| Chain sequence(s) |
A: EIVLTKSPATLSLSPGERATLSCRVSQNVSSNLAWYQQKPGQAPRLLIYDTSNRATGIPARFSGSGPGTDFTLTISSLEPEDFAVYYCQQRRNWPLTFGGGTKVEIKGGGGSGGGGSGGGGSEVQLVESGGGLVQPGGSLRLSCAASGFTFSRYAMSWVRQAPGKGLEWVSSISASGATTYYADPVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDQDFDILTGYLNWFDPWGQGTLVTVSS
B: AQEVQQSPHCTTVPVGASVNITCSTSGGLRGIYLRQLGPQPQDIIYYEDGVVPTTDRRFRGRIDFSGSQDNLTITMHRLQLSDTGTYTCQAITEVNVYGSGTLVLVTEEQSQGWHRCSDAPPRASALPAPPTGSALPDPQTASALPDPPAASALP 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] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[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/19fcbffce65e074/tmp/folded.pdb (00:04:57)
[INFO] Main: Simulation completed successfully. (00:12:23)
|
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 | E | A | -1.5956 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7269 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.6275 | |
| 6 | K | A | -0.8314 | |
| 7 | S | A | -0.7879 | |
| 8 | P | A | -0.4319 | |
| 9 | A | A | -0.3884 | |
| 10 | T | A | -0.4975 | |
| 11 | L | A | -0.2931 | |
| 12 | S | A | -0.7028 | |
| 13 | L | A | -1.0251 | |
| 14 | S | A | -1.3501 | |
| 15 | P | A | -1.6031 | |
| 16 | G | A | -1.7466 | |
| 17 | E | A | -2.3371 | |
| 18 | R | A | -2.5534 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5316 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.8665 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.2603 | |
| 25 | V | A | 0.0000 | |
| 26 | S | A | -1.1838 | |
| 27 | Q | A | -2.2561 | |
| 28 | N | A | -2.4386 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -1.0947 | |
| 31 | S | A | -0.8473 | |
| 32 | N | A | -0.9031 | |
| 33 | L | A | 0.0000 | |
| 34 | A | A | 0.0000 | |
| 35 | W | A | 0.0000 | |
| 36 | Y | A | 0.0000 | |
| 37 | Q | A | 0.0000 | |
| 38 | Q | A | 0.0000 | |
| 39 | K | A | -1.2752 | |
| 40 | P | A | -0.8610 | |
| 41 | G | A | -1.1861 | |
| 42 | Q | A | -1.5294 | |
| 43 | A | A | -1.1269 | |
| 44 | P | A | 0.0000 | |
| 45 | R | A | -1.3059 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | -0.7024 | |
| 50 | D | A | -0.9175 | |
| 51 | T | A | 0.0000 | |
| 52 | S | A | -1.0880 | |
| 53 | N | A | -1.3395 | |
| 54 | R | A | -1.8099 | |
| 55 | A | A | 0.0000 | |
| 56 | T | A | -0.7229 | |
| 57 | G | A | -0.7812 | |
| 58 | I | A | 0.0000 | |
| 59 | P | A | -0.5253 | |
| 60 | A | A | -0.4371 | |
| 61 | R | A | -0.8323 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.7254 | |
| 64 | G | A | 0.0000 | |
| 65 | S | A | -0.6914 | |
| 66 | G | A | -0.8686 | |
| 67 | P | A | -0.9761 | |
| 68 | G | A | -1.4946 | |
| 69 | T | A | -1.8890 | |
| 70 | D | A | -1.9943 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.7016 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.5811 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.3164 | |
| 77 | S | A | -1.6606 | |
| 78 | L | A | 0.0000 | |
| 79 | E | A | -1.9334 | |
| 80 | P | A | -1.7835 | |
| 81 | E | A | -2.5696 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | -0.8552 | |
| 84 | A | A | 0.0000 | |
| 85 | V | A | -0.2644 | |
