| Chain sequence(s) |
A: EIVLTQSPATLSLSPGERVILSCRVNQSVSSYLAWYQQKPGQAPRLLIYNTSNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCNQRRNWPLTFGGGTKVEIKGGGGSGGGGSGGGGSEVQLVESGGGLVQPGGSLRLSCAASGFTFSRYSMSWVRQAPGKGLEWVSSTSASGATTFYADPVKGRFTISRDNSKKTLYLQMNSLRAEDTAVYYCAKDQDFDILTGYLNWFDPWGQGTLVTVSS
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] (00:00:01)
[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. (00:00:02)
[INFO] FoldX: Starting FoldX energy minimization (00:00:03)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:04:42)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/fdd68894f96166/tmp/folded.pdb (00:04:42)
[INFO] Main: Simulation completed successfully. (00:07:45)
|
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 | -1.7495 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.1877 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.7836 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.4788 | |
| 8 | P | A | -0.0812 | |
| 9 | A | A | -0.2758 | |
| 10 | T | A | -0.4067 | |
| 11 | L | A | -0.2748 | |
| 12 | S | A | -0.9210 | |
| 13 | L | A | -1.2355 | |
| 14 | S | A | -1.7118 | |
| 15 | P | A | -1.8205 | |
| 16 | G | A | -1.8082 | |
| 17 | E | A | -2.1957 | |
| 18 | R | A | -2.2952 | |
| 19 | V | A | 0.0000 | |
| 20 | I | A | 0.9863 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.5500 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.6092 | |
| 25 | V | A | 0.0000 | |
| 26 | N | A | -2.0746 | |
| 27 | Q | A | -2.1942 | |
| 28 | S | A | -1.5371 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.6297 | |
| 31 | S | A | -0.3335 | |
| 32 | Y | A | 0.0417 | |
| 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 | -1.3537 | |
| 40 | P | A | -0.9739 | |
| 41 | G | A | -1.4456 | |
| 42 | Q | A | -2.0821 | |
| 43 | A | A | -1.4040 | |
| 44 | P | A | 0.0000 | |
| 45 | R | A | -1.5325 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | -0.2496 | |
| 50 | N | A | -0.2592 | |
| 51 | T | A | 0.0000 | |
| 52 | S | A | -0.9240 | |
| 53 | N | A | -1.0910 | |
| 54 | R | A | -1.3427 | |
| 55 | A | A | -1.0099 | |
| 56 | T | A | -0.5854 | |
| 57 | G | A | -0.7223 | |
| 58 | I | A | 0.0000 | |
| 59 | P | A | -0.4156 | |
| 60 | A | A | -0.3391 | |
| 61 | R | A | -0.6736 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.4524 | |
| 64 | G | A | 0.0000 | |
| 65 | S | A | -0.7573 | |
| 66 | G | A | -1.0993 | |
| 67 | S | A | -1.0215 | |
| 68 | G | A | -1.2302 | |
| 69 | T | A | -1.9646 | |
| 70 | D | A | -2.3692 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.4244 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | 0.0638 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.0816 | |
| 77 | S | A | -1.7127 | |
| 78 | L | A | 0.0000 | |
| 79 | E | A | -2.0862 | |
| 80 | P | A | -2.0287 | |
| 81 | E | A | -2.3238 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | -0.6246 | |
| 84 | A | A | 0.0000 | |
| 85 | V | A | -0.2047 | |
| 86 | Y | A | 0.0000 | |
| 87 | Y | A | 0.0000 | |
