| Chain sequence(s) |
A: EIVLTQSPATLSLSPGERATLSCRVSQNVSSNLAWYQQKPGQAPRLLIYDTSNRATGIPARFSGSGSGRDFTLTISSLEPEDFAVYYCQQRRNWPLTFGGGTKVEIKGGGGSGGGGSGGGGSEVQLVESGGGLVQPGGSLRLSCAASGFTFSRYAMSWVRQAPGKGLEWVSAISASGATTYYADPVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDQDFDILTGYLNWFDPWGQGTLVTVSS
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] (00:00:03)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:03)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:03)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:03)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:05)
[INFO] FoldX: Starting FoldX energy minimization (00:00:05)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:09:25)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/1b692c2f887e980/tmp/folded.pdb (00:09:25)
[INFO] Main: Simulation completed successfully. (00:15:57)
|
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 | -1.7921 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7433 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.6770 | |
| 6 | Q | A | -0.6440 | |
| 7 | S | A | -0.7063 | |
| 8 | P | A | -0.3185 | |
| 9 | A | A | -0.3553 | |
| 10 | T | A | -0.4409 | |
| 11 | L | A | -0.2421 | |
| 12 | S | A | -0.6311 | |
| 13 | L | A | -0.9702 | |
| 14 | S | A | -1.3589 | |
| 15 | P | A | -1.7668 | |
| 16 | G | A | -1.9499 | |
| 17 | E | A | -2.5136 | |
| 18 | R | A | -2.6636 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.6335 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -1.0131 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -3.1533 | |
| 25 | V | A | 0.0000 | |
| 26 | S | A | -1.5642 | |
| 27 | Q | A | -2.6718 | |
| 28 | N | A | -3.0377 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -1.7440 | |
| 31 | S | A | -1.0947 | |
| 32 | N | A | -0.6242 | |
| 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 | -1.5640 | |
| 40 | P | A | -1.1146 | |
| 41 | G | A | -1.3229 | |
| 42 | Q | A | -1.7470 | |
| 43 | A | A | 0.0000 | |
| 44 | P | A | 0.0000 | |
| 45 | R | A | -1.3136 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | -0.5130 | |
| 50 | D | A | -0.5265 | |
| 51 | T | A | 0.0000 | |
| 52 | S | A | -0.9716 | |
| 53 | N | A | -1.2674 | |
| 54 | R | A | -1.4703 | |
| 55 | A | A | 0.0000 | |
| 56 | T | A | -0.7528 | |
| 57 | G | A | -0.6286 | |
| 58 | I | A | -0.4912 | |
| 59 | P | A | -0.3437 | |
| 60 | A | A | -0.3638 | |
| 61 | R | A | -0.9208 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.6407 | |
| 64 | G | A | -0.6512 | |
| 65 | S | A | -0.8607 | |
| 66 | G | A | -1.5626 | |
| 67 | S | A | -1.6859 | |
| 68 | G | A | -2.5304 | |
| 69 | R | A | -3.9278 | |
| 70 | D | A | -3.7630 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.9223 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.6272 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.5719 | |
| 77 | S | A | -1.9548 | |
| 78 | L | A | 0.0000 | |
| 79 | E | A | -2.4684 | |
| 80 | P | A | -1.8350 | |