| 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 | R | A | 0.0000 | |
| 92 | R | A | -1.1436 | |
| 93 | N | A | -1.1522 | |
| 94 | W | A | -0.8287 | |
| 95 | P | A | -0.8784 | |
| 96 | L | A | 0.0000 | |
| 97 | T | A | 0.0000 | |
| 98 | F | A | 0.1974 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -0.6757 | |
| 101 | G | A | -0.7532 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -1.0276 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | -0.8894 | |
| 106 | I | A | -0.7021 | |
| 107 | K | A | -1.8319 | |
| 108 | G | A | -1.4711 | |
| 109 | G | A | -1.2956 | |
| 110 | G | A | -1.1864 | |
| 111 | G | A | -1.2452 | |
| 112 | S | A | -1.0069 | |
| 113 | G | A | -1.5302 | |
| 114 | G | A | -1.5853 | |
| 115 | G | A | -1.7431 | |
| 116 | G | A | -1.7100 | |
| 117 | S | A | -1.3099 | |
| 118 | G | A | -1.4478 | |
| 119 | G | A | -1.2652 | |
| 120 | G | A | -1.4680 | |
| 121 | G | A | -1.6725 | |
| 122 | S | A | -1.7495 | |
| 123 | E | A | -2.4418 | |
| 124 | V | A | -1.5538 | |
| 125 | Q | A | -1.7477 | |
| 126 | L | A | 0.0000 | |
| 127 | V | A | 0.0461 | |
| 128 | E | A | 0.0000 | |
| 129 | S | A | -0.3979 | |
| 130 | G | A | -0.7778 | |
| 131 | G | A | 0.0772 | |
| 132 | G | A | 0.5872 | |
| 133 | L | A | 1.3150 | |
| 134 | V | A | 0.0000 | |
| 135 | Q | A | -1.3528 | |
| 136 | P | A | -1.4907 | |
| 137 | G | A | -1.3412 | |
| 138 | G | A | -0.9245 | |
| 139 | S | A | -1.3149 | |
| 140 | L | A | -1.1126 | |
| 141 | R | A | -2.2296 | |
| 142 | L | A | 0.0000 | |
| 143 | S | A | -0.5719 | |
| 144 | C | A | 0.0000 | |
| 145 | A | A | -0.4330 | |
| 146 | A | A | 0.0000 | |
| 147 | S | A | -1.0084 | |
| 148 | G | A | -1.3275 | |
| 149 | F | A | -0.8757 | |
| 150 | T | A | -0.6913 | |
| 151 | F | A | 0.0000 | |
| 152 | S | A | -1.5791 | |
| 153 | R | A | -2.0728 | |
| 154 | Y | A | 0.0000 | |
| 155 | A | A | 0.0000 | |
| 156 | M | A | 0.0000 | |
| 157 | S | A | 0.0000 | |
| 158 | W | A | 0.0000 | |
| 159 | V | A | 0.0000 | |
| 160 | R | A | 0.0000 | |
| 161 | Q | A | -0.6515 | |
| 162 | A | A | -1.0559 | |
| 163 | P | A | -0.8425 | |
| 164 | G | A | -1.4543 | |
| 165 | K | A | -2.2486 | |
| 166 | G | A | -1.3273 | |
| 167 | L | A | 0.0000 | |
| 168 | E | A | -0.9292 | |
| 169 | W | A | 0.0000 | |
| 170 | V | A | 0.0000 | |
| 171 | S | A | 0.0000 | |
| 172 | S | A | 0.0000 | |
| 173 | I | A | 0.0000 | |
| 174 | S | A | 0.0000 | |
| 175 | A | A | 0.0000 | |
| 176 | S | A | -0.7742 | |
| 177 | G | A | -0.3757 | |
| 178 | A | A | -0.1108 | |
| 179 | T | A | 0.0000 | |
| 180 | T | A | 0.0682 | |
| 181 | Y | A | -0.1003 | |
| 182 | Y | A | -0.7585 | |
| 183 | A | A | 0.0000 | |
| 184 | D | A | -2.4527 | |
| 185 | P | A | -1.8506 | |
| 186 | V | A | 0.0000 | |
| 187 | K | A | -2.6076 | |
| 188 | G | A | -1.7810 | |
| 189 | R | A | -1.4366 | |
| 190 | F | A | 0.0000 | |
| 191 | T | A | -0.9089 | |
| 192 | I | A | 0.0000 | |
| 193 | S | A | -0.4028 | |
| 194 | R | A | -0.9072 | |
| 195 | D | A | -1.4501 | |
| 196 | N | A | -1.8062 | |
| 197 | S | A | -1.5464 | |
| 198 | K | A | -2.3350 | |
| 199 | N | A | -1.7088 | |
