| Chain sequence(s) |
A: DIVMTQTPLSLPVTPGEPASISCRSSQSLVHSNGNTYLEWYLQKPGQSPQLLIYKLSYRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFKGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
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] (00:00:00)
[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 (00:04:10)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/816d39a45639353/tmp/folded.pdb (00:04:10)
[INFO] Main: Simulation completed successfully. (00:07:18)
|
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 | D | A | -1.3489 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7420 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.2530 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | -0.0542 | |
| 8 | P | A | 0.3814 | |
| 9 | L | A | 1.1703 | |
| 10 | S | A | 0.0120 | |
| 11 | L | A | -0.3526 | |
| 12 | P | A | -1.2451 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.6076 | |
| 15 | P | A | -1.9543 | |
| 16 | G | A | -1.7936 | |
| 17 | E | A | -2.0443 | |
| 18 | P | A | -2.0736 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.8712 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.9067 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.1970 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -0.9908 | |
| 27 | Q | A | -1.5444 | |
| 28 | S | A | -0.8918 | |
| 29 | L | A | 0.0000 | |
| 30 | V | A | 0.3050 | |
| 31 | H | A | -0.3829 | |
| 32 | S | A | -0.6982 | |
| 33 | N | A | -1.3140 | |
| 34 | G | A | -0.8830 | |
| 35 | N | A | -0.5836 | |
| 36 | T | A | -0.1162 | |
| 37 | Y | A | 0.0000 | |
| 38 | L | A | 0.0000 | |
| 39 | E | A | 0.0000 | |
| 40 | W | A | 0.0000 | |
| 41 | Y | A | 0.0000 | |
| 42 | L | A | 0.0000 | |
| 43 | Q | A | -0.9009 | |
| 44 | K | A | -1.5520 | |
| 45 | P | A | -1.1874 | |
| 46 | G | A | -1.4785 | |
| 47 | Q | A | -2.1221 | |
| 48 | S | A | -1.3167 | |
| 49 | P | A | 0.0000 | |
| 50 | Q | A | -1.1446 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | 0.3813 | |
| 55 | K | A | 0.0611 | |
| 56 | L | A | -0.0059 | |
| 57 | S | A | 0.1163 | |
| 58 | Y | A | 0.8049 | |
| 59 | R | A | -0.7363 | |
| 60 | F | A | -0.1184 | |
| 61 | S | A | -0.4170 | |
| 62 | G | A | -1.0021 | |
| 63 | V | A | 0.0000 | |
| 64 | P | A | -1.3302 | |
| 65 | D | A | -2.4351 | |
| 66 | R | A | -2.1644 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.2664 | |
| 69 | G | A | -0.6316 | |
| 70 | S | A | -0.7341 | |
| 71 | G | A | -1.0591 | |
| 72 | S | A | -0.7582 | |
| 73 | G | A | -0.7295 | |
| 74 | T | A | -1.5014 | |
| 75 | D | A | -2.1932 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -1.1721 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -2.1119 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.3505 | |
| 82 | R | A | -3.2258 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.5628 | |
| 85 | A | A | -1.8243 | |
| 86 | E | A | -2.5559 | |
| 87 | D | A | 0.0000 | |
| 88 | V | A | -1.2019 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | -0.1789 | |
