| Chain sequence(s) |
A: DIVMTQTPLSLPVTPGEPASISCRSSQSLVHSNGNTYLEWYLQKPGQSPQLLIYKLSYRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFKGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
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 (00:00:02)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:05:10)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/1c11f708748008b/tmp/folded.pdb (00:05:10)
[INFO] Main: Simulation completed successfully. (00:07:53)
|
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 | -1.3771 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7273 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.2869 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | -0.0696 | |
| 8 | P | A | 0.4166 | |
| 9 | L | A | 1.1953 | |
| 10 | S | A | 0.0190 | |
| 11 | L | A | -0.3888 | |
| 12 | P | A | -1.3363 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.7861 | |
| 15 | P | A | -2.0680 | |
| 16 | G | A | -1.9559 | |
| 17 | E | A | -2.4238 | |
| 18 | P | A | -2.2760 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.9078 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.9236 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.2868 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -1.0110 | |
| 27 | Q | A | -1.5721 | |
| 28 | S | A | -0.8922 | |
| 29 | L | A | 0.0000 | |
| 30 | V | A | 0.5658 | |
| 31 | H | A | -0.2752 | |
| 32 | S | A | -0.6010 | |
| 33 | N | A | -1.2531 | |
| 34 | G | A | -0.7884 | |
| 35 | N | A | -0.5078 | |
| 36 | T | A | -0.0131 | |
| 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 | -0.9165 | |
| 44 | K | A | -1.6607 | |
| 45 | P | A | -1.1695 | |
| 46 | G | A | -1.5295 | |
| 47 | Q | A | -2.1200 | |
| 48 | S | A | -1.2654 | |
| 49 | P | A | 0.0000 | |
| 50 | Q | A | -1.0168 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | 0.2449 | |
| 55 | K | A | 0.0064 | |
| 56 | L | A | -0.0206 | |
| 57 | S | A | 0.0841 | |
| 58 | Y | A | 0.7233 | |
| 59 | R | A | -0.8399 | |
| 60 | A | A | -0.4505 | |
| 61 | S | A | -0.5658 | |
| 62 | G | A | -1.0597 | |
| 63 | V | A | -0.8785 | |
| 64 | P | A | -1.3538 | |
| 65 | D | A | -2.2706 | |
| 66 | R | A | -2.2398 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.2821 | |
| 69 | G | A | 0.0000 | |
| 70 | S | A | -0.7333 | |
| 71 | G | A | -1.0506 | |
| 72 | S | A | -0.7101 | |
| 73 | G | A | -0.6542 | |
| 74 | T | A | -1.4496 | |
| 75 | D | A | -2.1038 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -1.1827 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -2.2397 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.4551 | |
| 82 | R | A | -3.1891 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.5478 | |
| 85 | A | A | -1.9188 | |
| 86 | E | A | -2.5620 | |
| 87 | D | A | 0.0000 | |
| 88 | V | A | -1.3210 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | -0.1894 | |
| 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 | -1.0856 | |
| 99 | V | A | -0.4663 | |
| 100 | P | A | -0.5097 | |
| 101 | F | A | 0.0000 | |
| 102 | T | A | -0.0138 | |
| 103 | F | A | 0.3188 | |
| 104 | G | A | 0.0000 | |
| 105 | S | A | -0.0421 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.7227 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -2.0351 | |
| 111 | I | A | -2.0340 | |
| 112 | K | A | -2.4606 | |
| 113 | G | A | -1.7755 | |
| 114 | G | A | -1.6463 | |
| 115 | G | A | -1.4406 | |
| 116 | G | A | -1.7531 | |
| 117 | S | A | -1.2336 | |
| 118 | G | A | -1.7240 | |
| 119 | G | A | -1.6397 | |
| 120 | G | A | -1.7431 | |
| 121 | G | A | -1.6652 | |
| 122 | S | A | -1.0680 | |
| 123 | G | A | -1.2925 | |
| 124 | G | A | -1.2539 | |
| 125 | G | A | -1.1770 | |
