| Chain sequence(s) |
A: DVLMTQTPLSLPVTLGDQASISCRSSQSIVHSNGYTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLRISGVEAEDLGVYYCFQGSHVPWTFGGGTKLEIKVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
B: QVQLQQSGAELARPGASVKLSCKASGYTFTNYGITWVKQRTGQGLEWIGEIYPRSGNTYYNEKFKGKATLTADKSSSTASMELRSLTSEDSAVYFCATKGLWYFDVWGTGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 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 (00:05:34)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/24e9e396e6b8bc/tmp/folded.pdb (00:05:34)
[INFO] Main: Simulation completed successfully. (00:07:48)
|
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 | -1.3797 | |
| 2 | V | A | 0.0000 | |
| 3 | L | A | 0.4635 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.4727 | |
| 6 | Q | A | -0.3171 | |
| 7 | T | A | -0.1454 | |
| 8 | P | A | 0.4025 | |
| 9 | L | A | 1.1841 | |
| 10 | S | A | 0.3007 | |
| 11 | L | A | 0.0734 | |
| 12 | P | A | -0.6738 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -0.8310 | |
| 15 | L | A | -0.5166 | |
| 16 | G | A | -1.4234 | |
| 17 | D | A | -2.4643 | |
| 18 | Q | A | -2.6155 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -1.0490 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.9140 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.2823 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -0.9695 | |
| 27 | Q | A | -1.3208 | |
| 28 | S | A | -0.8527 | |
| 29 | I | A | 0.0000 | |
| 30 | V | A | 0.4528 | |
| 31 | H | A | -0.2610 | |
| 32 | S | A | -0.7398 | |
| 33 | N | A | -1.2067 | |
| 34 | G | A | -0.4675 | |
| 35 | Y | A | 0.5109 | |
| 36 | T | A | 0.2999 | |
| 37 | Y | A | 0.2769 | |
| 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 | -1.5308 | |
| 45 | P | A | -1.2148 | |
| 46 | G | A | -1.2889 | |
| 47 | Q | A | -1.6050 | |
| 48 | S | A | -0.9971 | |
| 49 | P | A | 0.0000 | |
| 50 | K | A | -1.3092 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | -0.3863 | |
| 55 | K | A | -0.5223 | |
| 56 | V | A | -0.4412 | |
| 57 | S | A | -0.8802 | |
| 58 | N | A | -1.2449 | |
| 59 | R | A | -1.6042 | |
| 60 | F | A | -0.6557 | |
| 61 | S | A | -0.5527 | |
| 62 | G | A | -0.8214 | |
| 63 | V | A | -0.9388 | |
| 64 | P | A | -1.3102 | |
| 65 | D | A | -2.2172 | |
| 66 | R | A | -1.9608 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.5061 | |
| 69 | G | A | 0.0000 | |
| 70 | S | A | -0.9390 | |
| 71 | G | A | -0.9269 | |
| 72 | S | A | -0.6354 | |
| 73 | G | A | -0.7775 | |
| 74 | T | A | -1.4319 | |
| 75 | D | A | -1.9826 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -1.1310 | |
| 78 | L | A | 0.0000 | |
| 79 | R | A | -2.0888 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.0591 | |
| 82 | G | A | -1.7081 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.2108 | |
| 85 | A | A | -2.1396 | |
| 86 | E | A | -2.6819 | |
| 87 | D | A | 0.0000 | |
| 88 | L | A | 0.0000 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | -0.1455 | |
| 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 | 0.3007 | |
| 97 | S | A | 0.0000 | |
| 98 | H | A | 0.3866 | |
| 99 | V | A | 1.2546 | |
| 100 | P | A | 0.1180 | |
| 101 | W | A | 0.5472 | |
| 102 | T | A | 0.1678 | |
| 103 | F | A | 0.0000 | |
| 104 | G | A | 0.0000 | |