| 91 | Y | A | 0.0000 | |
| 92 | Y | A | 0.0000 | |
| 93 | C | A | 0.0000 | |
| 94 | F | A | 0.0000 | |
| 95 | Q | A | 0.0000 | |
| 96 | G | A | 0.0000 | |
| 97 | S | A | 0.0000 | |
| 98 | H | A | -0.8673 | |
| 99 | V | A | -0.5068 | |
| 100 | P | A | -0.4914 | |
| 101 | F | A | 0.0000 | |
| 102 | T | A | 0.0286 | |
| 103 | F | A | 0.3133 | |
| 104 | G | A | 0.0000 | |
| 105 | S | A | -0.0533 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.7575 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -1.8603 | |
| 111 | I | A | -1.8664 | |
| 112 | K | A | -2.3024 | |
| 113 | G | A | -1.7198 | |
| 114 | G | A | -1.6461 | |
| 115 | G | A | -1.4181 | |
| 116 | G | A | -1.6819 | |
| 117 | S | A | -1.2641 | |
| 118 | G | A | -1.5705 | |
| 119 | G | A | -1.6366 | |
| 120 | G | A | -1.7113 | |
| 121 | G | A | -1.7756 | |
| 122 | S | A | -1.0697 | |
| 123 | G | A | -1.4248 | |
| 124 | G | A | -1.3272 | |
| 125 | G | A | -1.2025 | |
| 126 | G | A | -1.0509 | |
| 127 | S | A | -0.8795 | |
| 128 | V | A | -0.8023 | |
| 129 | Q | A | -1.5183 | |
| 130 | L | A | 0.0000 | |
| 131 | V | A | -0.5403 | |
| 132 | Q | A | 0.0000 | |
| 133 | S | A | -0.7928 | |
| 134 | G | A | -0.7181 | |
| 135 | A | A | -0.0941 | |
| 136 | E | A | -0.2527 | |
| 137 | V | A | 0.8080 | |
| 138 | K | A | -1.0285 | |
| 139 | K | A | -2.2152 | |
| 140 | P | A | -2.3085 | |
| 141 | G | A | -1.6246 | |
| 142 | A | A | -1.2730 | |
| 143 | S | A | -1.3934 | |
| 144 | V | A | 0.0000 | |
| 145 | K | A | -2.0830 | |
| 146 | V | A | 0.0000 | |
| 147 | S | A | -0.8172 | |
| 148 | C | A | 0.0000 | |
| 149 | K | A | -1.3642 | |
| 150 | A | A | 0.0000 | |
| 151 | S | A | -0.8681 | |
| 152 | G | A | -0.7698 | |
| 153 | Y | A | -0.2343 | |
| 154 | T | A | -0.0862 | |
| 155 | F | A | 0.0000 | |
| 156 | T | A | 0.0711 | |
| 157 | D | A | 0.0000 | |
| 158 | Y | A | 0.0000 | |
| 159 | I | A | 0.0000 | |
| 160 | M | A | 0.0000 | |
| 161 | L | A | 0.0000 | |
| 162 | W | A | 0.0000 | |
| 163 | V | A | 0.0000 | |
| 164 | R | A | -0.4044 | |
| 165 | Q | A | -0.6599 | |
| 166 | A | A | -1.0473 | |
| 167 | P | A | -1.0431 | |
| 168 | G | A | -1.2115 | |
| 169 | Q | A | -1.6962 | |
| 170 | G | A | -0.9894 | |
| 171 | L | A | 0.0000 | |
| 172 | E | A | -0.5952 | |
| 173 | W | A | 0.0000 | |
| 174 | M | A | 0.0000 | |
| 175 | G | A | 0.0000 | |
| 176 | N | A | 0.0000 | |
| 177 | I | A | 0.0000 | |
| 178 | D | A | 0.0000 | |
| 179 | P | A | 0.0000 | |
| 180 | Y | A | 0.3340 | |
| 181 | Y | A | 0.5208 | |
| 182 | G | A | 0.0131 | |
| 183 | S | A | 0.0000 | |
| 184 | T | A | -0.3406 | |
| 185 | G | A | 0.0000 | |
| 186 | Y | A | -0.3438 | |
| 187 | A | A | 0.0000 | |
| 188 | L | A | -0.0167 | |
| 189 | K | A | -1.4500 | |
| 190 | F | A | 0.0000 | |
| 191 | K | A | -1.6205 | |
| 192 | G | A | -1.3600 | |
| 193 | R | A | -1.3409 | |
| 194 | V | A | 0.0000 | |
| 195 | T | A | -0.8564 | |
| 196 | M | A | 0.0000 | |
| 197 | T | A | -0.5941 | |
| 198 | R | A | -1.0786 | |