| 126 | G | A | -0.9961 | |
| 127 | S | A | -0.9559 | |
| 128 | V | A | 0.0000 | |
| 129 | Q | A | -1.3456 | |
| 130 | L | A | 0.0000 | |
| 131 | V | A | 0.2363 | |
| 132 | Q | A | 0.0000 | |
| 133 | S | A | -0.5802 | |
| 134 | G | A | -0.6593 | |
| 135 | A | A | -0.1483 | |
| 136 | E | A | -0.3135 | |
| 137 | V | A | 0.7590 | |
| 138 | K | A | -1.0508 | |
| 139 | K | A | -2.2074 | |
| 140 | P | A | -2.2880 | |
| 141 | G | A | -1.6183 | |
| 142 | A | A | -1.2704 | |
| 143 | S | A | -1.3351 | |
| 144 | V | A | 0.0000 | |
| 145 | K | A | -1.8179 | |
| 146 | V | A | 0.0000 | |
| 147 | S | A | -0.6011 | |
| 148 | C | A | 0.0000 | |
| 149 | K | A | -0.9208 | |
| 150 | A | A | 0.0000 | |
| 151 | S | A | -0.7293 | |
| 152 | G | A | -0.8322 | |
| 153 | Y | A | -0.2765 | |
| 154 | T | A | -0.0699 | |
| 155 | F | A | 0.0000 | |
| 156 | T | A | 0.1314 | |
| 157 | D | A | 0.0000 | |
| 158 | Y | A | 0.2354 | |
| 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 | 0.0000 | |
| 165 | Q | A | -0.5729 | |
| 166 | A | A | -1.0119 | |
| 167 | P | A | -1.0233 | |
| 168 | G | A | -1.2133 | |
| 169 | Q | A | -1.6777 | |
| 170 | G | A | -0.9510 | |
| 171 | L | A | 0.0000 | |
| 172 | E | A | -0.5367 | |
| 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 | 0.3671 | |
| 181 | Y | A | 0.5493 | |
| 182 | G | A | -0.0459 | |
| 183 | S | A | -0.1927 | |
| 184 | T | A | -0.2307 | |
| 185 | G | A | 0.0000 | |
| 186 | Y | A | -0.2985 | |
| 187 | A | A | 0.0000 | |
| 188 | L | A | 0.1342 | |
| 189 | K | A | -1.3366 | |
| 190 | F | A | 0.0000 | |
| 191 | K | A | -1.2251 | |
| 192 | G | A | -1.1660 | |
| 193 | R | A | -1.2092 | |
| 194 | V | A | 0.0000 | |
| 195 | T | A | -0.7746 | |
| 196 | M | A | 0.0000 | |
| 197 | T | A | -0.6592 | |
| 198 | R | A | -1.1741 | |
| 199 | D | A | -1.3220 | |
| 200 | T | A | -0.7320 | |
| 201 | S | A | -0.5996 | |
| 202 | T | A | -0.6931 | |
| 203 | S | A | -0.7795 | |
| 204 | T | A | 0.0000 | |
| 205 | V | A | 0.0000 | |
| 206 | Y | A | -0.8104 | |
| 207 | M | A | 0.0000 | |
| 208 | E | A | -1.4320 | |
| 209 | L | A | 0.0000 | |
| 210 | S | A | -1.1396 | |
| 211 | S | A | -1.2583 | |
| 212 | L | A | 0.0000 | |
| 213 | R | A | -3.1397 | |
| 214 | S | A | -2.4197 | |
| 215 | E | A | -2.5884 | |
| 216 | D | A | 0.0000 | |
| 217 | T | A | -0.8650 | |
| 218 | A | A | 0.0000 | |
| 219 | V | A | 0.2043 | |
| 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 | 0.0000 | |
| 228 | Y | A | 0.1952 | |
| 229 | G | A | 0.0000 | |
| 230 | S | A | 0.0000 | |
| 231 | D | A | -0.2672 | |
| 232 | Y | A | -0.3703 | |
| 233 | W | A | -0.3813 | |
| 234 | G | A | 0.0000 | |
| 235 | Q | A | -1.2997 | |
| 236 | G | A | -0.5618 | |
| 237 | T | A | 0.0000 | |
| 238 | T | A | -0.0272 | |
| 239 | V | A | 0.0000 | |
| 240 | T | A | -0.3933 | |
| 241 | V | A | 0.0000 | |
| 242 | S | A | -1.1272 | |
| 243 | S | A | -1.0249 | |
| 1 | A | B | -0.3861 | |
| 2 | Q | B | -1.4178 | |
| 3 | E | B | -2.1814 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -2.0066 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.4292 | |
| 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 | -1.0524 | |
| 15 | V | B | -0.6528 | |
| 16 | G | B | -1.2760 | |
| 17 | A | B | 0.0000 | |
| 18 | S | B | -0.8105 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -0.9739 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8331 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.6022 | |
| 25 | T | B | -1.5470 | |
| 26 | S | B | -1.4745 | |
| 27 | G | B | -1.1377 | |
| 28 | G | B | -1.3606 | |
| 29 | L | B | -1.6196 | |
| 30 | R | B | -2.4117 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.1932 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.5837 | |