| 88 | C | A | 0.0000 | |
| 89 | N | A | 0.0000 | |
| 90 | Q | A | 0.0000 | |
| 91 | R | A | 0.0000 | |
| 92 | R | A | -0.5164 | |
| 93 | N | A | -0.9992 | |
| 94 | W | A | -0.6846 | |
| 95 | P | A | -0.7098 | |
| 96 | L | A | 0.0000 | |
| 97 | T | A | -0.1455 | |
| 98 | F | A | 0.1544 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -0.7334 | |
| 101 | G | A | -0.6419 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -0.7428 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | -1.2954 | |
| 106 | I | A | -1.7742 | |
| 107 | K | A | -2.2925 | |
| 108 | G | A | -1.7912 | |
| 109 | G | A | -1.7689 | |
| 110 | G | A | -1.3887 | |
| 111 | G | A | -1.4288 | |
| 112 | S | A | -1.2880 | |
| 113 | G | A | -1.6543 | |
| 114 | G | A | -1.6379 | |
| 115 | G | A | -1.7357 | |
| 116 | G | A | -1.6110 | |
| 117 | S | A | -1.1181 | |
| 118 | G | A | -1.2701 | |
| 119 | G | A | -1.2426 | |
| 120 | G | A | -1.5099 | |
| 121 | G | A | -1.6654 | |
| 122 | S | A | -1.7643 | |
| 123 | E | A | -2.3941 | |
| 124 | V | A | -1.5259 | |
| 125 | Q | A | -1.6722 | |
| 126 | L | A | 0.0000 | |
| 127 | V | A | 0.0748 | |
| 128 | E | A | 0.0000 | |
| 129 | S | A | -0.4290 | |
| 130 | G | A | -0.8013 | |
| 131 | G | A | 0.0653 | |
| 132 | G | A | 0.5822 | |
| 133 | L | A | 1.3095 | |
| 134 | V | A | 0.0000 | |
| 135 | Q | A | -1.5257 | |
| 136 | P | A | -1.8759 | |
| 137 | G | A | -1.6170 | |
| 138 | G | A | -1.1136 | |
| 139 | S | A | -1.4386 | |
| 140 | L | A | -1.1331 | |
| 141 | R | A | -2.2566 | |
| 142 | L | A | 0.0000 | |
| 143 | S | A | -0.5951 | |
| 144 | C | A | 0.0000 | |
| 145 | A | A | -0.4985 | |
| 146 | A | A | 0.0000 | |
| 147 | S | A | -0.9393 | |
| 148 | G | A | -1.1687 | |
| 149 | F | A | -0.7170 | |
| 150 | T | A | -0.6559 | |
| 151 | F | A | 0.0000 | |
| 152 | S | A | -1.5587 | |
| 153 | R | A | -2.0101 | |
| 154 | Y | A | -0.9046 | |
| 155 | S | 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 | -0.6325 | |
| 162 | A | A | -1.0542 | |
| 163 | P | A | -0.8420 | |
| 164 | G | A | -1.4517 | |
| 165 | K | A | -2.2655 | |
| 166 | G | A | -1.3640 | |
| 167 | L | A | 0.0000 | |
| 168 | E | A | -0.9202 | |
| 169 | W | A | 0.0000 | |
| 170 | V | A | 0.0000 | |
| 171 | S | A | 0.0000 | |
| 172 | S | A | 0.0000 | |
| 173 | T | A | 0.0000 | |
| 174 | S | A | -0.3632 | |
| 175 | A | A | 0.0000 | |
| 176 | S | A | -0.7203 | |
| 177 | G | A | -0.3398 | |
| 178 | A | A | -0.0769 | |
| 179 | T | A | 0.0494 | |
| 180 | T | A | 0.1973 | |
| 181 | F | A | 0.1604 | |
| 182 | Y | A | -0.6262 | |
| 183 | A | A | 0.0000 | |
| 184 | D | A | -2.4063 | |
| 185 | P | A | -1.8286 | |
| 186 | V | A | 0.0000 | |
| 187 | K | A | -2.5617 | |
| 188 | G | A | -1.7772 | |
| 189 | R | A | -1.4460 | |
| 190 | F | A | 0.0000 | |
| 191 | T | A | -0.8900 | |
| 192 | I | A | 0.0000 | |
| 193 | S | A | -0.4246 | |
| 194 | R | A | -0.9734 | |
| 195 | D | A | -1.5447 | |
| 196 | N | A | -1.9302 | |
| 197 | S | A | -1.6487 | |
| 198 | K | A | -2.4862 | |
