| Chain sequence(s) |
A: DIVMTQTPLSLPVTPGEPASISCRSSQSIVHSNGNTYLEWYLQKPGQSPQLLIYKLSYRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYNLKFKGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
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 (00:04:55)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/48589d1b38b190a/tmp/folded.pdb (00:04:55)
[INFO] Main: Simulation completed successfully. (00:07:13)
|
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 | -1.4168 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7498 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.2902 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | -0.0475 | |
| 8 | P | A | 0.4587 | |
| 9 | L | A | 1.2583 | |
| 10 | S | A | 0.2042 | |
| 11 | L | A | -0.1455 | |
| 12 | P | A | -1.0262 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.6410 | |
| 15 | P | A | -1.9018 | |
| 16 | G | A | -1.8367 | |
| 17 | E | A | -2.2085 | |
| 18 | P | A | -2.1462 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.8725 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.8986 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.2627 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -0.9285 | |
| 27 | Q | A | -1.3190 | |
| 28 | S | A | -0.8434 | |
| 29 | I | A | 0.0000 | |
| 30 | V | A | 0.2638 | |
| 31 | H | A | -0.5848 | |
| 32 | S | A | -0.8025 | |
| 33 | N | A | -1.5412 | |
| 34 | G | A | -0.9978 | |
| 35 | N | A | -0.6772 | |
| 36 | T | A | -0.0728 | |
| 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 | -0.8131 | |
| 44 | K | A | -1.5088 | |
| 45 | P | A | -1.1420 | |
| 46 | G | A | -1.3607 | |
| 47 | Q | A | -1.8521 | |
| 48 | S | A | -1.1256 | |
| 49 | P | A | 0.0000 | |
| 50 | Q | A | -1.0420 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | 0.0000 | |
| 55 | K | A | 0.0000 | |
| 56 | L | A | -0.0666 | |
| 57 | S | A | -0.1988 | |
| 58 | Y | A | 0.0154 | |
| 59 | R | A | -1.2652 | |
| 60 | A | A | -0.8826 | |
| 61 | S | A | -0.6251 | |
| 62 | G | A | -1.0598 | |
| 63 | V | A | 0.0000 | |
| 64 | P | A | -1.4130 | |
| 65 | D | A | -2.4909 | |
| 66 | R | A | -2.3294 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.4144 | |
| 69 | G | A | -0.7723 | |
| 70 | S | A | -0.7658 | |
| 71 | G | A | -1.0353 | |
| 72 | S | A | -0.7406 | |
| 73 | G | A | -0.6962 | |
| 74 | T | A | -1.4209 | |
| 75 | D | A | -2.0628 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -1.1555 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -2.1286 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.3878 | |
| 82 | R | A | -3.2502 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.2705 | |
| 85 | A | A | -1.5587 | |
| 86 | E | A | -2.2578 | |
| 87 | D | A | 0.0000 | |
| 88 | V | A | -0.9166 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | 0.0072 | |
| 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 | -1.3130 | |
| 99 | V | A | -0.7354 | |
| 100 | P | A | -0.6851 | |
| 101 | F | A | 0.0000 | |
| 102 | T | A | -0.0561 | |
| 103 | F | A | 0.3180 | |
| 104 | G | A | 0.0000 | |
| 105 | S | A | -0.0322 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.3688 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -1.4558 | |
| 111 | I | A | -1.6867 | |
| 112 | K | A | -2.2935 | |
| 113 | G | A | -1.7583 | |
| 114 | G | A | -1.6858 | |
| 115 | G | A | -1.3435 | |
| 116 | G | A | -1.2288 | |
| 117 | S | A | -1.2403 | |
| 118 | G | A | -1.4966 | |
| 119 | G | A | -1.6604 | |
| 120 | G | A | -1.5709 | |
| 121 | G | A | -1.7202 | |
| 122 | S | A | -1.2218 | |
| 123 | G | A | -1.2743 | |
| 124 | G | A | -1.2319 | |
| 125 | G | A | -1.1962 | |
| 126 | G | A | -1.0129 | |