| 36 | Q | B | 0.0000 | |
| 37 | L | B | -0.1489 | |
| 38 | G | B | -0.6734 | |
| 39 | P | B | -1.0613 | |
| 40 | Q | B | -1.4536 | |
| 41 | P | B | -1.0081 | |
| 42 | Q | B | -1.1335 | |
| 43 | D | B | -0.9925 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.4509 | |
| 47 | Y | B | 0.0574 | |
| 48 | E | B | -0.8761 | |
| 49 | D | B | -1.8978 | |
| 50 | G | B | -0.4074 | |
| 51 | V | B | 1.2431 | |
| 52 | V | B | 1.9188 | |
| 53 | P | B | 0.7135 | |
| 54 | T | B | 0.0316 | |
| 55 | T | B | -1.1140 | |
| 56 | D | B | 0.0000 | |
| 57 | R | B | -3.0872 | |
| 58 | R | B | -2.5841 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -3.2199 | |
| 61 | G | B | -2.2814 | |
| 62 | R | B | -2.1683 | |
| 63 | I | B | -1.5585 | |
| 64 | D | B | -1.9377 | |
| 65 | F | B | -0.6723 | |
| 66 | S | B | -0.9442 | |
| 67 | G | B | -1.0563 | |
| 68 | S | B | -1.3634 | |
| 69 | Q | B | -1.7550 | |
| 70 | D | B | -1.9170 | |
| 71 | N | B | -2.0239 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0018 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.9206 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.7522 | |
| 78 | R | B | -2.2775 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -1.0228 | |
| 81 | L | B | 0.1123 | |
| 82 | S | B | -0.1005 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | -0.0828 | |
| 85 | G | B | -0.0923 | |
| 86 | T | B | 0.0000 | |
| 87 | Y | B | 0.0000 | |
| 88 | T | B | 0.0000 | |
| 89 | C | B | 0.0000 | |
| 90 | Q | B | -0.0184 | |
| 91 | A | B | 0.0000 | |
| 92 | I | B | -0.4049 | |
| 93 | T | B | -1.0555 | |
| 94 | E | B | -1.4420 | |
| 95 | V | B | 0.4757 | |
| 96 | N | B | -0.4683 | |
| 97 | V | B | 0.0521 | |
| 98 | Y | B | -0.1303 | |
| 99 | G | B | 0.0000 | |
| 100 | S | B | -1.1319 | |
| 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 | -2.7718 | |
| 109 | E | B | -3.1050 | |
| 110 | Q | B | -2.5257 | |
| 111 | S | B | -1.5179 | |
| 112 | Q | B | -2.2558 | |
| 113 | G | B | -1.5379 | |
| 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 | -0.3848 | |
| 120 | A | B | 0.0000 | |
| 121 | P | B | -0.5076 | |
| 122 | P | B | -1.0712 | |
| 123 | R | B | -2.1732 | |
| 124 | A | B | -0.4647 | |
| 125 | S | B | -0.2774 | |
| 126 | A | B | 0.5207 | |
| 127 | L | B | 1.4070 | |
| 128 | P | B | 0.3967 | |
| 129 | A | B | 0.4079 | |
| 130 | P | B | -0.2543 | |
| 131 | P | B | -0.6206 | |
| 132 | T | B | -0.5316 | |
| 133 | G | B | -0.4325 | |
| 134 | S | B | -0.0793 | |
| 135 | A | B | 0.1862 | |
| 136 | L | B | 0.7893 | |
| 137 | P | B | -0.6750 | |
| 138 | D | B | -1.9755 | |
| 139 | P | B | -1.5211 | |
| 140 | Q | B | -1.9398 | |
| 141 | T | B | -1.0116 | |
| 142 | A | B | -0.1961 | |
| 143 | S | B | 0.0122 | |
| 144 | A | B | 0.3634 | |
| 145 | L | B | 0.9076 | |
| 146 | P | B | -0.4984 | |
| 147 | D | B | -1.6913 | |
| 148 | P | B | -1.0499 | |
| 149 | P | B | -0.8806 | |
| 150 | A | B | -0.4358 | |
| 151 | A | B | 0.1203 | |
| 152 | S | B | 0.2175 | |
| 153 | A | B | 0.6659 | |
| 154 | L | B | 1.4033 | |
| 155 | P | B | 0.4775 |
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 | -0.3542 | 3.8923 | View | CSV | PDB |
| 4.5 | -0.3923 | 3.8923 | View | CSV | PDB |
| 5.0 | -0.439 | 3.8923 | View | CSV | PDB |
| 5.5 | -0.4869 | 3.8923 | View | CSV | PDB |
| 6.0 | -0.5282 | 3.8923 | View | CSV | PDB |
| 6.5 | -0.5576 | 3.8923 | View | CSV | PDB |
| 7.0 | -0.5737 | 3.8923 | View | CSV | PDB |
| 7.5 | -0.5796 | 3.8923 | View | CSV | PDB |
| 8.0 | -0.5791 | 3.8923 | View | CSV | PDB |
| 8.5 | -0.5732 | 3.8923 | View | CSV | PDB |
| 9.0 | -0.5613 | 3.8923 | 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