| Chain sequence(s) |
A: QVQLVESGGGVVQPGRSLRLSCTASGFTFSHYGMYWVRQAPGKGLEWVAVIWYDGSYEYNEDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDRVGLFDYWGQGTLVTVSSASTKGPEVQLVESGGGLVQPGGSLRLSCAASGYTFTNYGMNWVRQAPGKGLEWVGWINTYTGEPTYAADFKRRFTFSLDTSKSTAYLQMNSLRAEDTAVYYCAKYPHYYGSSHWYFDVWGQGTLVTVSS
B: EIVLTQSPGTLSLSPGERATLSCRASQSISSSYLAWYQQKPGQAPRLLIYGPSSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYAGSLTFGPGTKVDIKRTVAAPSVFIFPPDIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKVLIYFTSSLHSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYSTVPWTFGQGTKVEIK 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] (00:00:00)
[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 (00:03:44)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/4b6851c770eb562/tmp/folded.pdb (00:03:44)
[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 | Q | A | -1.4009 | |
| 2 | V | A | -0.7113 | |
| 3 | Q | A | -0.7450 | |
| 4 | L | A | 0.0000 | |
| 5 | V | A | 0.3861 | |
| 6 | E | A | 0.0000 | |
| 7 | S | A | -0.5479 | |
| 8 | G | A | -0.9055 | |
| 9 | G | A | -0.3704 | |
| 10 | G | A | 0.1991 | |
| 11 | V | A | 0.8524 | |
| 12 | V | A | 0.0000 | |
| 13 | Q | A | -0.9924 | |
| 14 | P | A | -1.6532 | |
| 15 | G | A | -1.9561 | |
| 16 | R | A | -2.4851 | |
| 17 | S | A | -1.8923 | |
| 18 | L | A | -1.2017 | |
| 19 | R | A | -1.8748 | |
| 20 | L | A | 0.0000 | |
| 21 | S | A | -0.5539 | |
| 22 | C | A | 0.0000 | |
| 23 | T | A | -0.4294 | |
| 24 | A | A | 0.0000 | |
| 25 | S | A | -0.6949 | |
| 26 | G | A | -0.9448 | |
| 27 | F | A | -0.4596 | |
| 28 | T | A | -0.3458 | |
| 29 | F | A | 0.0000 | |
| 30 | S | A | -0.9428 | |
| 31 | H | A | -0.8841 | |
| 32 | Y | A | 0.0694 | |
| 33 | G | A | 0.0000 | |
| 34 | M | A | 0.0000 | |
| 35 | Y | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | V | A | 0.0000 | |
| 38 | R | A | 0.0000 | |
| 39 | Q | A | 0.0000 | |
| 40 | A | A | -1.0516 | |
| 41 | P | A | -0.5584 | |
| 42 | G | A | -0.8108 | |
| 43 | K | A | -1.9644 | |
| 44 | G | A | -1.1917 | |
| 45 | L | A | 0.0000 | |
| 46 | E | A | -1.0702 | |
| 47 | W | A | 0.0000 | |
| 48 | V | A | 0.0000 | |
| 49 | A | A | 0.0000 | |
| 50 | V | A | 0.0000 | |
| 51 | I | A | 0.0000 | |
| 52 | W | A | 0.2276 | |
| 53 | Y | A | -0.1378 | |
| 54 | D | A | -1.6332 | |
| 55 | G | A | -0.8916 | |
| 56 | S | A | -0.4232 | |
| 57 | Y | A | 0.2104 | |
| 58 | E | A | -0.7913 | |
| 59 | Y | A | -0.2741 | |
| 60 | N | A | -1.3430 | |
| 61 | E | A | -1.7888 | |
| 62 | D | A | -2.6329 | |
| 63 | S | A | -1.8333 | |
| 64 | V | A | 0.0000 | |
| 65 | K | A | -2.6432 | |
| 66 | G | A | -1.7504 | |
| 67 | R | A | 0.0000 | |
| 68 | F | A | 0.0000 | |
| 69 | T | A | -0.9814 | |
| 70 | I | A | 0.0000 | |
| 71 | S | A | -0.5572 | |
| 72 | R | A | -1.1261 | |
| 73 | D | A | -1.8830 | |
| 74 | N | A | -2.0084 | |
| 75 | S | A | -1.6302 | |
| 76 | K | A | -2.4108 | |
