| Chain sequence(s) |
A: DIVMTQTPLSLSVTPGQPASISCRSSQSLVHSNGKTYLEWYLQKPGQSPQLLIYKLSYRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYNLKFQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
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 (00:04:27)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/8724b91a497c475/tmp/folded.pdb (00:04:27)
[INFO] Main: Simulation completed successfully. (00:07:43)
|
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 | -1.3390 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7252 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.2720 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | -0.0043 | |
| 8 | P | A | 0.4434 | |
| 9 | L | A | 1.2397 | |
| 10 | S | A | 0.1273 | |
| 11 | L | A | -0.3654 | |
| 12 | S | A | -1.1651 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.6418 | |
| 15 | P | A | -1.7390 | |
| 16 | G | A | -1.6405 | |
| 17 | Q | A | -1.9168 | |
| 18 | P | A | -2.0071 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.9167 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.9081 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.2634 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -0.9972 | |
| 27 | Q | A | -1.5790 | |
| 28 | S | A | -0.9558 | |
| 29 | L | A | 0.0000 | |
| 30 | V | A | 0.2156 | |
| 31 | H | A | -0.4406 | |
| 32 | S | A | -0.7244 | |
| 33 | N | A | -1.2140 | |
| 34 | G | A | -0.8626 | |
| 35 | K | A | -0.7117 | |
| 36 | T | A | -0.2438 | |
| 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 | 0.0000 | |
| 44 | K | A | -1.4260 | |
| 45 | P | A | -1.0008 | |
| 46 | G | A | -1.4292 | |
| 47 | Q | A | -2.0442 | |
| 48 | S | A | -1.1883 | |
| 49 | P | A | 0.0000 | |
| 50 | Q | A | -0.8796 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | 0.0000 | |
| 55 | K | A | -0.2634 | |
| 56 | L | A | -0.1647 | |
| 57 | S | A | -0.0760 | |
| 58 | Y | A | 0.3972 | |
| 59 | R | A | -0.9072 | |
| 60 | A | A | -0.7404 | |
| 61 | S | A | -0.5738 | |
| 62 | G | A | -1.0248 | |
| 63 | V | A | 0.0000 | |
| 64 | P | A | -1.3781 | |
| 65 | D | A | -2.4226 | |
| 66 | R | A | -2.2569 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.2998 | |
| 69 | G | A | -0.7088 | |
| 70 | S | A | -0.7573 | |
| 71 | G | A | -0.9775 | |
| 72 | S | A | -0.7148 | |
| 73 | G | A | -0.7217 | |
| 74 | T | A | -1.4663 | |
| 75 | D | A | -2.0555 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -1.1573 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -2.2031 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.3332 | |
| 82 | R | A | -3.1319 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.2448 | |
| 85 | A | A | -1.9362 | |
| 86 | E | A | -2.4443 | |
| 87 | D | A | 0.0000 | |
| 88 | V | A | -1.0207 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | 0.0218 | |
| 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 | -0.9175 | |
| 99 | V | A | -0.3328 | |
| 100 | P | A | -0.4625 | |
| 101 | F | A | 0.0000 | |
| 102 | T | A | 0.0222 | |
| 103 | F | A | 0.3243 | |
| 104 | G | A | 0.0000 | |
| 105 | S | A | -0.0047 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.4260 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -1.7220 | |
| 111 | I | A | -1.9093 | |
| 112 | K | A | -2.3732 | |
| 113 | G | A | -1.8168 | |
| 114 | G | A | -1.7184 | |
| 115 | G | A | -1.3489 | |
| 116 | G | A | -1.4594 | |
| 117 | S | A | -1.3150 | |
| 118 | G | A | -1.5954 | |
| 119 | G | A | -1.6456 | |
| 120 | G | A | -1.6561 | |
| 121 | G | A | -1.7330 | |
| 122 | S | A | -1.0776 | |
| 123 | G | A | -1.1721 | |
| 124 | G | A | -1.2002 | |
| 125 | G | A | -1.1148 | |
| 126 | G | A | -0.8966 | |
| 127 | S | A | -0.8228 | |