| 105 | G | A | -0.4156 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.5464 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -0.9807 | |
| 111 | I | A | 0.0000 | |
| 112 | K | A | -1.0387 | |
| 113 | V | A | 0.5300 | |
| 114 | A | A | -0.0316 | |
| 115 | A | A | 0.0563 | |
| 116 | P | A | 0.0000 | |
| 117 | S | A | -0.1904 | |
| 118 | V | A | 0.0000 | |
| 119 | F | A | 0.0000 | |
| 120 | I | A | 0.0000 | |
| 121 | F | A | 0.0000 | |
| 122 | P | A | -0.4575 | |
| 123 | P | A | 0.0000 | |
| 124 | S | A | 0.0000 | |
| 125 | D | A | -3.0906 | |
| 126 | E | A | -3.1359 | |
| 127 | Q | A | 0.0000 | |
| 128 | L | A | -2.3231 | |
| 129 | K | A | -2.9501 | |
| 130 | S | A | -1.8675 | |
| 131 | G | A | -1.3467 | |
| 132 | T | A | -1.3203 | |
| 133 | A | A | 0.0000 | |
| 134 | S | A | 0.0000 | |
| 135 | V | A | 0.0000 | |
| 136 | V | A | 0.0000 | |
| 137 | C | A | 0.0000 | |
| 138 | L | A | 0.0000 | |
| 139 | L | A | 0.0000 | |
| 140 | N | A | 0.0000 | |
| 141 | N | A | -0.6363 | |
| 142 | F | A | 0.0000 | |
| 143 | Y | A | -0.8325 | |
| 144 | P | A | -1.6102 | |
| 145 | R | A | -3.0995 | |
| 146 | E | A | -3.2429 | |
| 147 | A | A | -2.3835 | |
| 148 | K | A | -2.5229 | |
| 149 | V | A | -1.1842 | |
| 150 | Q | A | -0.8205 | |
| 151 | W | A | 0.0000 | |
| 152 | K | A | -0.7327 | |
| 153 | V | A | 0.0000 | |
| 154 | D | A | -1.8903 | |
| 155 | N | A | -1.4309 | |
| 156 | A | A | -0.4364 | |
| 157 | L | A | 0.2976 | |
| 158 | Q | A | -0.3084 | |
| 159 | S | A | -0.5635 | |
| 160 | G | A | -0.8695 | |
| 161 | N | A | -0.7722 | |
| 162 | S | A | -0.9636 | |
| 163 | Q | A | -1.0638 | |
| 164 | E | A | -1.3120 | |
| 165 | S | A | -0.6467 | |
| 166 | V | A | -0.7377 | |
| 167 | T | A | -0.8102 | |
| 168 | E | A | -1.6198 | |
| 169 | Q | A | 0.0000 | |
| 170 | D | A | -2.0529 | |
| 171 | S | A | -2.4389 | |
| 172 | K | A | -3.1133 | |
| 173 | D | A | -2.4808 | |
| 174 | S | A | 0.0000 | |
| 175 | T | A | 0.0000 | |
| 176 | Y | A | 0.0000 | |
| 177 | S | A | 0.0000 | |
| 178 | L | A | 0.0000 | |
| 179 | S | A | 0.0000 | |
| 180 | S | A | 0.0000 | |
| 181 | T | A | -0.5175 | |
| 182 | L | A | 0.0000 | |
| 183 | T | A | -0.4228 | |
| 184 | L | A | -0.6667 | |
| 185 | S | A | -1.0921 | |
| 186 | K | A | -2.0645 | |
| 187 | A | A | -1.8796 | |
| 188 | D | A | -2.6814 | |
| 189 | Y | A | 0.0000 | |
| 190 | E | A | -3.0693 | |
| 191 | K | A | -3.4036 | |
| 192 | H | A | -2.7950 | |
| 193 | K | A | -2.8093 | |
| 194 | V | A | -1.4346 | |
| 195 | Y | A | 0.0000 | |
| 196 | A | A | 0.0000 | |
| 197 | C | A | 0.0000 | |
| 198 | E | A | -0.8215 | |
| 199 | V | A | 0.0000 | |
| 200 | T | A | -1.2836 | |
| 201 | H | A | 0.0000 | |
| 202 | Q | A | -1.7325 | |
| 203 | G | A | -0.3884 | |
| 204 | L | A | -0.3513 | |
| 205 | S | A | -0.4562 | |
| 206 | S | A | -0.4465 | |
| 207 | P | A | -0.6035 | |
| 208 | V | A | -0.0681 | |
| 209 | T | A | -0.4829 | |
| 210 | K | A | -0.7921 | |
| 211 | S | A | -0.6276 | |
| 212 | F | A | 0.0000 | |
| 213 | N | A | -1.6349 | |
| 214 | R | A | -2.0971 | |
| 215 | G | A | -1.7455 | |
| 216 | E | A | -2.1166 | |
| 217 | C | A | -0.6602 | |
| 1 | Q | B | -1.4397 | |
| 2 | V | B | -0.8778 | |
| 3 | Q | B | -1.8040 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -2.0017 | |
