| 146 | L | A | 0.0000 | |
| 147 | G | A | 0.0000 | |
| 148 | C | A | 0.0000 | |
| 149 | L | A | 0.0000 | |
| 150 | V | A | 0.0000 | |
| 151 | K | A | 0.0000 | |
| 152 | D | A | -0.6602 | |
| 153 | Y | A | 0.0000 | |
| 154 | F | A | 0.0000 | |
| 155 | P | A | 0.0000 | |
| 156 | E | A | -0.5298 | |
| 157 | P | A | -0.6056 | |
| 158 | V | A | -0.5349 | |
| 159 | T | A | -0.4588 | |
| 160 | V | A | -0.2971 | |
| 161 | S | A | -0.4256 | |
| 162 | W | A | 0.0000 | |
| 163 | N | A | -0.9766 | |
| 164 | S | A | -0.7775 | |
| 165 | G | A | -0.6225 | |
| 166 | A | A | -0.2816 | |
| 167 | L | A | -0.0311 | |
| 168 | T | A | -0.1994 | |
| 169 | S | A | -0.2252 | |
| 170 | G | A | -0.2366 | |
| 171 | V | A | 0.1307 | |
| 172 | H | A | -0.3688 | |
| 173 | T | A | -0.1980 | |
| 174 | F | A | 0.0000 | |
| 175 | P | A | -0.3813 | |
| 176 | A | A | 0.2775 | |
| 177 | V | A | 0.6848 | |
| 178 | L | A | 1.4431 | |
| 179 | Q | A | 0.4176 | |
| 180 | S | A | -0.0408 | |
| 181 | S | A | -0.2584 | |
| 182 | G | A | -0.0737 | |
| 183 | L | A | 0.0185 | |
| 184 | Y | A | 0.6012 | |
| 185 | S | A | 0.0000 | |
| 186 | L | A | 0.0000 | |
| 187 | S | A | 0.0000 | |
| 188 | S | A | 0.0000 | |
| 189 | V | A | 0.0000 | |
| 190 | V | A | 0.0000 | |
| 191 | T | A | -0.1830 | |
| 192 | V | A | 0.0000 | |
| 193 | P | A | -0.6232 | |
| 194 | S | A | -0.8494 | |
| 195 | S | A | -0.5804 | |
| 196 | S | A | -0.6303 | |
| 197 | L | A | -0.8130 | |
| 198 | G | A | -1.0352 | |
| 199 | T | A | -0.7305 | |
| 200 | Q | A | -1.2484 | |
| 201 | T | A | -1.2219 | |
| 202 | Y | A | 0.0000 | |
| 203 | I | A | -1.5620 | |
| 204 | C | A | 0.0000 | |
| 205 | N | A | -1.5795 | |
| 206 | V | A | 0.0000 | |
| 207 | N | A | -1.6305 | |
| 208 | H | A | 0.0000 | |
| 209 | K | A | -2.4578 | |
| 210 | P | A | -1.5394 | |
| 211 | S | A | -1.8771 | |
| 212 | N | A | -2.3376 | |
| 213 | T | A | -1.9704 | |
| 214 | K | A | -2.6014 | |
| 215 | V | A | -1.7894 | |
| 216 | D | A | -2.6793 | |
| 217 | K | A | -2.4248 | |
| 218 | R | A | -2.8436 | |
| 219 | V | A | 0.0000 | |
| 220 | E | A | -2.9086 | |
| 221 | P | A | -1.9620 | |
| 222 | K | A | -2.8776 | |
| 223 | S | A | -2.1669 | |
| 224 | C | A | -2.5149 | |
| 225 | D | A | -3.3473 | |
| 226 | K | A | -3.3899 | |
| 227 | T | A | -2.7562 | |
| 228 | H | A | -2.4405 | |
| 1 | D | B | -2.2196 | |
| 2 | I | B | 0.0000 | |
| 3 | Q | B | -2.1904 | |
| 4 | M | B | 0.0000 | |
| 5 | T | B | -0.9439 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.5897 | |
| 8 | P | B | -0.6172 | |
| 9 | S | B | -0.8589 | |
| 10 | S | B | -0.9119 | |
| 11 | L | B | -0.5304 | |
| 12 | S | B | -0.7157 | |
| 13 | A | B | -0.9278 | |
| 14 | S | B | -0.8626 | |
| 15 | V | B | -0.2120 | |
| 16 | G | B | -0.9839 | |
| 17 | D | B | -2.0214 | |
| 18 | R | B | -2.4116 | |
