| Chain sequence(s) |
A: EIVLTQSPATLSLSPGERATLSCRVSQNVSSNLAWYQQKPGQAPRLLIYDTSNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRRNWPLTFGGGTKVEIKGGGGSGGGGSGGGGSEVKLLESGGGLVQPGGSLRLSCAASGFTFSRYAMSWVRQAPGKGLEWVSSISASGATTYYADPVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDQDFDILTGYLNWFDPWGQGTLVTVSS
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. (00:00:06)
[INFO] FoldX: Starting FoldX energy minimization (00:00:06)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:11:15)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/6bf73f6f159b4a0/tmp/folded.pdb (00:11:15)
[INFO] Main: Simulation completed successfully. (00:17:02)
|
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 | -1.7902 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7038 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.6456 | |
| 6 | Q | A | -0.6856 | |
| 7 | S | A | -0.7734 | |
| 8 | P | A | -0.3619 | |
| 9 | A | A | -0.3741 | |
| 10 | T | A | -0.4522 | |
| 11 | L | A | -0.2653 | |
| 12 | S | A | -0.6624 | |
| 13 | L | A | -0.9718 | |
| 14 | S | A | -1.2950 | |
| 15 | P | A | -1.5572 | |
| 16 | G | A | -1.7637 | |
| 17 | E | A | -2.3523 | |
| 18 | R | A | -2.6582 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.6618 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.9758 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.4754 | |
| 25 | V | A | 0.0000 | |
| 26 | S | A | -1.2465 | |
| 27 | Q | A | -2.2990 | |
| 28 | N | A | -2.4681 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -1.2191 | |
| 31 | S | A | -0.8362 | |
| 32 | N | A | -0.8868 | |
| 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 | -1.2804 | |
| 40 | P | A | -0.9012 | |
| 41 | G | A | -1.2002 | |
| 42 | Q | A | -1.6334 | |
| 43 | A | A | -1.2353 | |
| 44 | P | A | 0.0000 | |
| 45 | R | A | -1.4943 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | -0.5495 | |
| 50 | D | A | -0.8604 | |
| 51 | T | A | 0.0000 | |
| 52 | S | A | -1.0480 | |
| 53 | N | A | -1.3601 | |
| 54 | R | A | -1.5945 | |
| 55 | A | A | 0.0000 | |
| 56 | T | A | -0.6081 | |
| 57 | G | A | -0.7436 | |
| 58 | I | A | 0.0000 | |
| 59 | P | A | -0.4644 | |
| 60 | A | A | -0.3880 | |
| 61 | R | A | -0.6979 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.6676 | |
| 64 | G | A | 0.0000 | |
| 65 | S | A | -0.7786 | |
| 66 | G | A | -1.0758 | |
| 67 | S | A | -1.0953 | |
| 68 | G | A | 0.0000 | |
| 69 | T | A | -2.0973 | |
| 70 | D | A | -2.4008 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.8131 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.5952 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.3376 | |
| 77 | S | A | -1.7009 | |
| 78 | L | A | 0.0000 | |
| 79 | E | A | -2.0791 | |
| 80 | P | A | -1.5368 | |
| 81 | E | A | -2.2795 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | -0.5901 | |
| 84 | A | A | 0.0000 | |
| 85 | V | A | -0.2523 | |
| 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 | -1.1407 | |
| 93 | N | A | -1.1950 | |
| 94 | W | A | -0.8533 | |
| 95 | P | A | -0.9009 | |
| 96 | L | A | 0.0000 | |
| 97 | T | A | 0.0000 | |
| 98 | F | A | 0.1836 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -0.7721 | |
| 101 | G | A | -0.7292 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -0.9078 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | -0.7714 | |
| 106 | I | A | -0.4768 | |
| 107 | K | A | -1.7110 | |
| 108 | G | A | -1.4543 | |
| 109 | G | A | -1.3069 | |
| 110 | G | A | -1.1934 | |
| 111 | G | A | -1.0844 | |
| 112 | S | A | -1.0789 | |
| 113 | G | A | -1.2319 | |
| 114 | G | A | -1.5045 | |
| 115 | G | A | -1.4531 | |
| 116 | G | A | -1.6252 | |
| 117 | S | A | -1.0831 | |
| 118 | G | A | -1.4141 | |
| 119 | G | A | -1.2308 | |
| 120 | G | A | -1.4392 | |
| 121 | G | A | -1.6527 | |
| 122 | S | A | -1.7907 | |
| 123 | E | A | -2.4858 | |