| 6 | Q | B | -1.2668 | |
| 7 | S | B | -1.2439 | |
| 8 | G | B | -1.2562 | |
| 9 | A | B | -0.9292 | |
| 10 | E | B | -1.2676 | |
| 11 | L | B | -0.8853 | |
| 12 | A | B | 0.0000 | |
| 13 | R | B | -2.2221 | |
| 14 | P | B | -1.6042 | |
| 15 | G | B | -1.3654 | |
| 16 | A | B | -1.1640 | |
| 17 | S | B | -1.4283 | |
| 18 | V | B | 0.0000 | |
| 19 | K | B | -2.1933 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -1.0814 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -1.7970 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.2509 | |
| 26 | G | B | -0.9781 | |
| 27 | Y | B | -0.4303 | |
| 28 | T | B | -0.4110 | |
| 29 | F | B | 0.0000 | |
| 30 | T | B | -1.4842 | |
| 31 | N | B | -1.0793 | |
| 32 | Y | B | -0.0777 | |
| 33 | G | B | -0.3775 | |
| 34 | I | B | 0.0000 | |
| 35 | T | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | K | B | -0.5847 | |
| 39 | Q | B | -0.9637 | |
| 40 | R | B | -1.5931 | |
| 41 | T | B | -1.0060 | |
| 42 | G | B | -1.3121 | |
| 43 | Q | B | -1.8938 | |
| 44 | G | B | -1.2525 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -0.9158 | |
| 47 | W | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | G | B | 0.0000 | |
| 50 | E | B | 0.0000 | |
| 51 | I | B | 0.0000 | |
| 52 | Y | B | -0.4146 | |
| 53 | P | B | 0.0000 | |
| 54 | R | B | -2.6688 | |
| 55 | S | B | -1.6923 | |
| 56 | G | B | -1.7510 | |
| 57 | N | B | -1.3576 | |
| 58 | T | B | -0.0142 | |
| 59 | Y | B | 0.7883 | |
| 60 | Y | B | -0.2568 | |
| 61 | N | B | 0.0000 | |
| 62 | E | B | -3.0754 | |
| 63 | K | B | -3.1876 | |
| 64 | F | B | 0.0000 | |
| 65 | K | B | -2.9238 | |
| 66 | G | B | -2.0372 | |
| 67 | K | B | -1.8882 | |
| 68 | A | B | 0.0000 | |
| 69 | T | B | -0.8505 | |
| 70 | L | B | 0.0000 | |
| 71 | T | B | -0.7711 | |
| 72 | A | B | -1.6602 | |
| 73 | D | B | -2.6091 | |
| 74 | K | B | -2.9213 | |
| 75 | S | B | -1.5084 | |
| 76 | S | B | -1.3468 | |
| 77 | S | B | -1.4593 | |
| 78 | T | B | -1.5288 | |
| 79 | A | B | 0.0000 | |
| 80 | S | B | 0.0000 | |
| 81 | M | B | 0.0000 | |
| 82 | E | B | -1.5696 | |
| 83 | L | B | 0.0000 | |
| 84 | R | B | -1.4438 | |
| 85 | S | B | -1.1347 | |
| 86 | L | B | 0.0000 | |
| 87 | T | B | -1.3848 | |
| 88 | S | B | -1.4522 | |
| 89 | E | B | -2.0553 | |
| 90 | D | B | 0.0000 | |
| 91 | S | B | -0.8857 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | 0.0767 | |
| 94 | Y | B | 0.0000 | |
| 95 | F | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | T | B | 0.0000 | |
| 99 | K | B | -0.2605 | |
| 100 | G | B | 0.5508 | |
| 101 | L | B | 1.5891 | |
| 102 | W | B | 1.0010 | |
| 103 | Y | B | 0.3544 | |
| 104 | F | B | 0.0000 | |
| 105 | D | B | -0.1213 | |
| 106 | V | B | -0.1588 | |
| 107 | W | B | -0.6374 | |
| 108 | G | B | 0.0000 | |
| 109 | T | B | -0.7903 | |
| 110 | G | B | -0.5249 | |
| 111 | T | B | 0.0000 | |
| 112 | T | B | -0.3713 | |
| 113 | V | B | 0.0000 | |
| 114 | T | B | -0.7907 | |
| 115 | V | B | 0.0000 | |
| 116 | S | B | -0.9607 | |
| 117 | S | B | -1.0389 | |
| 118 | A | B | -0.5852 | |
| 119 | S | B | -0.6596 | |
| 120 | T | B | -0.7079 | |
| 121 | K | B | -1.0994 | |
| 122 | G | B | -1.2374 | |
| 123 | P | B | 0.0000 | |