| 81 | E | A | -2.6637 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | -0.8846 | |
| 84 | A | A | 0.0000 | |
| 85 | V | A | -0.2886 | |
| 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 | -0.7950 | |
| 93 | N | A | -1.2089 | |
| 94 | W | A | -0.8213 | |
| 95 | P | A | -0.8667 | |
| 96 | L | A | 0.0000 | |
| 97 | T | A | 0.0000 | |
| 98 | F | A | 0.1677 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -0.7752 | |
| 101 | G | A | -0.7227 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -0.9046 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | -0.8107 | |
| 106 | I | A | -0.4125 | |
| 107 | K | A | -1.7030 | |
| 108 | G | A | -1.4014 | |
| 109 | G | A | -1.2045 | |
| 110 | G | A | -1.2041 | |
| 111 | G | A | -1.2236 | |
| 112 | S | A | -1.0545 | |
| 113 | G | A | -1.3626 | |
| 114 | G | A | -1.5825 | |
| 115 | G | A | -1.7149 | |
| 116 | G | A | -1.7580 | |
| 117 | S | A | -1.2057 | |
| 118 | G | A | -1.5744 | |
| 119 | G | A | -1.2351 | |
| 120 | G | A | -1.5555 | |
| 121 | G | A | -1.6120 | |
| 122 | S | A | -1.7577 | |
| 123 | E | A | -2.4694 | |
| 124 | V | A | -1.6987 | |
| 125 | Q | A | -1.6128 | |
| 126 | L | A | 0.0000 | |
| 127 | V | A | 0.6946 | |
| 128 | E | A | 0.0000 | |
| 129 | S | A | -0.2889 | |
| 130 | G | A | -0.6722 | |
| 131 | G | A | 0.0160 | |
| 132 | G | A | 0.5493 | |
| 133 | L | A | 1.2597 | |
| 134 | V | A | 0.0000 | |
| 135 | Q | A | -1.4127 | |
| 136 | P | A | -1.6459 | |
| 137 | G | A | -1.4702 | |
| 138 | G | A | -1.0405 | |
| 139 | S | A | -1.3513 | |
| 140 | L | A | -1.0930 | |
| 141 | R | A | -2.1589 | |
| 142 | L | A | 0.0000 | |
| 143 | S | A | -0.4421 | |
| 144 | C | A | 0.0000 | |
| 145 | A | A | -0.2344 | |
| 146 | A | A | 0.0000 | |
| 147 | S | A | -0.9477 | |
| 148 | G | A | -1.3289 | |
| 149 | F | A | -0.8440 | |
| 150 | T | A | -0.5022 | |
| 151 | F | A | 0.0000 | |
| 152 | S | A | -1.2364 | |
| 153 | R | A | -1.4288 | |
| 154 | Y | A | -0.6952 | |
| 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 | -0.6744 | |
| 162 | A | A | -1.0802 | |
| 163 | P | A | -0.8536 | |
| 164 | G | A | -1.4493 | |
| 165 | K | A | -2.2739 | |
| 166 | G | A | -1.3736 | |
| 167 | L | A | 0.0000 | |
| 168 | E | A | -0.9922 | |
| 169 | W | A | 0.0000 | |
| 170 | V | A | 0.0000 | |
| 171 | S | A | 0.0000 | |
| 172 | A | A | 0.0000 | |
| 173 | I | A | 0.0000 | |
| 174 | S | A | 0.0000 | |
| 175 | A | A | 0.0000 | |
| 176 | S | A | -0.6221 | |
| 177 | G | A | -0.3783 | |
| 178 | A | A | -0.1076 | |
| 179 | T | A | 0.0000 | |
| 180 | T | A | 0.0626 | |
| 181 | Y | A | -0.1005 | |
| 182 | Y | A | -0.7265 | |
| 183 | A | A | 0.0000 | |
| 184 | D | A | -2.6361 | |
| 185 | P | A | -1.7340 | |
| 186 | V | A | 0.0000 | |
| 187 | K | A | -2.5485 | |
| 188 | G | A | -1.7328 | |
| 189 | R | A | -1.5048 | |
| 190 | F | A | 0.0000 | |
| 191 | T | A | -0.8268 | |
| 192 | I | A | 0.0000 | |
| 193 | S | A | -0.4079 | |
| 194 | R | A | -0.9884 | |
| 195 | D | A | -1.6177 | |