| 124 | V | A | -1.7047 | |
| 125 | K | A | -1.9193 | |
| 126 | L | A | 0.0000 | |
| 127 | L | A | 0.1131 | |
| 128 | E | A | 0.0000 | |
| 129 | S | A | -0.4254 | |
| 130 | G | A | -0.8052 | |
| 131 | G | A | 0.0952 | |
| 132 | G | A | 0.6132 | |
| 133 | L | A | 1.3421 | |
| 134 | V | A | 0.0000 | |
| 135 | Q | A | -1.3990 | |
| 136 | P | A | -1.5832 | |
| 137 | G | A | -1.4119 | |
| 138 | G | A | -0.9971 | |
| 139 | S | A | -1.3457 | |
| 140 | L | A | -0.9688 | |
| 141 | R | A | -2.1696 | |
| 142 | L | A | 0.0000 | |
| 143 | S | A | -0.5499 | |
| 144 | C | A | 0.0000 | |
| 145 | A | A | -0.4356 | |
| 146 | A | A | 0.0000 | |
| 147 | S | A | -1.0272 | |
| 148 | G | A | -1.3434 | |
| 149 | F | A | -0.8515 | |
| 150 | T | A | -0.6066 | |
| 151 | F | A | 0.0000 | |
| 152 | S | A | -1.4000 | |
| 153 | R | A | -1.7174 | |
| 154 | Y | A | -0.8254 | |
| 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 | -0.6302 | |
| 162 | A | A | -1.0190 | |
| 163 | P | A | -0.8219 | |
| 164 | G | A | -1.4472 | |
| 165 | K | A | -2.2684 | |
| 166 | G | A | -1.3639 | |
| 167 | L | A | 0.0000 | |
| 168 | E | A | -0.9346 | |
| 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 | -0.6844 | |
| 177 | G | A | -0.3476 | |
| 178 | A | A | -0.1101 | |
| 179 | T | A | 0.0000 | |
| 180 | T | A | 0.0478 | |
| 181 | Y | A | -0.1432 | |
| 182 | Y | A | -0.8261 | |
| 183 | A | A | 0.0000 | |
| 184 | D | A | -2.7160 | |
| 185 | P | A | -1.8806 | |
| 186 | V | A | 0.0000 | |
| 187 | K | A | -2.6505 | |
| 188 | G | A | -1.8180 | |
| 189 | R | A | -1.6453 | |
| 190 | F | A | 0.0000 | |
| 191 | T | A | -0.8750 | |
| 192 | I | A | 0.0000 | |
| 193 | S | A | -0.3770 | |
| 194 | R | A | -0.9049 | |
| 195 | D | A | -1.4381 | |
| 196 | N | A | -1.7628 | |
| 197 | S | A | -1.5324 | |
| 198 | K | A | -2.3289 | |
| 199 | N | A | -1.6931 | |
| 200 | T | A | -1.0450 | |
| 201 | L | A | 0.0000 | |
| 202 | Y | A | -0.5601 | |
| 203 | L | A | 0.0000 | |
| 204 | Q | A | -1.3078 | |
| 205 | M | A | 0.0000 | |
| 206 | N | A | -1.5907 | |
| 207 | S | A | -1.2758 | |
| 208 | L | A | 0.0000 | |
| 209 | R | A | -2.2652 | |
| 210 | A | A | -1.7014 | |
| 211 | E | A | -2.2334 | |
| 212 | D | A | 0.0000 | |
| 213 | T | A | -0.3703 | |
| 214 | A | A | 0.0000 | |
| 215 | V | A | 0.7443 | |
| 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 | -1.1140 | |
| 224 | F | A | -1.2584 | |
| 225 | D | A | -1.7329 | |
| 226 | I | A | -0.3554 | |
| 227 | L | A | -0.4305 | |
| 228 | T | A | -0.8785 | |
| 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 | -0.9454 | |
| 236 | P | A | -1.0635 | |
| 237 | W | A | 0.0000 | |
| 238 | G | A | 0.0000 | |
| 239 | Q | A | -1.4154 | |
| 240 | G | A | -0.1963 | |
| 241 | T | A | 0.4715 | |
| 242 | L | A | 1.6760 | |
| 243 | V | A | 0.0000 | |
| 244 | T | A | 0.3217 | |
| 245 | V | A | 0.0000 | |
| 246 | S | A | -0.7492 | |
| 247 | S | A | -0.6871 | |
| 1 | A | B | -1.7983 | |
| 2 | Q | B | -2.0395 | |
| 3 | E | B | -2.5826 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -1.7886 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.9718 | |
| 8 | P | B | -0.9276 | |
| 9 | H | B | -0.6956 | |
| 10 | C | B | -0.3656 | |
| 11 | T | B | -0.5268 | |
| 12 | T | B | -0.0367 | |
| 13 | V | B | -0.2101 | |
| 14 | P | B | -0.9770 | |
| 15 | V | B | -0.6207 | |
| 16 | G | B | -0.7692 | |
| 17 | A | B | -0.4103 | |
| 18 | S | B | -0.7525 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -1.3944 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.9747 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.8028 | |
| 25 | T | B | -1.9280 | |
| 26 | S | B | -1.9651 | |
| 27 | G | B | -1.5463 | |
| 28 | G | B | -1.5801 | |
| 29 | L | B | -1.9410 | |
| 30 | R | B | -2.4044 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.1361 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.5340 | |