| 200 | T | A | -1.0632 | |
| 201 | L | A | 0.0000 | |
| 202 | Y | A | -0.5897 | |
| 203 | L | A | 0.0000 | |
| 204 | Q | A | -1.5089 | |
| 205 | M | A | 0.0000 | |
| 206 | N | A | -1.4659 | |
| 207 | S | A | -1.1804 | |
| 208 | L | A | 0.0000 | |
| 209 | R | A | -1.9738 | |
| 210 | A | A | -1.5814 | |
| 211 | E | A | -2.1437 | |
| 212 | D | A | 0.0000 | |
| 213 | T | A | -0.3587 | |
| 214 | A | A | 0.0000 | |
| 215 | V | A | 0.7200 | |
| 216 | Y | A | 0.0000 | |
| 217 | Y | A | 0.0000 | |
| 218 | C | A | 0.0000 | |
| 219 | A | A | 0.0000 | |
| 220 | K | A | 0.0000 | |
| 221 | D | A | 0.0000 | |
| 222 | Q | A | 0.0000 | |
| 223 | D | A | -1.1257 | |
| 224 | F | A | -0.9671 | |
| 225 | D | A | -1.4023 | |
| 226 | I | A | 0.4158 | |
| 227 | L | A | 0.0000 | |
| 228 | T | A | -0.6306 | |
| 229 | G | A | -0.3345 | |
| 230 | Y | A | 0.0000 | |
| 231 | L | A | 0.0000 | |
| 232 | N | A | 0.0000 | |
| 233 | W | A | 0.0000 | |
| 234 | F | A | 0.0000 | |
| 235 | D | A | -0.7435 | |
| 236 | P | A | -0.8991 | |
| 237 | W | A | 0.0000 | |
| 238 | G | A | 0.0000 | |
| 239 | Q | A | -1.3674 | |
| 240 | G | A | 0.0000 | |
| 241 | T | A | 0.4319 | |
| 242 | L | A | 1.5565 | |
| 243 | V | A | 0.0000 | |
| 244 | T | A | 0.3081 | |
| 245 | V | A | 0.0000 | |
| 246 | S | A | -0.7554 | |
| 247 | S | A | -0.5786 | |
| 1 | A | B | -1.7167 | |
| 2 | Q | B | -1.9823 | |
| 3 | E | B | -2.5894 | |
| 4 | V | B | -1.5890 | |
| 5 | Q | B | -1.6842 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.9649 | |
| 8 | P | B | -0.9588 | |
| 9 | H | B | -0.8068 | |
| 10 | C | B | -0.5180 | |
| 11 | T | B | -0.6157 | |
| 12 | T | B | -0.1062 | |
| 13 | V | B | -0.0401 | |
| 14 | P | B | -0.9784 | |
| 15 | V | B | -0.5378 | |
| 16 | G | B | -1.0597 | |
| 17 | A | B | -0.6027 | |
| 18 | S | B | -0.9999 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -1.3907 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.9522 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.7857 | |
| 25 | T | B | -1.8832 | |
| 26 | S | B | -1.9006 | |
| 27 | G | B | -1.5206 | |
| 28 | G | B | -1.5411 | |
| 29 | L | B | -1.5887 | |
| 30 | R | B | -2.3756 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.1102 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.5266 | |
| 36 | Q | B | 0.0000 | |
| 37 | L | B | 0.2589 | |
| 38 | G | B | -0.6475 | |
| 39 | P | B | -0.8999 | |
| 40 | Q | B | -1.5535 | |
| 41 | P | B | -1.1802 | |
| 42 | Q | B | -1.4174 | |
| 43 | D | B | -1.2567 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.0425 | |
| 47 | Y | B | -0.4454 | |
| 48 | E | B | -1.3848 | |
| 49 | D | B | -1.9825 | |
| 50 | G | B | -1.2658 | |
| 51 | V | B | -0.6441 | |
| 52 | V | B | 0.0000 | |
| 53 | P | B | 0.0000 | |
| 54 | T | B | -0.3853 | |
| 55 | T | B | 0.0000 | |
| 56 | D | B | 0.0000 | |
| 57 | R | B | -2.1257 | |
| 58 | R | B | -1.5567 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | 0.0000 | |
| 61 | G | B | -1.3283 | |
| 62 | R | B | -1.4518 | |
| 63 | I | B | 0.0000 | |
| 64 | D | B | 0.0000 | |
| 65 | F | B | 0.0000 | |
