| Chain sequence(s) |
A: DIVMTQTPLSLPVTPGEPASISCRSSQSIVHSNGNTYLEWYLQKPGQSPQLLIYKLSYRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFKGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
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. (00:00:02)
[INFO] FoldX: Starting FoldX energy minimization (00:00:02)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:05:21)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/3a31752c11f74ea/tmp/folded.pdb (00:05:21)
[INFO] Main: Simulation completed successfully. (00:07:42)
|
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 | -1.2864 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7584 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.3150 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | -0.0731 | |
| 8 | P | A | 0.3832 | |
| 9 | L | A | 1.1638 | |
| 10 | S | A | 0.0044 | |
| 11 | L | A | -0.3705 | |
| 12 | P | A | -1.2680 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.6203 | |
| 15 | P | A | -1.8830 | |
| 16 | G | A | -1.7995 | |
| 17 | E | A | -2.1265 | |
| 18 | P | A | -2.1218 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.8835 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.9315 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.3314 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -0.9099 | |
| 27 | Q | A | -1.2832 | |
| 28 | S | A | -0.8425 | |
| 29 | I | A | 0.0000 | |
| 30 | V | A | 0.1161 | |
| 31 | H | A | -0.5031 | |
| 32 | S | A | -0.7799 | |
| 33 | N | A | -1.4212 | |
| 34 | G | A | -0.9385 | |
| 35 | N | A | -0.6713 | |
| 36 | T | A | 0.0000 | |
| 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 | -0.6941 | |
| 44 | K | A | -1.3054 | |
| 45 | P | A | -1.0284 | |
| 46 | G | A | -1.1125 | |
| 47 | Q | A | -1.3297 | |
| 48 | S | A | -0.8970 | |
| 49 | P | A | 0.0000 | |
| 50 | Q | A | -0.9175 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | 0.0000 | |
| 55 | K | A | -0.2696 | |
| 56 | L | A | -0.2620 | |
| 57 | S | A | -0.2974 | |
| 58 | Y | A | 0.1569 | |
| 59 | R | A | -1.2342 | |
| 60 | A | A | 0.0000 | |
| 61 | S | A | -0.4548 | |
| 62 | G | A | -1.0633 | |
| 63 | V | A | 0.0000 | |
| 64 | P | A | -1.4195 | |
| 65 | D | A | -2.4968 | |
| 66 | R | A | -2.3417 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.4005 | |
| 69 | G | A | 0.0000 | |
| 70 | S | A | -0.8009 | |
| 71 | G | A | -1.0667 | |
| 72 | S | A | -0.8428 | |
| 73 | G | A | -0.7911 | |
| 74 | T | A | -1.5559 | |
| 75 | D | A | -2.2938 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -1.1968 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -2.1672 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.3960 | |
| 82 | R | A | -3.2346 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.2748 | |
| 85 | A | A | -1.6123 | |
| 86 | E | A | -2.2426 | |
| 87 | D | A | 0.0000 | |
| 88 | V | A | -1.2482 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | -0.2027 | |
| 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 | -0.5475 | |
| 99 | V | A | -0.2266 | |
| 100 | P | A | -0.4159 | |
| 101 | F | A | 0.0000 | |
| 102 | T | A | 0.0432 | |
| 103 | F | A | 0.3176 | |
| 104 | G | A | 0.0000 | |
| 105 | S | A | -0.0435 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.7989 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -1.8780 | |
| 111 | I | A | -1.8398 | |
| 112 | K | A | -2.3017 | |
| 113 | G | A | -1.6896 | |
| 114 | G | A | -1.5586 | |
| 115 | G | A | -1.4233 | |
| 116 | G | A | -1.6975 | |
| 117 | S | A | -1.2383 | |
| 118 | G | A | -1.6165 | |
| 119 | G | A | -1.6185 | |
| 120 | G | A | -1.5461 | |
| 121 | G | A | -1.4239 | |
| 122 | S | A | -0.9811 | |
| 123 | G | A | -1.2637 | |
| 124 | G | A | -1.1974 | |