| 77 | N | A | -1.8073 | |
| 78 | T | A | 0.0000 | |
| 79 | L | A | 0.0000 | |
| 80 | Y | A | 0.0000 | |
| 81 | L | A | 0.0000 | |
| 82 | Q | A | -1.1402 | |
| 83 | M | A | 0.0000 | |
| 84 | N | A | -1.8310 | |
| 85 | S | A | -1.6106 | |
| 86 | L | A | 0.0000 | |
| 87 | R | A | -2.3622 | |
| 88 | A | A | -1.5593 | |
| 89 | E | A | -2.2106 | |
| 90 | D | A | 0.0000 | |
| 91 | T | A | -0.6417 | |
| 92 | A | A | 0.0000 | |
| 93 | V | A | 0.0000 | |
| 94 | Y | A | 0.0000 | |
| 95 | Y | A | 0.0000 | |
| 96 | C | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | R | A | 0.0000 | |
| 99 | D | A | 0.1040 | |
| 100 | R | A | -0.0442 | |
| 101 | V | A | 1.4088 | |
| 102 | G | A | 0.5600 | |
| 103 | L | A | 0.0000 | |
| 104 | F | A | 0.0000 | |
| 105 | D | A | -0.1475 | |
| 106 | Y | A | 0.0118 | |
| 107 | W | A | -0.0488 | |
| 108 | G | A | 0.0000 | |
| 109 | Q | A | -0.8016 | |
| 110 | G | A | 0.0000 | |
| 111 | T | A | -0.1836 | |
| 112 | L | A | 0.2742 | |
| 113 | V | A | 0.0000 | |
| 114 | T | A | 0.0414 | |
| 115 | V | A | 0.0000 | |
| 116 | S | A | -0.4877 | |
| 117 | S | A | -0.4514 | |
| 118 | A | A | -0.4806 | |
| 119 | S | A | -0.8144 | |
| 120 | T | A | -0.8872 | |
| 121 | K | A | -2.0772 | |
| 122 | G | A | -1.2587 | |
| 123 | P | A | -1.4558 | |
| 124 | E | A | -2.1302 | |
| 125 | V | A | -0.4962 | |
| 126 | Q | A | -0.7064 | |
| 127 | L | A | 0.0000 | |
| 128 | V | A | 0.3757 | |
| 129 | E | A | 0.0000 | |
| 130 | S | A | -0.3570 | |
| 131 | G | A | -0.5781 | |
| 132 | G | A | 0.1573 | |
| 133 | G | A | 0.8818 | |
| 134 | L | A | 1.3879 | |
| 135 | V | A | -0.0187 | |
| 136 | Q | A | -1.2831 | |
| 137 | P | A | -1.5162 | |
| 138 | G | A | -1.3704 | |
| 139 | G | A | -0.9438 | |
| 140 | S | A | -1.1848 | |
| 141 | L | A | -0.9160 | |
| 142 | R | A | -1.9288 | |
| 143 | L | A | 0.0000 | |
| 144 | S | A | -0.4562 | |
| 145 | C | A | 0.0000 | |
| 146 | A | A | -0.2019 | |
| 147 | A | A | 0.0000 | |
| 148 | S | A | -0.6662 | |
| 149 | G | A | -0.7303 | |
| 150 | Y | A | -0.0529 | |
| 151 | T | A | 0.0336 | |
| 152 | F | A | 0.0000 | |
| 153 | T | A | 0.1544 | |
| 154 | N | A | 0.0000 | |
| 155 | Y | A | 0.0000 | |
| 156 | G | A | 0.0000 | |
| 157 | M | A | 0.0000 | |
| 158 | N | A | 0.0000 | |
| 159 | W | A | 0.0000 | |
| 160 | V | A | 0.0000 | |
| 161 | R | A | 0.0000 | |
| 162 | Q | A | -0.7157 | |
| 163 | A | A | -1.0837 | |
| 164 | P | A | -0.8261 | |
| 165 | G | A | -1.4521 | |
| 166 | K | A | -2.4010 | |
| 167 | G | A | -1.6946 | |
| 168 | L | A | 0.0000 | |
| 169 | E | A | -1.3079 | |
| 170 | W | A | 0.0000 | |
| 171 | V | A | 0.0000 | |
| 172 | G | A | 0.0000 | |
| 173 | W | A | 0.0000 | |
| 174 | I | A | 0.0000 | |
| 175 | N | A | 0.0000 | |
| 176 | T | A | 0.0000 | |
| 177 | Y | A | 0.4348 | |
| 178 | T | A | -0.1209 | |
| 179 | G | A | -0.3228 | |
| 180 | E | A | -0.3859 | |