| 128 | V | A | -0.6126 | |
| 129 | Q | A | -1.0858 | |
| 130 | L | A | 0.0000 | |
| 131 | V | A | 0.5381 | |
| 132 | Q | A | 0.0000 | |
| 133 | S | A | -0.4885 | |
| 134 | G | A | -0.6287 | |
| 135 | A | A | -0.1255 | |
| 136 | E | A | -0.2486 | |
| 137 | V | A | 0.8336 | |
| 138 | K | A | -0.9711 | |
| 139 | K | A | -2.1734 | |
| 140 | P | A | -2.2840 | |
| 141 | G | A | -1.5990 | |
| 142 | A | A | -1.2509 | |
| 143 | S | A | -1.3139 | |
| 144 | V | A | 0.0000 | |
| 145 | K | A | -1.7870 | |
| 146 | V | A | 0.0000 | |
| 147 | S | A | -0.4647 | |
| 148 | C | A | 0.0000 | |
| 149 | K | A | -0.5081 | |
| 150 | A | A | 0.0000 | |
| 151 | S | A | -0.5711 | |
| 152 | G | A | -0.7326 | |
| 153 | Y | A | -0.2001 | |
| 154 | T | A | -0.0494 | |
| 155 | F | A | 0.0000 | |
| 156 | T | A | 0.1401 | |
| 157 | D | A | 0.0000 | |
| 158 | Y | A | 0.2057 | |
| 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 | -0.4042 | |
| 165 | Q | A | -0.6500 | |
| 166 | A | A | -1.0452 | |
| 167 | P | A | -1.0447 | |
| 168 | G | A | -1.2113 | |
| 169 | Q | A | -1.6937 | |
| 170 | G | A | -0.9654 | |
| 171 | L | A | 0.0000 | |
| 172 | E | A | -0.5739 | |
| 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 | 0.3594 | |
| 181 | Y | A | 0.4883 | |
| 182 | G | A | -0.0413 | |
| 183 | S | A | -0.2264 | |
| 184 | T | A | -0.2511 | |
| 185 | G | A | 0.0000 | |
| 186 | Y | A | -0.2815 | |
| 187 | N | A | 0.0000 | |
| 188 | L | A | 0.0775 | |
| 189 | K | A | -1.3886 | |
| 190 | F | A | 0.0000 | |
| 191 | Q | A | -1.4266 | |
| 192 | G | A | -1.2571 | |
| 193 | R | A | -1.2679 | |
| 194 | V | A | 0.0000 | |
| 195 | T | A | -0.7801 | |
| 196 | M | A | 0.0000 | |
| 197 | T | A | -0.5680 | |
| 198 | R | A | -0.9554 | |
| 199 | D | A | -1.1578 | |
| 200 | T | A | -0.6623 | |
| 201 | S | A | -0.5562 | |
| 202 | T | A | -0.5877 | |
| 203 | S | A | -0.6347 | |
| 204 | T | A | 0.0000 | |
| 205 | V | A | 0.0000 | |
| 206 | Y | A | -0.6945 | |
| 207 | M | A | 0.0000 | |
| 208 | E | A | -1.3947 | |
| 209 | L | A | 0.0000 | |
| 210 | S | A | -1.1406 | |
| 211 | S | A | -1.2488 | |
| 212 | L | A | 0.0000 | |
| 213 | R | A | -3.1393 | |
| 214 | S | A | -2.4231 | |
| 215 | E | A | -2.5743 | |
| 216 | D | A | 0.0000 | |
| 217 | T | A | -0.8790 | |
| 218 | A | A | 0.0000 | |
| 219 | V | A | 0.1591 | |
| 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 | -0.1120 | |
| 228 | Y | A | 0.0107 | |
| 229 | G | A | 0.0000 | |
| 230 | S | A | 0.0000 | |
| 231 | D | A | -0.4497 | |
| 232 | Y | A | -0.2750 | |
| 233 | W | A | -0.3324 | |
| 234 | G | A | 0.0000 | |
| 235 | Q | A | -1.2477 | |
| 236 | G | A | -0.5594 | |
| 237 | T | A | 0.0000 | |
| 238 | T | A | -0.0360 | |
| 239 | V | A | 0.0000 | |
| 240 | T | A | -0.3724 | |
| 241 | V | A | 0.0000 | |
| 242 | S | A | -0.9076 | |
| 243 | S | A | -1.2035 | |
| 1 | A | B | -0.3117 | |
| 2 | Q | B | -0.9940 | |
| 3 | E | B | -1.7431 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -1.7491 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.4224 | |
| 8 | P | B | 0.0000 | |
| 9 | H | B | 0.0000 | |
| 10 | C | B | 0.0000 | |
| 11 | T | B | 0.0000 | |
| 12 | T | B | 0.0000 | |
| 13 | V | B | 0.0000 | |
| 14 | P | B | -0.9287 | |
| 15 | V | B | -0.4927 | |
| 16 | G | B | -1.2114 | |
| 17 | A | B | 0.0000 | |
| 18 | S | B | -0.7630 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -0.8724 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8775 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.7516 | |
| 25 | T | B | -1.7592 | |
| 26 | S | B | -1.4802 | |
| 27 | G | B | -1.1830 | |
| 28 | G | B | -1.4118 | |
| 29 | L | B | -1.7071 | |