| 125 | G | A | -1.2129 | |
| 126 | G | A | -1.0394 | |
| 127 | S | A | -0.8917 | |
| 128 | V | A | -0.7265 | |
| 129 | Q | A | -1.5222 | |
| 130 | L | A | 0.0000 | |
| 131 | V | A | -0.5807 | |
| 132 | Q | A | 0.0000 | |
| 133 | S | A | -0.7832 | |
| 134 | G | A | -0.7108 | |
| 135 | A | A | -0.0776 | |
| 136 | E | A | -0.1841 | |
| 137 | V | A | 0.8652 | |
| 138 | K | A | -0.8955 | |
| 139 | K | A | -2.0912 | |
| 140 | P | A | -2.1187 | |
| 141 | G | A | -1.4505 | |
| 142 | A | A | -0.9872 | |
| 143 | S | A | -1.2778 | |
| 144 | V | A | 0.0000 | |
| 145 | K | A | -1.9608 | |
| 146 | V | A | 0.0000 | |
| 147 | S | A | -0.7868 | |
| 148 | C | A | 0.0000 | |
| 149 | K | A | -1.3869 | |
| 150 | A | A | 0.0000 | |
| 151 | S | A | -0.8951 | |
| 152 | G | A | -0.7821 | |
| 153 | Y | A | -0.2263 | |
| 154 | T | A | -0.0453 | |
| 155 | F | A | 0.0000 | |
| 156 | T | A | 0.0856 | |
| 157 | D | A | 0.0000 | |
| 158 | Y | A | 0.1113 | |
| 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 | -0.4208 | |
| 165 | Q | A | -0.6785 | |
| 166 | A | A | -1.0569 | |
| 167 | P | A | -1.0443 | |
| 168 | G | A | -1.2148 | |
| 169 | Q | A | -1.6990 | |
| 170 | G | A | -0.9913 | |
| 171 | L | A | 0.0000 | |
| 172 | E | A | -0.5943 | |
| 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 | 0.2475 | |
| 181 | Y | A | 0.3787 | |
| 182 | G | A | -0.1046 | |
| 183 | S | A | -0.1902 | |
| 184 | T | A | -0.0523 | |
| 185 | G | A | 0.0000 | |
| 186 | Y | A | -0.3019 | |
| 187 | A | A | 0.0000 | |
| 188 | L | A | -0.1303 | |
| 189 | K | A | -1.5361 | |
| 190 | F | A | 0.0000 | |
| 191 | K | A | -1.9252 | |
| 192 | G | A | -1.4693 | |
| 193 | R | A | -1.3347 | |
| 194 | V | A | 0.0000 | |
| 195 | T | A | -0.8777 | |
| 196 | M | A | 0.0000 | |
| 197 | T | A | -0.5602 | |
| 198 | R | A | -0.9957 | |
| 199 | D | A | -1.2095 | |
| 200 | T | A | -0.6662 | |
| 201 | S | A | -0.5560 | |
| 202 | T | A | -0.7023 | |
| 203 | S | A | -0.8041 | |
| 204 | T | A | 0.0000 | |
| 205 | V | A | 0.0000 | |
| 206 | Y | A | -0.8064 | |
| 207 | M | A | 0.0000 | |
| 208 | E | A | -1.4727 | |
| 209 | L | A | 0.0000 | |
| 210 | S | A | -1.0357 | |
| 211 | S | A | -1.0541 | |
| 212 | L | A | 0.0000 | |
| 213 | R | A | -2.7395 | |
| 214 | S | A | -2.2297 | |
| 215 | E | A | -2.4695 | |
| 216 | D | A | 0.0000 | |
| 217 | T | A | -0.8738 | |
| 218 | A | A | 0.0000 | |
| 219 | V | A | 0.1116 | |
| 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 | 0.3600 | |
| 228 | Y | A | 1.0293 | |
| 229 | G | A | 0.0000 | |
| 230 | S | A | 0.2098 | |
| 231 | D | A | 0.0000 | |
| 232 | Y | A | -0.0791 | |
| 233 | W | A | -0.2947 | |
| 234 | G | A | 0.0000 | |
| 235 | Q | A | -1.3070 | |
| 236 | G | A | -0.5876 | |
| 237 | T | A | 0.0000 | |
| 238 | T | A | -0.0295 | |
| 239 | V | A | 0.0000 | |
| 240 | T | A | -0.3033 | |
| 241 | V | A | 0.0000 | |
| 242 | S | A | -1.0270 | |
| 243 | S | A | -0.9105 | |
| 1 | A | B | -0.5487 | |
| 2 | Q | B | -1.2984 | |
| 3 | E | B | -1.8586 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -1.7540 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.4893 | |
| 8 | P | B | 0.0000 | |
| 9 | H | B | -0.3006 | |
| 10 | C | B | 0.0000 | |
| 11 | T | B | 0.0000 | |
| 12 | T | B | 0.0000 | |
| 13 | V | B | 0.0000 | |
| 14 | P | B | -1.1239 | |
| 15 | V | B | -0.7997 | |
| 16 | G | B | -1.3043 | |
| 17 | A | B | 0.0000 | |
| 18 | S | B | -0.8082 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -0.9543 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8930 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.7204 | |
| 25 | T | B | -1.7150 | |
| 26 | S | B | -1.5239 | |
| 27 | G | B | -1.2048 | |
| 28 | G | B | -1.4621 | |
| 29 | L | B | -1.6804 | |