| 124 | S | B | -0.4068 | |
| 125 | V | B | 0.0000 | |
| 126 | F | B | 0.0000 | |
| 127 | P | B | -1.2142 | |
| 128 | L | B | 0.0000 | |
| 129 | A | B | -1.0619 | |
| 130 | P | B | 0.0000 | |
| 131 | S | B | -0.7693 | |
| 132 | S | B | -0.7314 | |
| 133 | K | B | -1.0361 | |
| 134 | S | B | 0.0000 | |
| 135 | T | B | -0.6734 | |
| 136 | S | B | -0.7088 | |
| 137 | G | B | -0.8107 | |
| 138 | G | B | -0.8771 | |
| 139 | T | B | -0.5923 | |
| 140 | A | B | 0.0000 | |
| 141 | A | B | 0.0000 | |
| 142 | L | B | 0.0000 | |
| 143 | G | B | 0.0000 | |
| 144 | C | B | 0.0000 | |
| 145 | L | B | 0.0000 | |
| 146 | V | B | 0.0000 | |
| 147 | K | B | 0.0000 | |
| 148 | D | B | -0.3448 | |
| 149 | Y | B | 0.0000 | |
| 150 | F | B | 0.0000 | |
| 151 | P | B | 0.0000 | |
| 152 | E | B | -0.4935 | |
| 153 | P | B | -0.7243 | |
| 154 | V | B | 0.0000 | |
| 155 | T | B | -0.5770 | |
| 156 | V | B | -0.3711 | |
| 157 | S | B | -0.3256 | |
| 158 | W | B | 0.0000 | |
| 159 | N | B | -0.6100 | |
| 160 | S | B | -0.5787 | |
| 161 | G | B | -0.5020 | |
| 162 | A | B | -0.2316 | |
| 163 | L | B | 0.0237 | |
| 164 | T | B | -0.1571 | |
| 165 | S | B | -0.3590 | |
| 166 | G | B | -0.4084 | |
| 167 | V | B | 0.1961 | |
| 168 | H | B | 0.0000 | |
| 169 | T | B | 0.0802 | |
| 170 | F | B | 0.0000 | |
| 171 | P | B | -0.1908 | |
| 172 | A | B | 0.2800 | |
| 173 | V | B | 0.6238 | |
| 174 | L | B | 1.2613 | |
| 175 | Q | B | 0.3390 | |
| 176 | S | B | -0.0845 | |
| 177 | S | B | -0.2107 | |
| 178 | G | B | 0.0316 | |
| 179 | L | B | 0.2018 | |
| 180 | Y | B | 0.4953 | |
| 181 | S | B | 0.0000 | |
| 182 | L | B | 0.0000 | |
| 183 | S | B | 0.0000 | |
| 184 | S | B | 0.0000 | |
| 185 | V | B | 0.0000 | |
| 186 | V | B | 0.0000 | |
| 187 | T | B | -0.1326 | |
| 188 | V | B | 0.0000 | |
| 189 | P | B | -0.6155 | |
| 190 | S | B | -0.5751 | |
| 191 | S | B | -0.5856 | |
| 192 | S | B | -0.5690 | |
| 193 | L | B | -0.7962 | |
| 194 | G | B | -0.9514 | |
| 195 | T | B | -0.6922 | |
| 196 | Q | B | -1.1555 | |
| 197 | T | B | -0.9997 | |
| 198 | Y | B | 0.0000 | |
| 199 | I | B | -1.0216 | |
| 200 | C | B | 0.0000 | |
| 201 | N | B | -1.2917 | |
| 202 | V | B | 0.0000 | |
| 203 | N | B | -1.8495 | |
| 204 | H | B | 0.0000 | |
| 205 | K | B | -2.3163 | |
| 206 | P | B | -1.4996 | |
| 207 | S | B | -1.6655 | |
| 208 | N | B | -2.3609 | |
| 209 | T | B | -1.9595 | |
| 210 | K | B | -2.5656 | |
| 211 | V | B | -1.5641 | |
| 212 | D | B | -2.0180 | |
| 213 | K | B | -1.9604 | |
| 214 | K | B | -2.1775 | |
| 215 | V | B | 0.0000 | |
| 216 | E | B | -2.5568 | |
| 217 | P | B | -1.3979 | |
| 218 | K | B | -1.3472 | |
| 219 | S | B | -0.8198 |
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 | -0.753 | 2.1262 | View | CSV | PDB |
| 4.5 | -0.7957 | 2.1203 | View | CSV | PDB |
| 5.0 | -0.8453 | 2.1169 | View | CSV | PDB |
| 5.5 | -0.8918 | 2.1204 | View | CSV | PDB |
| 6.0 | -0.9239 | 2.138 | View | CSV | PDB |
| 6.5 | -0.9325 | 2.1732 | View | CSV | PDB |
| 7.0 | -0.9173 | 2.2208 | View | CSV | PDB |
| 7.5 | -0.8862 | 2.2746 | View | CSV | PDB |
| 8.0 | -0.8461 | 2.3313 | View | CSV | PDB |
| 8.5 | -0.7993 | 2.3901 | View | CSV | PDB |
| 9.0 | -0.7465 | 2.4502 | 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