| 30 | R | B | -2.3856 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.1420 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | 0.0000 | |
| 36 | Q | B | -0.6750 | |
| 37 | L | B | -0.4860 | |
| 38 | G | B | -0.8794 | |
| 39 | P | B | -1.0913 | |
| 40 | Q | B | -1.5645 | |
| 41 | P | B | -1.1369 | |
| 42 | Q | B | -1.2332 | |
| 43 | D | B | -0.8384 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.5208 | |
| 47 | Y | B | 0.1524 | |
| 48 | E | B | -0.6951 | |
| 49 | D | B | -1.2592 | |
| 50 | G | B | 0.0027 | |
| 51 | V | B | 1.6772 | |
| 52 | V | B | 2.1478 | |
| 53 | P | B | 0.8717 | |
| 54 | T | B | -0.0882 | |
| 55 | T | B | -1.1846 | |
| 56 | D | B | -1.9147 | |
| 57 | R | B | -2.9717 | |
| 58 | R | B | -2.1565 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -3.1265 | |
| 61 | G | B | -2.2311 | |
| 62 | R | B | -2.1072 | |
| 63 | I | B | -1.5904 | |
| 64 | D | B | -1.9603 | |
| 65 | F | B | -0.6810 | |
| 66 | S | B | -0.9100 | |
| 67 | G | B | -1.2457 | |
| 68 | S | B | -1.5545 | |
| 69 | Q | B | -1.9451 | |
| 70 | D | B | -2.6047 | |
| 71 | N | B | -2.3160 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0284 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.9184 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.7081 | |
| 78 | R | B | -2.1925 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -0.9547 | |
| 81 | L | B | 0.2082 | |
| 82 | S | B | -0.0235 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | -0.0298 | |
| 85 | G | B | -0.1503 | |
| 86 | T | B | -0.1365 | |
| 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 | -0.4238 | |
| 93 | T | B | -0.8920 | |
| 94 | E | B | -1.2600 | |
| 95 | V | B | 0.7266 | |
| 96 | N | B | 0.0933 | |
| 97 | V | B | 0.0669 | |
| 98 | Y | B | -0.2328 | |
| 99 | G | B | 0.0000 | |
| 100 | S | B | -0.5565 | |
| 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 | -2.5878 | |
| 109 | E | B | -2.8162 | |
| 110 | Q | B | -2.4884 | |
| 111 | S | B | -1.4927 | |
| 112 | Q | B | -2.1839 | |
| 113 | G | B | -1.4980 | |
| 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 | -0.2908 | |
| 120 | A | B | -0.3180 | |
| 121 | P | B | -0.5791 | |
| 122 | P | B | -0.9218 | |
| 123 | R | B | -1.8408 | |
| 124 | A | B | -0.9015 | |
| 125 | S | B | -0.7243 | |
| 126 | A | B | -0.5513 | |
| 127 | L | B | -0.3192 | |
| 128 | P | B | -0.1150 | |
| 129 | A | B | -0.1858 | |
| 130 | P | B | -0.3980 | |
| 131 | P | B | -0.5504 | |
| 132 | T | B | -0.4691 | |
| 133 | G | B | -0.6223 | |
| 134 | S | B | -0.4142 | |
| 135 | A | B | -0.4846 | |
| 136 | L | B | -0.3774 | |
| 137 | P | B | -1.2476 | |
| 138 | D | B | -2.2962 | |
| 139 | P | B | -1.7309 | |
| 140 | Q | B | -1.9754 | |
| 141 | T | B | -1.0800 | |
| 142 | A | B | -0.2078 | |
| 143 | S | B | 0.0225 | |
| 144 | A | B | 0.3287 | |
| 145 | L | B | 0.8760 | |
| 146 | P | B | -0.5044 | |
| 147 | D | B | -1.6731 | |
| 148 | P | B | -1.0343 | |
| 149 | P | B | -0.9098 | |
| 150 | A | B | -0.4804 | |
| 151 | A | B | 0.1249 | |
| 152 | S | B | 0.2400 | |
| 153 | A | B | 0.6692 | |
| 154 | L | B | 1.3996 | |
| 155 | P | B | 0.4802 |
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 | -0.3901 | 3.7611 | View | CSV | PDB |
| 4.5 | -0.428 | 3.5879 | View | CSV | PDB |
| 5.0 | -0.4728 | 3.3893 | View | CSV | PDB |
| 5.5 | -0.5177 | 3.181 | View | CSV | PDB |
| 6.0 | -0.5562 | 2.9694 | View | CSV | PDB |
| 6.5 | -0.584 | 2.8641 | View | CSV | PDB |
| 7.0 | -0.6004 | 2.8641 | View | CSV | PDB |
| 7.5 | -0.6082 | 2.8641 | View | CSV | PDB |
| 8.0 | -0.6104 | 2.8641 | View | CSV | PDB |
| 8.5 | -0.6073 | 2.8641 | View | CSV | PDB |
| 9.0 | -0.5984 | 2.8641 | 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