| 30 | R | B | -2.4432 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.0435 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.7912 | |
| 36 | Q | B | 0.0000 | |
| 37 | L | B | -0.7124 | |
| 38 | G | B | -1.1880 | |
| 39 | P | B | -1.2006 | |
| 40 | Q | B | -1.5810 | |
| 41 | P | B | -1.3153 | |
| 42 | Q | B | -1.2269 | |
| 43 | D | B | -1.0730 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.3186 | |
| 47 | Y | B | 0.0602 | |
| 48 | E | B | -0.9171 | |
| 49 | D | B | -1.5710 | |
| 50 | G | B | -0.2379 | |
| 51 | V | B | 1.3668 | |
| 52 | V | B | 1.9870 | |
| 53 | P | B | 0.7504 | |
| 54 | T | B | -0.0334 | |
| 55 | T | B | -1.3637 | |
| 56 | D | B | -2.0950 | |
| 57 | R | B | -3.0748 | |
| 58 | R | B | -2.3934 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -3.2210 | |
| 61 | G | B | -2.2759 | |
| 62 | R | B | -2.1540 | |
| 63 | I | B | -1.6119 | |
| 64 | D | B | -1.9853 | |
| 65 | F | B | -0.7218 | |
| 66 | S | B | -0.9381 | |
| 67 | G | B | -1.2541 | |
| 68 | S | B | -1.5660 | |
| 69 | Q | B | -1.9625 | |
| 70 | D | B | -2.4612 | |
| 71 | N | B | -2.2285 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0484 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.9547 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.7591 | |
| 78 | R | B | -2.2759 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -1.0734 | |
| 81 | L | B | 0.2190 | |
| 82 | S | B | -0.1282 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | -0.0838 | |
| 85 | G | B | -0.1989 | |
| 86 | T | B | -0.2624 | |
| 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 | -0.5932 | |
| 93 | T | B | -1.0698 | |
| 94 | E | B | -1.4039 | |
| 95 | V | B | 0.7130 | |
| 96 | N | B | 0.0402 | |
| 97 | V | B | -0.0197 | |
| 98 | Y | B | -0.0900 | |
| 99 | G | B | 0.0000 | |
| 100 | S | B | -0.5839 | |
| 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 | -1.1937 | |
| 108 | E | B | -2.1861 | |
| 109 | E | B | -2.8897 | |
| 110 | Q | B | -2.5818 | |
| 111 | S | B | -1.8199 | |
| 112 | Q | B | -1.4596 | |
| 113 | G | B | -1.0690 | |
| 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 | -0.1768 | |
| 120 | A | B | -0.2711 | |
| 121 | P | B | -0.6312 | |
| 122 | P | B | -1.2691 | |
| 123 | R | B | -1.9640 | |
| 124 | A | B | -0.7120 | |
| 125 | S | B | -0.3544 | |
| 126 | A | B | 0.5368 | |
| 127 | L | B | 1.4261 | |
| 128 | P | B | 0.5840 | |
| 129 | A | B | 0.1837 | |
| 130 | P | B | -0.0577 | |
| 131 | P | B | -0.6203 | |
| 132 | T | B | -0.5322 | |
| 133 | G | B | -0.4570 | |
| 134 | S | B | -0.0742 | |
| 135 | A | B | 0.1819 | |
| 136 | L | B | 0.7942 | |
| 137 | P | B | -0.6658 | |
| 138 | D | B | -1.9644 | |
| 139 | P | B | -1.5351 | |
| 140 | Q | B | -1.9234 | |
| 141 | T | B | -1.0365 | |
| 142 | A | B | -0.2180 | |
| 143 | S | B | 0.0251 | |
| 144 | A | B | 0.3739 | |
| 145 | L | B | 0.9101 | |
| 146 | P | B | -0.4950 | |
| 147 | D | B | -1.6920 | |
| 148 | P | B | -1.0645 | |
| 149 | P | B | -0.8596 | |
| 150 | A | B | -0.4230 | |
| 151 | A | B | 0.1061 | |
| 152 | S | B | 0.1968 | |
| 153 | A | B | 0.6636 | |
| 154 | L | B | 1.4067 | |
| 155 | P | B | 0.4729 |
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 | -0.3419 | 4.055 | View | CSV | PDB |
| 4.5 | -0.381 | 4.055 | View | CSV | PDB |
| 5.0 | -0.4285 | 4.055 | View | CSV | PDB |
| 5.5 | -0.4764 | 4.055 | View | CSV | PDB |
| 6.0 | -0.5173 | 4.055 | View | CSV | PDB |
| 6.5 | -0.5456 | 4.055 | View | CSV | PDB |
| 7.0 | -0.5601 | 4.055 | View | CSV | PDB |
| 7.5 | -0.5645 | 4.055 | View | CSV | PDB |
| 8.0 | -0.5627 | 4.055 | View | CSV | PDB |
| 8.5 | -0.5558 | 4.055 | View | CSV | PDB |
| 9.0 | -0.543 | 4.055 | 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