| 181 | P | A | -0.4888 | |
| 182 | T | A | -0.2730 | |
| 183 | Y | A | 0.0000 | |
| 184 | A | A | 0.0000 | |
| 185 | A | A | -1.5240 | |
| 186 | D | A | -2.5944 | |
| 187 | F | A | 0.0000 | |
| 188 | K | A | -3.0952 | |
| 189 | R | A | -3.0964 | |
| 190 | R | A | 0.0000 | |
| 191 | F | A | 0.0000 | |
| 192 | T | A | -1.0699 | |
| 193 | F | A | 0.0000 | |
| 194 | S | A | -0.1693 | |
| 195 | L | A | -0.2348 | |
| 196 | D | A | -0.9158 | |
| 197 | T | A | -0.7997 | |
| 198 | S | A | -1.1586 | |
| 199 | K | A | -1.9458 | |
| 200 | S | A | -1.0286 | |
| 201 | T | A | 0.0000 | |
| 202 | A | A | 0.0000 | |
| 203 | Y | A | -0.4088 | |
| 204 | L | A | 0.0000 | |
| 205 | Q | A | -1.1061 | |
| 206 | M | A | 0.0000 | |
| 207 | N | A | -1.4972 | |
| 208 | S | A | -1.2988 | |
| 209 | L | A | 0.0000 | |
| 210 | R | A | -2.1543 | |
| 211 | A | A | -1.6418 | |
| 212 | E | A | -2.1840 | |
| 213 | D | A | 0.0000 | |
| 214 | T | A | -0.3413 | |
| 215 | A | A | 0.0000 | |
| 216 | V | A | 0.7126 | |
| 217 | Y | A | 0.0000 | |
| 218 | Y | A | 0.0000 | |
| 219 | C | A | 0.0000 | |
| 220 | A | A | 0.0000 | |
| 221 | K | A | 0.0000 | |
| 222 | Y | A | 0.0000 | |
| 223 | P | A | -0.1304 | |
| 224 | H | A | -0.3466 | |
| 225 | Y | A | 0.0000 | |
| 226 | Y | A | 0.0000 | |
| 227 | G | A | 0.0000 | |
| 228 | S | A | -0.6312 | |
| 229 | S | A | -0.4164 | |
| 230 | H | A | -0.0047 | |
| 231 | W | A | 0.1494 | |
| 232 | Y | A | 0.0000 | |
| 233 | F | A | 0.0000 | |
| 234 | D | A | -0.3415 | |
| 235 | V | A | -0.0974 | |
| 236 | W | A | 0.0000 | |
| 237 | G | A | 0.0000 | |
| 238 | Q | A | -1.3107 | |
| 239 | G | A | -0.3918 | |
| 240 | T | A | 0.4650 | |
| 241 | L | A | 1.5234 | |
| 242 | V | A | 0.0000 | |
| 243 | T | A | 0.3663 | |
| 244 | V | A | 0.0000 | |
| 245 | S | A | -0.7049 | |
| 246 | S | A | -0.5313 | |
| 1 | E | B | -1.6412 | |
| 2 | I | B | 0.0000 | |
| 3 | V | B | 0.8431 | |
| 4 | L | B | 0.0000 | |
| 5 | T | B | -0.4051 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.6984 | |
| 8 | P | B | -0.5069 | |
| 9 | G | B | -0.7148 | |
| 10 | T | B | -0.5451 | |
| 11 | L | B | -0.2165 | |
| 12 | S | B | -0.5921 | |
| 13 | L | B | -0.9456 | |
| 14 | S | B | -1.4939 | |
| 15 | P | B | -1.6678 | |
| 16 | G | B | -2.1148 | |
| 17 | E | B | -2.7737 | |
| 18 | R | B | -3.2099 | |
| 19 | A | B | 0.0000 | |
| 20 | T | B | -0.6534 | |
| 21 | L | B | 0.0000 | |
| 22 | S | B | -0.8103 | |
| 23 | C | B | 0.0000 | |
| 24 | R | B | -1.8548 | |
| 25 | A | B | 0.0000 | |
| 26 | S | B | -0.8526 | |
| 27 | Q | B | -1.4387 | |
| 28 | S | B | -1.1858 | |
| 29 | I | B | 0.0000 | |
| 30 | S | B | -0.1012 | |
| 31 | S | B | -0.2965 | |
| 32 | S | B | 0.1650 | |
| 33 | Y | B | 0.9592 | |
| 34 | L | B | 0.0000 | |
| 35 | A | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | Y | B | 0.0000 | |
| 38 | Q | B | 0.0000 | |
| 39 | Q | B | 0.0000 | |