| 19 | V | B | 0.0000 | |
| 20 | T | B | -0.7433 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.6756 | |
| 23 | C | B | 0.0000 | |
| 24 | R | B | -2.2086 | |
| 25 | S | B | 0.0000 | |
| 26 | S | B | -2.2792 | |
| 27 | Q | B | -2.7054 | |
| 28 | R | B | -2.5357 | |
| 29 | I | B | 0.0000 | |
| 30 | M | B | -0.5084 | |
| 31 | T | B | -0.1147 | |
| 32 | Y | B | 1.0134 | |
| 33 | L | B | 0.0000 | |
| 34 | N | 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 | -1.5770 | |
| 40 | P | B | -1.5163 | |
| 41 | G | B | -1.7632 | |
| 42 | K | B | -2.3772 | |
| 43 | A | B | -1.5081 | |
| 44 | P | B | 0.0000 | |
| 45 | K | B | -1.2885 | |
| 46 | L | B | 0.0000 | |
| 47 | L | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | Y | B | 0.3816 | mutated: FY49B |
| 50 | V | B | 0.6338 | |
| 51 | G | B | 0.0000 | mutated: AG51B |
| 52 | S | B | -0.6340 | |
| 53 | H | B | -0.7608 | |
| 54 | S | B | -0.8003 | |
| 55 | Q | B | -0.8149 | |
| 56 | S | B | -0.6972 | |
| 57 | G | B | -0.5849 | |
| 58 | V | B | -0.3972 | |
| 59 | P | B | -0.5215 | |
| 60 | S | B | -0.7335 | |
| 61 | R | B | -1.0412 | |
| 62 | F | B | 0.0000 | |
| 63 | R | B | -1.3936 | |
| 64 | G | B | 0.0000 | |
| 65 | S | B | -0.8676 | |
| 66 | G | B | -0.9848 | |
| 67 | S | B | -1.1316 | |
| 68 | E | B | -1.8559 | |
| 69 | T | B | -2.1913 | |
| 70 | D | B | -2.2132 | |
| 71 | F | B | 0.0000 | |
| 72 | T | B | -0.7899 | |
| 73 | L | B | 0.0000 | |
| 74 | T | B | -0.9179 | |
| 75 | I | B | 0.0000 | |
| 76 | S | B | -1.4634 | |
| 77 | G | B | -1.2303 | |
| 78 | L | B | 0.0000 | |
| 79 | Q | B | -0.9556 | |
| 80 | P | B | -1.6204 | |
| 81 | E | B | -1.9931 | |
| 82 | D | B | 0.0000 | |
| 83 | S | B | 0.0000 | |
| 84 | A | B | 0.0000 | |
| 85 | T | B | -0.8397 | |
| 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 | S | B | 0.0000 | |
| 92 | F | B | 1.6164 | |
| 93 | F | B | 1.7842 | mutated: WF93B |
| 94 | T | B | 0.8787 | |
| 95 | P | B | 0.0513 | |
| 96 | L | B | 0.2919 | |
| 97 | T | B | -0.4334 | |
| 98 | F | B | 0.0000 | |
| 99 | G | B | 0.0000 | |
| 100 | G | B | -1.2371 | |
| 101 | G | B | -0.9932 | |
| 102 | T | B | 0.0000 | |
| 103 | K | B | -1.6774 | |
| 104 | V | B | 0.0000 | |
| 105 | E | B | -1.1337 | |
| 106 | I | B | 0.0000 | |
| 107 | K | B | -1.0577 | |
| 108 | R | B | -0.7840 | |
| 109 | T | B | -0.0713 | |
| 110 | V | B | 0.3685 | |
| 111 | A | B | -0.0161 | |
| 112 | A | B | -0.0693 | |
| 113 | P | B | 0.0000 | |
| 114 | S | B | -0.2093 | |
| 115 | V | B | 0.0000 | |
| 116 | F | B | 0.0040 | |
| 117 | I | B | 0.0055 | |
| 118 | F | B | 0.0000 | |
| 119 | P | B | -0.5083 | |
| 120 | P | B | -0.7928 | |
| 121 | S | B | -1.4082 | |
| 122 | D | B | -2.7470 | |
| 123 | E | B | -2.3635 | |
| 124 | Q | B | 0.0000 | |
| 125 | L | B | -2.0768 | |