| 127 | S | A | -0.8526 | |
| 128 | V | A | -0.7466 | |
| 129 | Q | A | -1.1746 | |
| 130 | L | A | 0.0000 | |
| 131 | V | A | 0.0768 | |
| 132 | Q | A | 0.0000 | |
| 133 | S | A | -0.6119 | |
| 134 | G | A | -0.7017 | |
| 135 | A | A | -0.1893 | |
| 136 | E | A | -0.3914 | |
| 137 | V | A | 0.7394 | |
| 138 | K | A | -1.0721 | |
| 139 | K | A | -2.2047 | |
| 140 | P | A | -2.2880 | |
| 141 | G | A | -1.6141 | |
| 142 | A | A | -1.2704 | |
| 143 | S | A | -1.3112 | |
| 144 | V | A | 0.0000 | |
| 145 | K | A | -1.7364 | |
| 146 | V | A | 0.0000 | |
| 147 | S | A | -0.5720 | |
| 148 | C | A | 0.0000 | |
| 149 | K | A | -0.8801 | |
| 150 | A | A | 0.0000 | |
| 151 | S | A | -0.6755 | |
| 152 | G | A | -0.7354 | |
| 153 | Y | A | -0.1948 | |
| 154 | T | A | -0.0384 | |
| 155 | F | A | 0.0000 | |
| 156 | T | A | 0.1186 | |
| 157 | D | A | 0.0000 | |
| 158 | Y | A | 0.0943 | |
| 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 | -0.5642 | |
| 166 | A | A | -1.0142 | |
| 167 | P | A | -1.0271 | |
| 168 | G | A | -1.2120 | |
| 169 | Q | A | -1.6772 | |
| 170 | G | A | -0.9491 | |
| 171 | L | A | 0.0000 | |
| 172 | E | A | -0.5310 | |
| 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 | 0.3695 | |
| 181 | Y | A | 0.5296 | |
| 182 | G | A | 0.0141 | |
| 183 | S | A | 0.0000 | |
| 184 | T | A | -0.4397 | |
| 185 | G | A | 0.0000 | |
| 186 | Y | A | -0.4001 | |
| 187 | N | A | 0.0000 | |
| 188 | L | A | -0.1375 | |
| 189 | K | A | -1.5349 | |
| 190 | F | A | 0.0000 | |
| 191 | K | A | -1.9177 | |
| 192 | G | A | -1.4855 | |
| 193 | R | A | -1.3871 | |
| 194 | V | A | 0.0000 | |
| 195 | T | A | -0.8416 | |
| 196 | M | A | 0.0000 | |
| 197 | T | A | -0.5641 | |
| 198 | R | A | -0.9874 | |
| 199 | D | A | -1.1895 | |
| 200 | T | A | -0.6616 | |
| 201 | S | A | -0.5594 | |
| 202 | T | A | -0.6370 | |
| 203 | S | A | -0.7160 | |
| 204 | T | A | 0.0000 | |
| 205 | V | A | 0.0000 | |
| 206 | Y | A | -0.7196 | |
| 207 | M | A | 0.0000 | |
| 208 | E | A | -1.3618 | |
| 209 | L | A | 0.0000 | |
| 210 | S | A | -1.1118 | |
| 211 | S | A | -1.2504 | |
| 212 | L | A | 0.0000 | |
| 213 | R | A | -3.1402 | |
| 214 | S | A | -2.4210 | |
| 215 | E | A | -2.5718 | |
| 216 | D | A | 0.0000 | |
| 217 | T | A | -0.9481 | |
| 218 | A | A | 0.0000 | |
| 219 | V | A | 0.2033 | |
| 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 | -0.3874 | |
| 228 | Y | A | -0.0279 | |
| 229 | G | A | 0.0000 | |
| 230 | S | A | 0.0000 | |
| 231 | D | A | -0.3486 | |
| 232 | Y | A | -0.2711 | |
| 233 | W | A | -0.3542 | |
| 234 | G | A | 0.0000 | |
| 235 | Q | A | -1.2665 | |
| 236 | G | A | -0.5477 | |
| 237 | T | A | 0.0000 | |
| 238 | T | A | -0.0508 | |
| 239 | V | A | 0.0000 | |
| 240 | T | A | -0.4157 | |
| 241 | V | A | 0.0000 | |
| 242 | S | A | -0.9126 | |
| 243 | S | A | -1.1949 | |
| 1 | A | B | -0.6865 | |
| 2 | Q | B | -1.3627 | |
| 3 | E | B | -2.2221 | |
| 4 | V | B | -1.6337 | |
| 5 | Q | B | -1.8303 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.4948 | |
| 8 | P | B | 0.0000 | |
| 9 | H | B | -0.4065 | |
| 10 | C | B | 0.0000 | |
| 11 | T | B | 0.0000 | |
| 12 | T | B | 0.0000 | |
| 13 | V | B | 0.0000 | |
| 14 | P | B | -0.9976 | |
| 15 | V | B | -0.6914 | |
| 16 | G | B | -1.2706 | |
| 17 | A | B | 0.0000 | |
| 18 | S | B | -0.7726 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -0.8332 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8466 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.7534 | |
| 25 | T | B | -1.8004 | |
| 26 | S | B | -1.6205 | |
| 27 | G | B | -1.2734 | |
| 28 | G | B | -1.4603 | |
| 29 | L | B | -1.5143 | |