| 196 | N | A | -1.7947 | |
| 197 | S | A | -1.5895 | |
| 198 | K | A | -2.3880 | |
| 199 | N | A | -1.7563 | |
| 200 | T | A | -1.0448 | |
| 201 | L | A | 0.0000 | |
| 202 | Y | A | -0.5658 | |
| 203 | L | A | 0.0000 | |
| 204 | Q | A | -1.2818 | |
| 205 | M | A | 0.0000 | |
| 206 | N | A | -1.5748 | |
| 207 | S | A | -1.3162 | |
| 208 | L | A | 0.0000 | |
| 209 | R | A | -2.2928 | |
| 210 | A | A | -1.7202 | |
| 211 | E | A | -2.2225 | |
| 212 | D | A | 0.0000 | |
| 213 | T | A | -0.4370 | |
| 214 | A | A | 0.0000 | |
| 215 | V | A | 0.6359 | |
| 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 | -1.5507 | |
| 224 | F | A | -1.2176 | |
| 225 | D | A | -1.8133 | |
| 226 | I | A | -0.4677 | |
| 227 | L | A | 0.2551 | |
| 228 | T | A | 0.2734 | |
| 229 | G | A | 0.0000 | |
| 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 | -0.9891 | |
| 236 | P | A | -1.0428 | |
| 237 | W | A | 0.0000 | |
| 238 | G | A | 0.0000 | |
| 239 | Q | A | -1.2292 | |
| 240 | G | A | 0.0000 | |
| 241 | T | A | 0.4455 | |
| 242 | L | A | 1.4091 | |
| 243 | V | A | 0.0000 | |
| 244 | T | A | 0.2117 | |
| 245 | V | A | 0.0000 | |
| 246 | S | A | -0.8118 | |
| 247 | S | A | -0.7102 | |
| 1 | A | B | -0.3670 | |
| 2 | Q | B | -1.0289 | |
| 3 | E | B | -2.0489 | |
| 4 | V | B | -1.4498 | |
| 5 | Q | B | -1.7096 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.8987 | |
| 8 | P | B | -0.8783 | |
| 9 | H | B | -0.8094 | |
| 10 | C | B | -0.6269 | |
| 11 | T | B | -0.6593 | |
| 12 | T | B | -0.2674 | |
| 13 | V | B | -0.3711 | |
| 14 | P | B | -1.1547 | |
| 15 | V | B | -0.8439 | |
| 16 | G | B | -0.8852 | |
| 17 | A | B | -0.4679 | |
| 18 | S | B | -0.7843 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -1.3919 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.9416 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.7732 | |
| 25 | T | B | -1.7538 | |
| 26 | S | B | -1.6247 | |
| 27 | G | B | -1.2684 | |
| 28 | G | B | -1.3886 | |
| 29 | L | B | -1.5021 | |
| 30 | R | B | -2.2494 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.1257 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.3294 | |
| 36 | Q | B | 0.0000 | |
| 37 | L | B | 0.3954 | |
| 38 | G | B | -0.5627 | |
| 39 | P | B | -0.8529 | |
| 40 | Q | B | -1.3444 | |
| 41 | P | B | -0.8481 | |
| 42 | Q | B | -0.9586 | |
| 43 | D | B | -1.0372 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.0766 | |
| 47 | Y | B | -0.3526 | |
| 48 | E | B | 0.0000 | |
| 49 | D | B | -1.8316 | |
| 50 | G | B | -1.2247 | |
| 51 | V | B | 0.0000 | |
| 52 | V | B | 0.0000 | |
| 53 | P | B | 0.0000 | |
| 54 | T | B | -0.0903 | |
| 55 | T | B | 0.0000 | |
| 56 | D | B | 0.0000 | |
| 57 | R | B | -1.6675 | |
| 58 | R | B | -1.3291 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | 0.0000 | |
| 61 | G | B | -0.9037 | |
| 62 | R | B | -0.9948 | |
| 63 | I | B | 0.0000 | |
| 64 | D | B | 0.0000 | |
| 65 | F | B | 0.0000 | |
| 66 | S | B | -0.7948 | |
