| Chain sequence(s) |
A: EIVLTKSPATLSLSPGERATLSCRVSQNVSSNLAWYQQKPGQAPRLLIYDTSNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRRNWPLTFGGGTKVEIKGGGGSGGGGSGGGGSEVQLVESGGGLVQPGGSLRLSCAASGFTFSRYAMSWVRQAPGKGLEWVSAISASGATTYYADPVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDQDFDILTGYLNWFDPWGQGTLVTVSS
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] (00:00:03)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:03)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:03)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:03)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:06)
[INFO] FoldX: Starting FoldX energy minimization (00:00:07)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:10:22)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/cfe0665fc0e8b1e/tmp/folded.pdb (00:10:22)
[INFO] Main: Simulation completed successfully. (00:16:39)
|
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 | E | A | -1.8047 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7436 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.6979 | |
| 6 | K | A | -0.9121 | |
| 7 | S | A | -0.7423 | |
| 8 | P | A | -0.3503 | |
| 9 | A | A | -0.2453 | |
| 10 | T | A | -0.2963 | |
| 11 | L | A | -0.3395 | |
| 12 | S | A | -0.7525 | |
| 13 | L | A | -1.2066 | |
| 14 | S | A | -1.6891 | |
| 15 | P | A | -1.9095 | |
| 16 | G | A | -1.7109 | |
| 17 | E | A | -2.2417 | |
| 18 | R | A | -2.6138 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.6607 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -1.0288 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.5436 | |
| 25 | V | A | 0.0000 | |
| 26 | S | A | -1.2344 | |
| 27 | Q | A | -2.3099 | |
| 28 | N | A | -2.5017 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -1.2409 | |
| 31 | S | A | -0.8940 | |
| 32 | N | A | -0.8940 | |
| 33 | L | A | 0.0000 | |
| 34 | A | A | 0.0000 | |
| 35 | W | A | 0.0000 | |
| 36 | Y | A | 0.0000 | |
| 37 | Q | A | -0.4538 | |
| 38 | Q | A | 0.0000 | |
| 39 | K | A | -1.1217 | |
| 40 | P | A | -0.8152 | |
| 41 | G | A | -1.2620 | |
| 42 | Q | A | -1.6533 | |
| 43 | A | A | -1.1600 | |
| 44 | P | A | 0.0000 | |
| 45 | R | A | -1.0469 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | 0.0000 | |
| 50 | D | A | -1.0942 | |
| 51 | T | A | 0.0000 | |
| 52 | S | A | -1.3018 | |
| 53 | N | A | -1.8143 | |
| 54 | R | A | -1.8393 | |
| 55 | A | A | 0.0000 | |
| 56 | T | A | -0.7415 | |
| 57 | G | A | -0.8419 | |
| 58 | I | A | 0.0000 | |
| 59 | P | A | -0.5063 | |
| 60 | A | A | -0.4191 | |
| 61 | R | A | -0.7046 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.7929 | |
| 64 | G | A | -0.8509 | |
| 65 | S | A | -0.8646 | |
| 66 | G | A | -1.1126 | |
| 67 | S | A | -1.2952 | |
| 68 | G | A | -1.6352 | |
| 69 | T | A | -2.0590 | |
| 70 | D | A | -2.2762 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.8426 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.6185 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.3265 | |
| 77 | S | A | -1.6342 | |
| 78 | L | A | 0.0000 | |
| 79 | E | A | -1.9761 | |
| 80 | P | A | -1.6744 | |