| 199 | D | A | -1.2643 | |
| 200 | T | A | -0.6875 | |
| 201 | S | A | -0.5773 | |
| 202 | T | A | -0.7149 | |
| 203 | S | A | -0.8205 | |
| 204 | T | A | 0.0000 | |
| 205 | V | A | 0.0000 | |
| 206 | Y | A | -0.8648 | |
| 207 | M | A | 0.0000 | |
| 208 | E | A | -1.5389 | |
| 209 | L | A | 0.0000 | |
| 210 | S | A | -1.1748 | |
| 211 | S | A | -1.2615 | |
| 212 | L | A | 0.0000 | |
| 213 | R | A | -3.1531 | |
| 214 | S | A | -2.4276 | |
| 215 | E | A | -2.5918 | |
| 216 | D | A | 0.0000 | |
| 217 | T | A | -0.9598 | |
| 218 | A | A | 0.0000 | |
| 219 | V | A | 0.1535 | |
| 220 | Y | A | 0.0000 | |
| 221 | Y | A | 0.0000 | |
| 222 | C | A | 0.0000 | |
| 223 | A | A | 0.0000 | |
| 224 | R | A | 0.0000 | |
| 225 | D | A | 0.0000 | |
| 226 | G | A | 0.0000 | |
| 227 | N | A | -0.0203 | |
| 228 | Y | A | 0.5140 | |
| 229 | G | A | 0.0000 | |
| 230 | S | A | 0.0000 | |
| 231 | D | A | -0.1076 | |
| 232 | Y | A | -0.3932 | |
| 233 | W | A | -0.4670 | |
| 234 | G | A | 0.0000 | |
| 235 | Q | A | -1.4686 | |
| 236 | G | A | -0.6879 | |
| 237 | T | A | 0.0000 | |
| 238 | T | A | -0.0240 | |
| 239 | V | A | 0.0000 | |
| 240 | T | A | -0.3811 | |
| 241 | V | A | 0.0000 | |
| 242 | S | A | -1.1349 | |
| 243 | S | A | -1.0372 | |
| 1 | A | B | -0.3288 | |
| 2 | Q | B | -1.3300 | |
| 3 | E | B | -2.1375 | |
| 4 | V | B | -1.5831 | |
| 5 | Q | B | -1.7374 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.4545 | |
| 8 | P | B | 0.0000 | |
| 9 | H | B | -0.3401 | |
| 10 | C | B | 0.0000 | |
| 11 | T | B | 0.0000 | |
| 12 | T | B | 0.0000 | |
| 13 | V | B | 0.0000 | |
| 14 | P | B | -0.8544 | |
| 15 | V | B | -0.5402 | |
| 16 | G | B | -1.2013 | |
| 17 | A | B | -0.6714 | |
| 18 | S | B | -0.7573 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -0.8746 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8277 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.7147 | |
| 25 | T | B | -1.7857 | |
| 26 | S | B | -1.5930 | |
| 27 | G | B | -1.2477 | |
| 28 | G | B | -1.4216 | |
| 29 | L | B | -1.4190 | |
| 30 | R | B | -2.3527 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.1324 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.5579 | |
| 36 | Q | B | -0.8302 | |
| 37 | L | B | -0.7054 | |
| 38 | G | B | -1.1712 | |
| 39 | P | B | -1.2892 | |
| 40 | Q | B | -1.5714 | |
| 41 | P | B | -1.2331 | |
| 42 | Q | B | -1.1219 | |
| 43 | D | B | -1.1484 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.4070 | |
| 47 | Y | B | 0.1958 | |
| 48 | E | B | -0.6307 | |
| 49 | D | B | -1.2629 | |
| 50 | G | B | -0.0113 | |
| 51 | V | B | 1.6576 | |
| 52 | V | B | 2.1300 | |
| 53 | P | B | 0.8330 | |
| 54 | T | B | -0.0036 | |
| 55 | T | B | -1.5198 | |
| 56 | D | B | -2.4135 | |
| 57 | R | B | -3.6461 | |
| 58 | R | B | -3.4336 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -3.5178 | |
| 61 | G | B | -2.4134 | |
| 62 | R | B | -2.2921 | |
| 63 | I | B | -1.5998 | |
| 64 | D | B | -1.9628 | |
| 65 | F | B | -0.6793 | |