| 67 | G | B | -1.3404 | |
| 68 | S | B | -1.5306 | |
| 69 | Q | B | -1.8712 | |
| 70 | D | B | -2.5063 | |
| 71 | N | B | -2.2753 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0099 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.6733 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -0.9663 | |
| 78 | R | B | -1.1926 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -0.9069 | |
| 81 | L | B | -0.0285 | |
| 82 | S | B | -0.1495 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | 0.0856 | |
| 85 | G | B | 0.2152 | |
| 86 | T | B | 0.2352 | |
| 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 | -0.3237 | |
| 93 | T | B | -0.9660 | |
| 94 | E | B | -1.3761 | |
| 95 | V | B | 0.4951 | |
| 96 | N | B | -0.3945 | |
| 97 | V | B | 0.0141 | |
| 98 | Y | B | 0.4465 | |
| 99 | G | B | -0.3017 | |
| 100 | S | B | -0.5167 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | L | B | 0.2803 | |
| 104 | V | B | 0.0000 | |
| 105 | L | B | 0.1722 | |
| 106 | V | B | 0.0000 | |
| 107 | T | B | -1.4529 | |
| 108 | E | B | -2.8743 | |
| 109 | E | B | -3.4601 | |
| 110 | Q | B | -2.9222 | |
| 111 | S | B | -2.3321 | |
| 112 | Q | B | -2.1847 | |
| 113 | G | B | -1.2382 | |
| 114 | W | B | -0.3593 | |
| 115 | H | B | -1.5828 | |
| 116 | R | B | -2.4487 | |
| 117 | C | B | -1.4385 | |
| 118 | S | B | -1.7742 | |
| 119 | D | B | -2.2289 | |
| 120 | A | B | -1.3997 | |
| 121 | P | B | -1.4467 | |
| 122 | P | B | -1.6107 | |
| 123 | R | B | -2.0742 | |
| 124 | A | B | -0.8043 | |
| 125 | S | B | -0.3440 | |
| 126 | A | B | 0.4082 | |
| 127 | L | B | 1.3686 | |
| 128 | P | B | 0.4013 | |
| 129 | A | B | 0.1509 | |
| 130 | P | B | -0.2471 | |
| 131 | P | B | -0.6144 | |
| 132 | T | B | -0.5154 | |
| 133 | G | B | -0.4883 | |
| 134 | S | B | -0.0492 | |
| 135 | A | B | 0.2797 | |
| 136 | L | B | 0.8637 | |
| 137 | P | B | -0.6120 | |
| 138 | D | B | -1.9856 | |
| 139 | P | B | -1.5249 | |
| 140 | Q | B | -1.8614 | |
| 141 | T | B | -0.9476 | |
| 142 | A | B | -0.1945 | |
| 143 | S | B | 0.0658 | |
| 144 | A | B | 0.2684 | |
| 145 | L | B | 0.8598 | |
| 146 | P | B | -0.5178 | |
| 147 | D | B | -1.6723 | |
| 148 | P | B | -1.0560 | |
| 149 | P | B | -1.1287 | |
| 150 | A | B | -0.6549 | |
| 151 | A | B | -0.0681 | |
| 152 | S | B | 0.2311 | |
| 153 | A | B | 0.6705 | |
| 154 | L | B | 1.4007 | |
| 155 | P | B | 0.4828 |
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 | -0.3366 | 3.8364 | View | CSV | PDB |
| 4.5 | -0.384 | 3.8364 | View | CSV | PDB |
| 5.0 | -0.4402 | 3.8364 | View | CSV | PDB |
| 5.5 | -0.4977 | 3.8364 | View | CSV | PDB |
| 6.0 | -0.5497 | 3.8364 | View | CSV | PDB |
| 6.5 | -0.5907 | 3.8364 | View | CSV | PDB |
| 7.0 | -0.6194 | 3.8364 | View | CSV | PDB |
| 7.5 | -0.6384 | 3.8364 | View | CSV | PDB |
| 8.0 | -0.6504 | 3.8364 | View | CSV | PDB |
| 8.5 | -0.6555 | 3.8364 | View | CSV | PDB |
| 9.0 | -0.6529 | 3.8364 | 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