| 40 | K | B | -0.9720 | |
| 41 | P | B | -0.3976 | |
| 42 | G | B | 0.0000 | |
| 43 | Q | B | -0.8720 | |
| 44 | A | B | -0.6365 | |
| 45 | P | B | 0.0000 | |
| 46 | R | B | -0.7083 | |
| 47 | L | B | 0.0000 | |
| 48 | L | B | 0.0000 | |
| 49 | I | B | 0.0000 | |
| 50 | Y | B | -0.0713 | |
| 51 | G | B | -0.0861 | |
| 52 | P | B | -0.4903 | |
| 53 | S | B | -0.7084 | |
| 54 | S | B | -0.7280 | |
| 55 | R | B | -1.4853 | |
| 56 | A | B | -0.7296 | |
| 57 | T | B | -0.5290 | |
| 58 | G | B | -0.7987 | |
| 59 | I | B | -0.9060 | |
| 60 | P | B | -1.2275 | |
| 61 | D | B | -2.3440 | |
| 62 | R | B | -1.9488 | |
| 63 | F | B | 0.0000 | |
| 64 | S | B | -0.8680 | |
| 65 | G | B | 0.0000 | |
| 66 | S | B | -0.6595 | |
| 67 | G | B | -1.0442 | |
| 68 | S | B | -0.9151 | |
| 69 | G | B | -1.0979 | |
| 70 | T | B | -1.5551 | |
| 71 | D | B | -1.9682 | |
| 72 | F | B | 0.0000 | |
| 73 | T | B | -0.7175 | |
| 74 | L | B | 0.0000 | |
| 75 | T | B | -0.7953 | |
| 76 | I | B | 0.0000 | |
| 77 | S | B | -2.3598 | |
| 78 | R | B | -3.4828 | |
| 79 | L | B | 0.0000 | |
| 80 | E | B | -2.5443 | |
| 81 | P | B | -1.6471 | |
| 82 | E | B | -2.2746 | |
| 83 | D | B | 0.0000 | |
| 84 | F | B | -0.6111 | |
| 85 | A | B | 0.0000 | |
| 86 | V | B | -0.2228 | |
| 87 | Y | B | 0.0000 | |
| 88 | Y | B | 0.0000 | |
| 89 | C | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | Q | B | 0.0000 | |
| 92 | Y | B | 0.5545 | |
| 93 | A | B | 0.0696 | |
| 94 | G | B | -0.6886 | |
| 95 | S | B | -0.8688 | |
| 96 | L | B | 0.0000 | |
| 97 | T | B | -0.0908 | |
| 98 | F | B | 0.2414 | |
| 99 | G | B | 0.0000 | |
| 100 | P | B | -0.4870 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | K | B | -0.6190 | |
| 104 | V | B | 0.0000 | |
| 105 | D | B | -0.6059 | |
| 106 | I | B | -0.2079 | |
| 107 | K | B | -1.4526 | |
| 108 | R | B | -1.7091 | |
| 109 | T | B | -0.2784 | |
| 110 | V | B | 1.0828 | |
| 111 | A | B | 0.5061 | |
| 112 | A | B | 0.5830 | |
| 113 | P | B | 0.8277 | |
| 114 | S | B | 1.4793 | |
| 115 | V | B | 3.5127 | |
| 116 | F | B | 4.3120 | |
| 117 | I | B | 4.3396 | |
| 118 | F | B | 3.3744 | |
| 119 | P | B | 0.9642 | |
| 120 | P | B | -0.6160 | |
| 121 | D | B | -1.9059 | |
| 122 | I | B | 0.0000 | |
| 123 | Q | B | -2.0329 | |
| 124 | M | B | 0.0000 | |
| 125 | T | B | -0.9564 | |
| 126 | Q | B | 0.0000 | |
| 127 | S | B | -0.6212 | |
| 128 | P | B | -0.5072 | |
| 129 | S | B | -0.8044 | |
| 130 | S | B | -0.8897 | |
| 131 | L | B | -0.7275 | |
| 132 | S | B | -1.1281 | |
| 133 | A | B | -1.1125 | |
| 134 | S | B | -1.0351 | |
| 135 | V | B | -0.1988 | |
| 136 | G | B | -0.9789 | |
| 137 | D | B | -2.0161 | |
| 138 | R | B | -2.3802 | |
| 139 | V | B | 0.0000 | |
| 140 | T | B | -0.6466 | |
| 141 | I | B | 0.0000 | |
| 142 | T | B | -0.5960 | |
| 143 | C | B | 0.0000 | |
| 144 | S | B | -1.3896 | |
| 145 | A | B | 0.0000 | |