| 30 | R | B | -2.3740 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.1046 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | 0.0000 | |
| 36 | Q | B | -0.7434 | |
| 37 | L | B | -0.5897 | |
| 38 | G | B | -1.2331 | |
| 39 | P | B | -1.3555 | |
| 40 | Q | B | -1.5837 | |
| 41 | P | B | -1.1454 | |
| 42 | Q | B | -1.1788 | |
| 43 | D | B | -1.1015 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.3813 | |
| 47 | Y | B | 0.2034 | |
| 48 | E | B | -0.5859 | |
| 49 | D | B | -1.1825 | |
| 50 | G | B | 0.0542 | |
| 51 | V | B | 1.7412 | |
| 52 | V | B | 2.1729 | |
| 53 | P | B | 0.8670 | |
| 54 | T | B | -0.0341 | |
| 55 | T | B | -1.3759 | |
| 56 | D | B | -2.0967 | |
| 57 | R | B | -2.9984 | |
| 58 | R | B | -2.2664 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -3.1726 | |
| 61 | G | B | -2.2683 | |
| 62 | R | B | -2.1674 | |
| 63 | I | B | -1.6072 | |
| 64 | D | B | -1.9720 | |
| 65 | F | B | -0.6977 | |
| 66 | S | B | -0.9177 | |
| 67 | G | B | -1.2287 | |
| 68 | S | B | -1.5094 | |
| 69 | Q | B | -1.9246 | |
| 70 | D | B | -2.4746 | |
| 71 | N | B | -2.2431 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0143 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.9063 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.7770 | |
| 78 | R | B | -2.3072 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -1.1077 | |
| 81 | L | B | 0.1229 | |
| 82 | S | B | -0.0794 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | -0.2168 | |
| 85 | G | B | -0.2712 | |
| 86 | T | B | -0.2519 | |
| 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 | -0.4565 | |
| 93 | T | B | -0.9811 | |
| 94 | E | B | -1.3177 | |
| 95 | V | B | 0.6431 | |
| 96 | N | B | -0.0173 | |
| 97 | V | B | -0.0577 | |
| 98 | Y | B | 0.0448 | |
| 99 | G | B | -0.5350 | |
| 100 | S | B | -0.5607 | |
| 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 | -2.8763 | |
| 109 | E | B | -3.3061 | |
| 110 | Q | B | -2.1927 | |
| 111 | S | B | -1.6588 | |
| 112 | Q | B | -2.5974 | |
| 113 | G | B | -1.8045 | |
| 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 | -0.7734 | |
| 120 | A | B | -0.6852 | |
| 121 | P | B | -0.9503 | |
| 122 | P | B | -1.3071 | |
| 123 | R | B | -2.0117 | |
| 124 | A | B | -0.9140 | |
| 125 | S | B | -0.7359 | |
| 126 | A | B | -0.1471 | |
| 127 | L | B | 0.0109 | |
| 128 | P | B | -0.0935 | |
| 129 | A | B | 0.0104 | |
| 130 | P | B | -0.4241 | |
| 131 | P | B | -0.5243 | |
| 132 | T | B | -0.4758 | |
| 133 | G | B | -0.4025 | |
| 134 | S | B | -0.0842 | |
| 135 | A | B | 0.1651 | |
| 136 | L | B | 0.7857 | |
| 137 | P | B | -0.6744 | |
| 138 | D | B | -1.9781 | |
| 139 | P | B | -1.5342 | |
| 140 | Q | B | -1.9532 | |
| 141 | T | B | -1.0287 | |
| 142 | A | B | -0.2132 | |
| 143 | S | B | 0.0294 | |
| 144 | A | B | 0.3575 | |
| 145 | L | B | 0.9036 | |
| 146 | P | B | -0.4972 | |
| 147 | D | B | -1.6896 | |
| 148 | P | B | -1.0531 | |
| 149 | P | B | -0.8797 | |
| 150 | A | B | -0.4407 | |
| 151 | A | B | 0.1162 | |
| 152 | S | B | 0.2286 | |
| 153 | A | B | 0.6665 | |
| 154 | L | B | 1.4026 | |
| 155 | P | B | 0.4742 |
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 | -0.3748 | 3.7417 | View | CSV | PDB |
| 4.5 | -0.4169 | 3.5813 | View | CSV | PDB |
| 5.0 | -0.4673 | 3.3889 | View | CSV | PDB |
| 5.5 | -0.518 | 3.1832 | View | CSV | PDB |
| 6.0 | -0.5609 | 2.973 | View | CSV | PDB |
| 6.5 | -0.5904 | 2.9365 | View | CSV | PDB |
| 7.0 | -0.6065 | 2.9365 | View | CSV | PDB |
| 7.5 | -0.6133 | 2.9365 | View | CSV | PDB |
| 8.0 | -0.6142 | 2.9365 | View | CSV | PDB |
| 8.5 | -0.6097 | 2.9365 | View | CSV | PDB |
| 9.0 | -0.5989 | 2.9365 | 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