| 81 | E | A | -2.3533 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | -0.6461 | |
| 84 | A | A | 0.0000 | |
| 85 | V | A | -0.1318 | |
| 86 | Y | A | 0.0000 | |
| 87 | Y | A | 0.0000 | |
| 88 | C | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | Q | A | 0.0000 | |
| 91 | R | A | 0.0000 | |
| 92 | R | A | -1.2956 | |
| 93 | N | A | -1.4992 | |
| 94 | W | A | -0.9384 | |
| 95 | P | A | -0.9104 | |
| 96 | L | A | 0.0000 | |
| 97 | T | A | 0.0000 | |
| 98 | F | A | 0.2119 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -0.8248 | |
| 101 | G | A | -0.7408 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -0.4722 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | -1.1489 | |
| 106 | I | A | -1.7121 | |
| 107 | K | A | -2.2351 | |
| 108 | G | A | -1.7612 | |
| 109 | G | A | -1.6558 | |
| 110 | G | A | -1.3977 | |
| 111 | G | A | -1.1722 | |
| 112 | S | A | -1.3586 | |
| 113 | G | A | -1.4808 | |
| 114 | G | A | -1.5610 | |
| 115 | G | A | -1.4173 | |
| 116 | G | A | -1.6708 | |
| 117 | S | A | -1.2438 | |
| 118 | G | A | -1.2229 | |
| 119 | G | A | -1.2917 | |
| 120 | G | A | -1.4304 | |
| 121 | G | A | -1.7255 | |
| 122 | S | A | -1.7326 | |
| 123 | E | A | -2.4470 | |
| 124 | V | A | -1.5524 | |
| 125 | Q | A | -1.7159 | |
| 126 | L | A | 0.0000 | |
| 127 | V | A | 0.1155 | |
| 128 | E | A | 0.0000 | |
| 129 | S | A | -0.3565 | |
| 130 | G | A | -0.7128 | |
| 131 | G | A | 0.0848 | |
| 132 | G | A | 0.5869 | |
| 133 | L | A | 1.2908 | |
| 134 | V | A | 0.0000 | |
| 135 | Q | A | -1.5159 | |
| 136 | P | A | -1.9176 | |
| 137 | G | A | -1.6797 | |
| 138 | G | A | -1.1833 | |
| 139 | S | A | -1.4376 | |
| 140 | L | A | -0.9979 | |
| 141 | R | A | -1.9215 | |
| 142 | L | A | 0.0000 | |
| 143 | S | A | -0.4624 | |
| 144 | C | A | 0.0000 | |
| 145 | A | A | -0.4270 | |
| 146 | A | A | 0.0000 | |
| 147 | S | A | -1.1510 | |
| 148 | G | A | -1.2729 | |
| 149 | F | A | -0.8349 | |
| 150 | T | A | -0.5133 | |
| 151 | F | A | 0.0000 | |
| 152 | S | A | -1.2886 | |
| 153 | R | A | -1.5268 | |
| 154 | Y | A | 0.0000 | |
| 155 | A | A | -0.3531 | |
| 156 | M | A | 0.0000 | |
| 157 | S | A | 0.0000 | |
| 158 | W | A | 0.0000 | |
| 159 | V | A | 0.0000 | |
| 160 | R | A | 0.0000 | |
| 161 | Q | A | -0.6965 | |
| 162 | A | A | -1.0929 | |
| 163 | P | A | -0.8750 | |
| 164 | G | A | -1.4899 | |
| 165 | K | A | -2.2836 | |
| 166 | G | A | -1.4093 | |
| 167 | L | A | 0.0000 | |
| 168 | E | A | -0.9047 | |
| 169 | W | A | 0.0000 | |
| 170 | V | A | 0.0000 | |
| 171 | S | A | 0.0000 | |
| 172 | A | A | 0.0000 | |
| 173 | I | A | 0.0000 | |
| 174 | S | A | 0.0000 | |
| 175 | A | A | 0.0000 | |
| 176 | S | A | -0.6790 | |
| 177 | G | A | -0.4041 | |
| 178 | A | A | -0.1166 | |
| 179 | T | A | -0.0483 | |
| 180 | T | A | 0.0980 | |
| 181 | Y | A | -0.0320 | |
| 182 | Y | A | -0.7021 | |
| 183 | A | A | 0.0000 | |
| 184 | D | A | -2.6747 | |
| 185 | P | A | -1.8357 | |
| 186 | V | A | 0.0000 | |
| 187 | K | A | -2.6121 | |
| 188 | G | A | -1.8522 | |
| 189 | R | A | -1.7562 | |
| 190 | F | A | 0.0000 | |
| 191 | T | A | -0.8759 | |
| 192 | I | A | 0.0000 | |
| 193 | S | A | -0.4049 | |