| 66 | S | B | -0.9102 | |
| 67 | G | B | -1.2257 | |
| 68 | S | B | -1.5082 | |
| 69 | Q | B | -1.8960 | |
| 70 | D | B | -2.4657 | |
| 71 | N | B | -2.2278 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0100 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.9123 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.7097 | |
| 78 | R | B | -2.2230 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -0.9661 | |
| 81 | L | B | 0.1604 | |
| 82 | S | B | -0.1628 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | -0.0903 | |
| 85 | G | B | -0.2771 | |
| 86 | T | B | -0.2596 | |
| 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 | -0.3658 | |
| 93 | T | B | -0.8618 | |
| 94 | E | B | -1.2815 | |
| 95 | V | B | 0.7534 | |
| 96 | N | B | 0.1079 | |
| 97 | V | B | 0.0058 | |
| 98 | Y | B | -0.2655 | |
| 99 | G | B | 0.0000 | |
| 100 | S | B | -0.5415 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | L | B | 0.0000 | |
| 104 | V | B | 0.0000 | |
| 105 | L | B | 0.0000 | |
| 106 | V | B | 0.0000 | |
| 107 | T | B | 0.0000 | |
| 108 | E | B | -2.8116 | |
| 109 | E | B | -3.2161 | |
| 110 | Q | B | -2.0871 | |
| 111 | S | B | -1.5445 | |
| 112 | Q | B | -2.4401 | |
| 113 | G | B | -1.6531 | |
| 114 | W | B | 0.0000 | |
| 115 | H | B | 0.0000 | |
| 116 | R | B | 0.0000 | |
| 117 | C | B | 0.0000 | |
| 118 | S | B | 0.0000 | |
| 119 | D | B | -0.3577 | |
| 120 | A | B | -0.5024 | |
| 121 | P | B | -0.7346 | |
| 122 | P | B | -1.1427 | |
| 123 | R | B | -1.9248 | |
| 124 | A | B | -0.9556 | |
| 125 | S | B | -0.7751 | |
| 126 | A | B | -0.6483 | |
| 127 | L | B | -0.4716 | |
| 128 | P | B | -0.2421 | |
| 129 | A | B | -0.2379 | |
| 130 | P | B | -0.4225 | |
| 131 | P | B | -0.5317 | |
| 132 | T | B | -0.4840 | |
| 133 | G | B | -0.4123 | |
| 134 | S | B | -0.0908 | |
| 135 | A | B | 0.1561 | |
| 136 | L | B | 0.7822 | |
| 137 | P | B | -0.6867 | |
| 138 | D | B | -1.9828 | |
| 139 | P | B | -1.5338 | |
| 140 | Q | B | -1.9692 | |
| 141 | T | B | -1.0324 | |
| 142 | A | B | -0.2074 | |
| 143 | S | B | 0.0233 | |
| 144 | A | B | 0.3523 | |
| 145 | L | B | 0.8907 | |
| 146 | P | B | -0.5014 | |
| 147 | D | B | -1.6813 | |
| 148 | P | B | -1.0451 | |
| 149 | P | B | -0.8894 | |
| 150 | A | B | -0.4476 | |
| 151 | A | B | 0.1178 | |
| 152 | S | B | 0.2137 | |
| 153 | A | B | 0.6658 | |
| 154 | L | B | 1.4040 | |
| 155 | P | B | 0.4747 |
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 | 3.7554 | View | CSV | PDB |
| 4.5 | -0.4181 | 3.5895 | View | CSV | PDB |
| 5.0 | -0.4681 | 3.3942 | View | CSV | PDB |
| 5.5 | -0.519 | 3.1872 | View | CSV | PDB |
| 6.0 | -0.5628 | 3.0838 | View | CSV | PDB |
| 6.5 | -0.5935 | 3.0838 | View | CSV | PDB |
| 7.0 | -0.6096 | 3.0838 | View | CSV | PDB |
| 7.5 | -0.6153 | 3.0838 | View | CSV | PDB |
| 8.0 | -0.6145 | 3.0838 | View | CSV | PDB |
| 8.5 | -0.6084 | 3.0838 | View | CSV | PDB |
| 9.0 | -0.5961 | 3.0838 | 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