| 126 | K | B | -2.5715 | |
| 127 | S | B | -1.6236 | |
| 128 | G | B | -1.2289 | |
| 129 | T | B | -0.9154 | |
| 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 | 0.0000 | |
| 138 | N | B | -0.8591 | |
| 139 | F | B | 0.0000 | |
| 140 | Y | B | 0.0000 | |
| 141 | P | B | -1.4775 | |
| 142 | R | B | -2.5995 | |
| 143 | E | B | -2.9748 | |
| 144 | A | B | -2.2085 | |
| 145 | K | B | -2.5706 | |
| 146 | V | B | -1.1323 | |
| 147 | Q | B | -0.6008 | |
| 148 | W | B | 0.0000 | |
| 149 | K | B | 0.0000 | |
| 150 | V | B | 0.0000 | |
| 151 | D | B | -1.7598 | |
| 152 | N | B | -1.3756 | |
| 153 | A | B | -0.1227 | |
| 154 | L | B | 0.8979 | |
| 155 | Q | B | -0.0653 | |
| 156 | S | B | -0.5463 | |
| 157 | G | B | -1.0665 | |
| 158 | N | B | -1.1869 | |
| 159 | S | B | -1.2224 | |
| 160 | Q | B | -1.2479 | |
| 161 | E | B | -2.0321 | |
| 162 | S | B | -0.9755 | |
| 163 | V | B | -0.9641 | |
| 164 | T | B | -1.1151 | |
| 165 | E | B | -2.2095 | |
| 166 | Q | B | 0.0000 | |
| 167 | D | B | -2.0799 | |
| 168 | S | B | -2.2487 | |
| 169 | K | B | -2.7000 | |
| 170 | D | B | -2.1409 | |
| 171 | S | B | 0.0000 | |
| 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 | -0.6241 | |
| 179 | L | B | 0.0000 | |
| 180 | T | B | -0.4125 | |
| 181 | L | B | -0.8279 | |
| 182 | S | B | -1.2063 | |
| 183 | K | B | -2.2552 | |
| 184 | A | B | -2.0793 | |
| 185 | D | B | -2.7498 | |
| 186 | Y | B | 0.0000 | |
| 187 | E | B | -3.8260 | |
| 188 | K | B | -3.7617 | |
| 189 | H | B | -3.0437 | |
| 190 | K | B | -3.2722 | |
| 191 | V | B | -1.6605 | |
| 192 | Y | B | 0.0000 | |
| 193 | A | B | 0.0000 | |
| 194 | C | B | 0.0000 | |
| 195 | E | B | -1.0539 | |
| 196 | V | B | 0.0000 | |
| 197 | T | B | -1.1773 | |
| 198 | H | B | 0.0000 | |
| 199 | Q | B | -1.6985 | |
| 200 | G | B | -0.4530 | |
| 201 | L | B | -0.2478 | |
| 202 | S | B | -0.4672 | |
| 203 | S | B | -0.4815 | |
| 204 | P | B | -0.6991 | |
| 205 | V | B | -0.1228 | |
| 206 | T | B | -0.5698 | |
| 207 | K | B | -0.8657 | |
| 208 | S | B | -0.7144 | |
| 209 | F | B | 0.0000 | |
| 210 | N | B | -1.9806 | |
| 211 | R | B | -2.9565 | |
| 212 | G | B | -2.7691 | |
| 213 | E | B | -3.1306 | |
| 214 | C | B | -2.1035 |
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 | -0.7872 | 4.7543 | View | CSV | PDB |
| 4.5 | -0.8323 | 4.7165 | View | CSV | PDB |
| 5.0 | -0.8854 | 4.665 | View | CSV | PDB |
| 5.5 | -0.9356 | 4.6069 | View | CSV | PDB |
| 6.0 | -0.9708 | 4.5461 | View | CSV | PDB |
| 6.5 | -0.9817 | 4.4845 | View | CSV | PDB |
| 7.0 | -0.9689 | 4.4227 | View | CSV | PDB |
| 7.5 | -0.9414 | 4.3612 | View | CSV | PDB |
| 8.0 | -0.9064 | 4.3005 | View | CSV | PDB |
| 8.5 | -0.8657 | 4.2426 | View | CSV | PDB |
| 9.0 | -0.819 | 4.192 | 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