| 194 | R | A | -0.9798 | |
| 195 | D | A | -1.6142 | |
| 196 | N | A | -1.8064 | |
| 197 | S | A | -1.5882 | |
| 198 | K | A | -2.4022 | |
| 199 | N | A | -1.7409 | |
| 200 | T | A | -1.1004 | |
| 201 | L | A | 0.0000 | |
| 202 | Y | A | -0.4923 | |
| 203 | L | A | 0.0000 | |
| 204 | Q | A | -1.3028 | |
| 205 | M | A | 0.0000 | |
| 206 | N | A | -1.9248 | |
| 207 | S | A | -1.6089 | |
| 208 | L | A | 0.0000 | |
| 209 | R | A | -2.9964 | |
| 210 | A | A | -2.0571 | |
| 211 | E | A | -2.4667 | |
| 212 | D | A | 0.0000 | |
| 213 | T | A | -0.5630 | |
| 214 | A | A | 0.0000 | |
| 215 | V | A | 0.6434 | |
| 216 | Y | A | 0.0000 | |
| 217 | Y | A | 0.0000 | |
| 218 | C | A | 0.0000 | |
| 219 | A | A | 0.0000 | |
| 220 | K | A | 0.0000 | |
| 221 | D | A | 0.0000 | |
| 222 | Q | A | 0.0000 | |
| 223 | D | A | -1.1928 | |
| 224 | F | A | -0.9330 | |
| 225 | D | A | -1.5087 | |
| 226 | I | A | 0.4470 | |
| 227 | L | A | 0.0000 | |
| 228 | T | A | -0.7413 | |
| 229 | G | A | 0.0000 | |
| 230 | Y | A | -0.1467 | |
| 231 | L | A | 0.0000 | |
| 232 | N | A | 0.0000 | |
| 233 | W | A | 0.0000 | |
| 234 | F | A | 0.0000 | |
| 235 | D | A | -0.6817 | |
| 236 | P | A | -0.8405 | |
| 237 | W | A | 0.0000 | |
| 238 | G | A | 0.0000 | |
| 239 | Q | A | -1.3913 | |
| 240 | G | A | 0.0000 | |
| 241 | T | A | 0.3771 | |
| 242 | L | A | 1.4281 | |
| 243 | V | A | 0.0000 | |
| 244 | T | A | 0.1562 | |
| 245 | V | A | 0.0000 | |
| 246 | S | A | -0.9186 | |
| 247 | S | A | -0.5822 | |
| 1 | A | B | -1.8956 | |
| 2 | Q | B | -2.0131 | |
| 3 | E | B | -2.7146 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -1.7916 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.9524 | |
| 8 | P | B | -0.8853 | |
| 9 | H | B | -0.8708 | |
| 10 | C | B | -0.4805 | |
| 11 | T | B | -0.5064 | |
| 12 | T | B | -0.0039 | |
| 13 | V | B | -0.2079 | |
| 14 | P | B | -0.9174 | |
| 15 | V | B | -0.6174 | |
| 16 | G | B | -0.8010 | |
| 17 | A | B | -0.4352 | |
| 18 | S | B | -0.7836 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -1.3980 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.9644 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.9653 | |
| 25 | T | B | -2.1047 | |
| 26 | S | B | -2.0142 | |
| 27 | G | B | -1.5684 | |
| 28 | G | B | -1.6457 | |
| 29 | L | B | -2.0834 | |
| 30 | R | B | -2.5147 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.0854 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.4823 | |
| 36 | Q | B | -0.4093 | |
| 37 | L | B | 0.2129 | |
| 38 | G | B | -0.4868 | |
| 39 | P | B | -0.8447 | |
| 40 | Q | B | -1.5037 | |
| 41 | P | B | -1.0839 | |
| 42 | Q | B | -1.1702 | |
| 43 | D | B | -1.2119 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | -0.0515 | |
| 47 | Y | B | 0.0000 | |
| 48 | E | B | -1.7351 | |
| 49 | D | B | -2.2708 | |
| 50 | G | B | -1.5175 | |
| 51 | V | B | 0.0000 | |
| 52 | V | B | 0.0000 | |
| 53 | P | B | 0.0000 | |
| 54 | T | B | -0.4360 | |
| 55 | T | B | 0.0000 | |
| 56 | D | B | -2.0422 | |
| 57 | R | B | -2.8478 | |
| 58 | R | B | -2.9861 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -1.7511 | |