| 199 | K | A | -2.0216 | |
| 200 | T | A | -1.2015 | |
| 201 | L | A | 0.0000 | |
| 202 | Y | A | -0.6295 | |
| 203 | L | A | 0.0000 | |
| 204 | Q | A | -1.5562 | |
| 205 | M | A | 0.0000 | |
| 206 | N | A | -1.6158 | |
| 207 | S | A | -1.4473 | |
| 208 | L | A | 0.0000 | |
| 209 | R | A | -2.9539 | |
| 210 | A | A | -2.0513 | |
| 211 | E | A | -2.4652 | |
| 212 | D | A | 0.0000 | |
| 213 | T | A | -0.5331 | |
| 214 | A | A | 0.0000 | |
| 215 | V | A | 0.7227 | |
| 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 | -0.6229 | |
| 223 | D | A | -0.6744 | |
| 224 | F | A | 0.0000 | |
| 225 | D | A | 0.0000 | |
| 226 | I | A | 0.9509 | |
| 227 | L | A | 0.6985 | |
| 228 | T | A | 0.5736 | |
| 229 | G | A | 0.6757 | |
| 230 | Y | A | 0.9918 | |
| 231 | L | A | 0.0000 | |
| 232 | N | A | -0.2177 | |
| 233 | W | A | 0.0000 | |
| 234 | F | A | 0.0000 | |
| 235 | D | A | -1.1033 | |
| 236 | P | A | -1.0767 | |
| 237 | W | A | 0.0000 | |
| 238 | G | A | 0.0000 | |
| 239 | Q | A | -1.3313 | |
| 240 | G | A | 0.0000 | |
| 241 | T | A | 0.4256 | |
| 242 | L | A | 1.4373 | |
| 243 | V | A | 0.0000 | |
| 244 | T | A | 0.1691 | |
| 245 | V | A | 0.0000 | |
| 246 | S | A | -0.9131 | |
| 247 | S | A | -0.5837 | |
| 1 | A | B | -1.8783 | |
| 2 | Q | B | -2.2048 | |
| 3 | E | B | -2.7187 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -1.8304 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.9298 | |
| 8 | P | B | -0.8980 | |
| 9 | H | B | -0.9671 | |
| 10 | C | B | -0.6107 | |
| 11 | T | B | -0.6616 | |
| 12 | T | B | -0.1596 | |
| 13 | V | B | -0.2462 | |
| 14 | P | B | -0.9841 | |
| 15 | V | B | -0.5193 | |
| 16 | G | B | -1.0492 | |
| 17 | A | B | -0.5945 | |
| 18 | S | B | -0.9989 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -1.3686 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -1.1363 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -2.0101 | |
| 25 | T | B | -2.2199 | |
| 26 | S | B | -2.0385 | |
| 27 | G | B | -1.5692 | |
| 28 | G | B | -1.6599 | |
| 29 | L | B | -1.9501 | |
| 30 | R | B | -2.6145 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.2685 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.1477 | |
| 36 | Q | B | 0.0000 | |
| 37 | L | B | 0.4440 | |
| 38 | G | B | -0.5611 | |
| 39 | P | B | -0.8499 | |
| 40 | Q | B | -1.3434 | |
| 41 | P | B | -0.7689 | |
| 42 | Q | B | -0.7381 | |
| 43 | D | B | -0.2491 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.3040 | |
| 47 | Y | B | -0.5208 | |
| 48 | E | B | -1.6448 | |
| 49 | D | B | -2.3785 | |
| 50 | G | B | -1.3519 | |
| 51 | V | B | -0.6776 | |
| 52 | V | B | -0.2816 | |
| 53 | P | B | -0.1535 | |
| 54 | T | B | 0.0000 | |
| 55 | T | B | 0.0000 | |
| 56 | D | B | 0.0000 | |
| 57 | R | B | -1.5470 | |
| 58 | R | B | -1.4270 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -1.5188 | |
| 61 | G | B | -1.5887 | |
| 62 | R | B | -1.5447 | |
| 63 | I | B | 0.0000 | |
| 64 | D | B | 0.0000 | |
| 65 | F | B | -0.1640 | |