| 146 | S | B | -1.7509 | |
| 147 | Q | B | -2.1601 | |
| 148 | D | B | -2.4277 | |
| 149 | I | B | 0.0000 | |
| 150 | S | B | -0.9793 | |
| 151 | N | B | -0.4998 | |
| 152 | Y | B | 0.3022 | |
| 153 | L | B | 0.0000 | |
| 154 | N | B | 0.0000 | |
| 155 | W | B | 0.0000 | |
| 156 | Y | B | 0.0000 | |
| 157 | Q | B | -0.8493 | |
| 158 | Q | B | 0.0000 | |
| 159 | K | B | -1.7369 | |
| 160 | P | B | -1.2025 | |
| 161 | G | B | -1.7098 | |
| 162 | K | B | -2.6332 | |
| 163 | A | B | -1.6741 | |
| 164 | P | B | 0.0000 | |
| 165 | K | B | -1.5016 | |
| 166 | V | B | 0.0000 | |
| 167 | L | B | 0.0000 | |
| 168 | I | B | 0.0000 | |
| 169 | Y | B | 0.6061 | |
| 170 | F | B | 0.7779 | |
| 171 | T | B | 0.0000 | |
| 172 | S | B | -0.0031 | |
| 173 | S | B | 0.2796 | |
| 174 | L | B | 0.4023 | |
| 175 | H | B | -0.2247 | |
| 176 | S | B | -0.3691 | |
| 177 | G | B | -0.5023 | |
| 178 | V | B | -0.3322 | |
| 179 | P | B | -0.3837 | |
| 180 | S | B | -0.4175 | |
| 181 | R | B | -0.7908 | |
| 182 | F | B | 0.0000 | |
| 183 | S | B | -0.3001 | |
| 184 | G | B | 0.0000 | |
| 185 | S | B | -0.6798 | |
| 186 | G | B | -1.0825 | |
| 187 | S | B | -1.2030 | |
| 188 | G | B | -1.6157 | |
| 189 | T | B | -1.9209 | |
| 190 | D | B | -2.3769 | |
| 191 | F | B | 0.0000 | |
| 192 | T | B | -0.6556 | |
| 193 | L | B | 0.0000 | |
| 194 | T | B | -0.5951 | |
| 195 | I | B | 0.0000 | |
| 196 | S | B | -1.3522 | |
| 197 | S | B | -1.2607 | |
| 198 | L | B | 0.0000 | |
| 199 | Q | B | -0.9507 | |
| 200 | P | B | -1.1916 | |
| 201 | E | B | -1.7566 | |
| 202 | D | B | 0.0000 | |
| 203 | F | B | -0.6652 | |
| 204 | A | B | 0.0000 | |
| 205 | T | B | -0.8313 | |
| 206 | Y | B | 0.0000 | |
| 207 | Y | B | 0.0000 | |
| 208 | C | B | 0.0000 | |
| 209 | Q | B | 0.0000 | |
| 210 | Q | B | 0.0000 | |
| 211 | Y | B | 0.0000 | |
| 212 | S | B | -0.1019 | |
| 213 | T | B | 0.0899 | |
| 214 | V | B | 0.6114 | |
| 215 | P | B | 0.0008 | |
| 216 | W | B | 0.0000 | |
| 217 | T | B | -0.7848 | |
| 218 | F | B | 0.0000 | |
| 219 | G | B | 0.0000 | |
| 220 | Q | B | -1.8414 | |
| 221 | G | B | 0.0000 | |
| 222 | T | B | 0.0000 | |
| 223 | K | B | -1.4034 | |
| 224 | V | B | 0.0000 | |
| 225 | E | B | -1.5990 | |
| 226 | I | B | -0.9812 | |
| 227 | K | B | -1.6921 |
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 | -0.4875 | 8.6986 | View | CSV | PDB |
| 4.5 | -0.5267 | 8.6389 | View | CSV | PDB |
| 5.0 | -0.5716 | 8.57 | View | CSV | PDB |
| 5.5 | -0.615 | 8.4974 | View | CSV | PDB |
| 6.0 | -0.6488 | 8.4235 | View | CSV | PDB |
| 6.5 | -0.6679 | 8.3494 | View | CSV | PDB |
| 7.0 | -0.6731 | 8.2755 | View | CSV | PDB |
| 7.5 | -0.669 | 8.2025 | View | CSV | PDB |
| 8.0 | -0.6586 | 8.1889 | View | CSV | PDB |
| 8.5 | -0.6424 | 8.1889 | View | CSV | PDB |
| 9.0 | -0.6201 | 8.1889 | 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