| 66 | S | B | -0.7963 | |
| 67 | G | B | -1.3527 | |
| 68 | S | B | -1.6005 | |
| 69 | Q | B | -1.9678 | |
| 70 | D | B | -2.5838 | |
| 71 | N | B | -2.2957 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0148 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.6813 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.4424 | |
| 78 | R | B | -2.1025 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -0.7274 | |
| 81 | L | B | 0.6143 | |
| 82 | S | B | 0.1789 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | 0.2845 | |
| 85 | G | B | 0.3805 | |
| 86 | T | B | 0.4092 | |
| 87 | Y | B | 0.0000 | |
| 88 | T | B | 0.0000 | |
| 89 | C | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | A | B | 0.0000 | |
| 92 | I | B | -0.4443 | |
| 93 | T | B | -1.1615 | |
| 94 | E | B | -1.4063 | |
| 95 | V | B | 0.4308 | |
| 96 | N | B | -0.5695 | |
| 97 | V | B | -0.0481 | |
| 98 | Y | B | 0.6103 | |
| 99 | G | B | -0.2021 | |
| 100 | S | B | -0.2311 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | L | B | 0.6591 | |
| 104 | V | B | 0.0000 | |
| 105 | L | B | 0.5902 | |
| 106 | V | B | 0.0000 | |
| 107 | T | B | -1.2595 | |
| 108 | E | B | -2.7815 | |
| 109 | E | B | -3.3078 | |
| 110 | Q | B | -3.0205 | |
| 111 | S | B | -2.4753 | |
| 112 | Q | B | -2.3956 | |
| 113 | G | B | -1.8704 | |
| 114 | W | B | -1.5849 | |
| 115 | H | B | -2.0004 | |
| 116 | R | B | -2.5346 | |
| 117 | C | B | -1.5086 | |
| 118 | S | B | -1.8099 | |
| 119 | D | B | -2.2674 | |
| 120 | A | B | -1.4285 | |
| 121 | P | B | -1.3506 | |
| 122 | P | B | -1.5410 | |
| 123 | R | B | -2.0379 | |
| 124 | A | B | -0.7696 | |
| 125 | S | B | -0.3586 | |
| 126 | A | B | 0.3599 | |
| 127 | L | B | 1.3691 | |
| 128 | P | B | 0.3945 | |
| 129 | A | B | 0.1719 | |
| 130 | P | B | -0.2523 | |
| 131 | P | B | -0.6160 | |
| 132 | T | B | -0.5301 | |
| 133 | G | B | -0.4551 | |
| 134 | S | B | -0.0557 | |
| 135 | A | B | 0.2073 | |
| 136 | L | B | 0.8164 | |
| 137 | P | B | -0.6357 | |
| 138 | D | B | -1.9708 | |
| 139 | P | B | -1.5315 | |
| 140 | Q | B | -1.8936 | |
| 141 | T | B | -0.9975 | |
| 142 | A | B | -0.2166 | |
| 143 | S | B | 0.0561 | |
| 144 | A | B | 0.3767 | |
| 145 | L | B | 0.9329 | |
| 146 | P | B | -0.4925 | |
| 147 | D | B | -1.7122 | |
| 148 | P | B | -1.0624 | |
| 149 | P | B | -0.8656 | |
| 150 | A | B | -0.4136 | |
| 151 | A | B | 0.1090 | |
| 152 | S | B | 0.2209 | |
| 153 | A | B | 0.6641 | |
| 154 | L | B | 1.4029 | |
| 155 | P | B | 0.4760 |
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 | -0.3495 | 3.8783 | View | CSV | PDB |
| 4.5 | -0.3935 | 3.8783 | View | CSV | PDB |
| 5.0 | -0.4467 | 3.8783 | View | CSV | PDB |
| 5.5 | -0.5018 | 3.8783 | View | CSV | PDB |
| 6.0 | -0.5512 | 3.8783 | View | CSV | PDB |
| 6.5 | -0.589 | 3.8783 | View | CSV | PDB |
| 7.0 | -0.6138 | 3.8783 | View | CSV | PDB |
| 7.5 | -0.629 | 3.8783 | View | CSV | PDB |
| 8.0 | -0.6379 | 3.8783 | View | CSV | PDB |
| 8.5 | -0.641 | 3.8783 | View | CSV | PDB |
| 9.0 | -0.6372 | 3.8783 | 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