| 36 | Q | B | 0.0000 | |
| 37 | L | B | 0.1700 | |
| 38 | G | B | -0.4894 | |
| 39 | P | B | -0.7785 | |
| 40 | Q | B | -1.3230 | |
| 41 | P | B | -0.9363 | |
| 42 | Q | B | -1.0899 | |
| 43 | D | B | -1.2607 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | -0.0013 | |
| 47 | Y | B | -0.4636 | |
| 48 | E | B | -1.4396 | |
| 49 | D | B | -1.9819 | |
| 50 | G | B | -1.2975 | |
| 51 | V | B | -0.6952 | |
| 52 | V | B | 0.0000 | |
| 53 | P | B | 0.0000 | |
| 54 | T | B | -0.3708 | |
| 55 | T | B | 0.0000 | |
| 56 | D | B | -1.5910 | |
| 57 | R | B | -2.4334 | |
| 58 | R | B | -1.5470 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | 0.0000 | |
| 61 | G | B | -1.1217 | |
| 62 | R | B | -1.0757 | |
| 63 | I | B | 0.0000 | |
| 64 | D | B | 0.0000 | |
| 65 | F | B | 0.0000 | |
| 66 | S | B | -0.7956 | |
| 67 | G | B | -1.3494 | |
| 68 | S | B | -1.5849 | |
| 69 | Q | B | -1.9072 | |
| 70 | D | B | -2.4718 | |
| 71 | N | B | -2.2578 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0079 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.6731 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -0.9180 | |
| 78 | R | B | -1.0869 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -0.7038 | |
| 81 | L | B | 0.2918 | |
| 82 | S | B | 0.0322 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | 0.2520 | |
| 85 | G | B | 0.0000 | |
| 86 | T | B | 0.3400 | |
| 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 | -0.5102 | |
| 93 | T | B | -1.2194 | |
| 94 | E | B | -1.4270 | |
| 95 | V | B | 0.4074 | |
| 96 | N | B | -0.3671 | |
| 97 | V | B | -0.1023 | |
| 98 | Y | B | 0.5535 | |
| 99 | G | B | -0.2645 | |
| 100 | S | B | -0.2815 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | L | B | 0.6414 | |
| 104 | V | B | 0.0000 | |
| 105 | L | B | 0.6668 | |
| 106 | V | B | 0.0000 | |
| 107 | T | B | -1.2605 | |
| 108 | E | B | -2.7618 | |
| 109 | E | B | -3.4226 | |
| 110 | Q | B | -2.8159 | |
| 111 | S | B | -2.4304 | |
| 112 | Q | B | -2.0870 | |
| 113 | G | B | -1.8501 | |
| 114 | W | B | -1.6650 | |
| 115 | H | B | -1.9501 | |
| 116 | R | B | -2.5226 | |
| 117 | C | B | -1.4762 | |
| 118 | S | B | -1.8087 | |
| 119 | D | B | -2.2739 | |
| 120 | A | B | -1.4476 | |
| 121 | P | B | -1.4604 | |
| 122 | P | B | -1.6021 | |
| 123 | R | B | -2.0498 | |
| 124 | A | B | -0.7793 | |
| 125 | S | B | -0.3871 | |
| 126 | A | B | 0.3213 | |
| 127 | L | B | 1.3694 | |
| 128 | P | B | 0.3921 | |
| 129 | A | B | 0.1728 | |
| 130 | P | B | -0.2510 | |
| 131 | P | B | -0.6230 | |
| 132 | T | B | -0.5365 | |
| 133 | G | B | -0.4475 | |
| 134 | S | B | -0.0730 | |
| 135 | A | B | 0.2016 | |
| 136 | L | B | 0.7906 | |
| 137 | P | B | -0.6702 | |
| 138 | D | B | -1.9704 | |
| 139 | P | B | -1.5283 | |
| 140 | Q | B | -1.9307 | |
| 141 | T | B | -1.0200 | |
| 142 | A | B | -0.2096 | |
| 143 | S | B | 0.0341 | |
| 144 | A | B | 0.3655 | |
| 145 | L | B | 0.9056 | |
| 146 | P | B | -0.5002 | |
| 147 | D | B | -1.6928 | |
| 148 | P | B | -1.0473 | |
| 149 | P | B | -0.8847 | |
| 150 | A | B | -0.4458 | |
| 151 | A | B | 0.1131 | |
| 152 | S | B | 0.2396 | |
| 153 | A | B | 0.6668 | |
| 154 | L | B | 1.3999 | |
| 155 | P | B | 0.4790 |
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 | -0.3771 | 3.8901 | View | CSV | PDB |
| 4.5 | -0.4224 | 3.8901 | View | CSV | PDB |
| 5.0 | -0.4766 | 3.8901 | View | CSV | PDB |
| 5.5 | -0.5323 | 3.8901 | View | CSV | PDB |
| 6.0 | -0.5822 | 3.8901 | View | CSV | PDB |
| 6.5 | -0.6203 | 3.8901 | View | CSV | PDB |
| 7.0 | -0.6451 | 3.8901 | View | CSV | PDB |
| 7.5 | -0.6599 | 3.8901 | View | CSV | PDB |
| 8.0 | -0.6678 | 3.8901 | View | CSV | PDB |
| 8.5 | -0.6692 | 3.8901 | View | CSV | PDB |
| 9.0 | -0.6631 | 3.8901 | 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