| 66 | S | B | -0.7233 | |
| 67 | G | B | -1.2975 | |
| 68 | S | B | -1.7627 | |
| 69 | Q | B | -2.2921 | |
| 70 | D | B | -2.8562 | |
| 71 | N | B | -2.5665 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0513 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.6231 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.4773 | |
| 78 | R | B | -2.0908 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -0.7501 | |
| 81 | L | B | 0.5403 | |
| 82 | S | B | 0.0722 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | 0.2786 | |
| 85 | G | B | 0.3079 | |
| 86 | T | B | 0.2543 | |
| 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 | -0.4894 | |
| 93 | T | B | -1.2245 | |
| 94 | E | B | -1.5662 | |
| 95 | V | B | 0.3698 | |
| 96 | N | B | -0.6589 | |
| 97 | V | B | -0.1818 | |
| 98 | Y | B | 0.4904 | |
| 99 | G | B | -0.3026 | |
| 100 | S | B | -0.3265 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | L | B | 0.3125 | |
| 104 | V | B | 0.0000 | |
| 105 | L | B | 0.4484 | |
| 106 | V | B | 0.0000 | |
| 107 | T | B | -1.1161 | |
| 108 | E | B | -2.6917 | |
| 109 | E | B | -3.2868 | |
| 110 | Q | B | -3.0020 | |
| 111 | S | B | -2.4554 | |
| 112 | Q | B | -2.3982 | |
| 113 | G | B | -1.9058 | |
| 114 | W | B | -1.9515 | |
| 115 | H | B | -2.0466 | |
| 116 | R | B | -2.4995 | |
| 117 | C | B | -1.5198 | |
| 118 | S | B | -1.7078 | |
| 119 | D | B | -2.1006 | |
| 120 | A | B | -1.4009 | |
| 121 | P | B | -1.4470 | |
| 122 | P | B | -1.6171 | |
| 123 | R | B | -2.0590 | |
| 124 | A | B | -0.7646 | |
| 125 | S | B | -0.3674 | |
| 126 | A | B | 0.3460 | |
| 127 | L | B | 1.3694 | |
| 128 | P | B | 0.3939 | |
| 129 | A | B | 0.1727 | |
| 130 | P | B | -0.2463 | |
| 131 | P | B | -0.6185 | |
| 132 | T | B | -0.5314 | |
| 133 | G | B | -0.4459 | |
| 134 | S | B | -0.0799 | |
| 135 | A | B | 0.2270 | |
| 136 | L | B | 0.8159 | |
| 137 | P | B | -0.6529 | |
| 138 | D | B | -1.9848 | |
| 139 | P | B | -1.5303 | |
| 140 | Q | B | -1.9191 | |
| 141 | T | B | -0.9961 | |
| 142 | A | B | -0.2038 | |
| 143 | S | B | 0.0324 | |
| 144 | A | B | 0.3790 | |
| 145 | L | B | 0.9235 | |
| 146 | P | B | -0.4946 | |
| 147 | D | B | -1.7040 | |
| 148 | P | B | -1.0551 | |
| 149 | P | B | -0.8794 | |
| 150 | A | B | -0.4297 | |
| 151 | A | B | 0.1181 | |
| 152 | S | B | 0.2193 | |
| 153 | A | B | 0.6665 | |
| 154 | L | B | 1.4026 | |
| 155 | P | B | 0.4795 |
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 | -0.3909 | 3.8783 | View | CSV | PDB |
| 4.5 | -0.4339 | 3.8783 | View | CSV | PDB |
| 5.0 | -0.4857 | 3.8783 | View | CSV | PDB |
| 5.5 | -0.5387 | 3.8783 | View | CSV | PDB |
| 6.0 | -0.5855 | 3.8783 | View | CSV | PDB |
| 6.5 | -0.6206 | 3.8783 | View | CSV | PDB |
| 7.0 | -0.6433 | 3.8783 | View | CSV | PDB |
| 7.5 | -0.6569 | 3.8783 | View | CSV | PDB |
| 8.0 | -0.6645 | 3.8783 | View | CSV | PDB |
| 8.5 | -0.6664 | 3.8783 | View | CSV | PDB |
| 9.0 | -0.6616 | 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