| 61 | G | B | -1.2336 | |
| 62 | R | B | -1.2862 | |
| 63 | I | B | 0.0000 | |
| 64 | D | B | 0.0000 | |
| 65 | F | B | 0.0000 | |
| 66 | S | B | -0.7902 | |
| 67 | G | B | -1.4268 | |
| 68 | S | B | -1.7872 | |
| 69 | Q | B | -2.2427 | |
| 70 | D | B | -3.0180 | |
| 71 | N | B | -2.4961 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0550 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.6736 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -0.9961 | |
| 78 | R | B | -1.1880 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -0.7859 | |
| 81 | L | B | 0.2670 | |
| 82 | S | B | 0.0489 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | 0.2105 | |
| 85 | G | B | 0.3419 | |
| 86 | T | B | 0.3252 | |
| 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 | -0.5871 | |
| 93 | T | B | 0.0000 | |
| 94 | E | B | -1.4688 | |
| 95 | V | B | 0.3190 | |
| 96 | N | B | -0.7242 | |
| 97 | V | B | -0.2568 | |
| 98 | Y | B | 0.4604 | |
| 99 | G | B | -0.3101 | |
| 100 | S | B | -0.3353 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | L | B | 0.5075 | |
| 104 | V | B | 0.0000 | |
| 105 | L | B | 0.6540 | |
| 106 | V | B | 0.0000 | |
| 107 | T | B | -1.2772 | |
| 108 | E | B | -2.7699 | |
| 109 | E | B | -3.4110 | |
| 110 | Q | B | -2.7862 | |
| 111 | S | B | -2.2494 | |
| 112 | Q | B | -2.0588 | |
| 113 | G | B | -1.9074 | |
| 114 | W | B | -1.6350 | |
| 115 | H | B | -1.9744 | |
| 116 | R | B | -2.5504 | |
| 117 | C | B | -1.5036 | |
| 118 | S | B | -1.8086 | |
| 119 | D | B | -2.3395 | |
| 120 | A | B | -1.4705 | |
| 121 | P | B | -1.5088 | |
| 122 | P | B | -1.6385 | |
| 123 | R | B | -2.0653 | |
| 124 | A | B | -0.7898 | |
| 125 | S | B | -0.3600 | |
| 126 | A | B | 0.3649 | |
| 127 | L | B | 1.3718 | |
| 128 | P | B | 0.3930 | |
| 129 | A | B | 0.1644 | |
| 130 | P | B | -0.2559 | |
| 131 | P | B | -0.6112 | |
| 132 | T | B | -0.5285 | |
| 133 | G | B | -0.4650 | |
| 134 | S | B | -0.0720 | |
| 135 | A | B | 0.2228 | |
| 136 | L | B | 0.8269 | |
| 137 | P | B | -0.6381 | |
| 138 | D | B | -1.9728 | |
| 139 | P | B | -1.5432 | |
| 140 | Q | B | -1.8986 | |
| 141 | T | B | -0.9835 | |
| 142 | A | B | -0.2127 | |
| 143 | S | B | 0.0408 | |
| 144 | A | B | 0.3926 | |
| 145 | L | B | 0.9384 | |
| 146 | P | B | -0.4912 | |
| 147 | D | B | -1.7090 | |
| 148 | P | B | -1.0733 | |
| 149 | P | B | -0.8486 | |
| 150 | A | B | -0.3995 | |
| 151 | A | B | 0.1003 | |
| 152 | S | B | 0.2011 | |
| 153 | A | B | 0.6603 | |
| 154 | L | B | 1.4059 | |
| 155 | P | B | 0.4721 |
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 | -0.389 | 3.8548 | View | CSV | PDB |
| 4.5 | -0.4356 | 3.8548 | View | CSV | PDB |
| 5.0 | -0.4911 | 3.8548 | View | CSV | PDB |
| 5.5 | -0.5482 | 3.8548 | View | CSV | PDB |
| 6.0 | -0.5994 | 3.8548 | View | CSV | PDB |
| 6.5 | -0.6393 | 3.8548 | View | CSV | PDB |
| 7.0 | -0.667 | 3.8548 | View | CSV | PDB |
| 7.5 | -0.6855 | 3.8548 | View | CSV | PDB |
| 8.0 | -0.6975 | 3.8548 | View | CSV | PDB |
| 8.5 | -0.7029 | 3.8548 | View | CSV | PDB |
| 9.0 | -0.7008 | 3.8548 | 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