| Chain sequence(s) |
A: LYSPSDPLTLLQADTVRGAVLGSRSAWAVEFFASWCGHCIAFAPTWKALAEDVKAWRPALYLAALDCAEETNSAVCRDFNIPGFPTVRFFKAFTKNGSGAVFPVAGADVQTLRERLIDALESHHDTWPPACPPLEPAKLEEIDGFFARNNEEYLALIFEKGGSYLGREVALDLSQHKGVAVRRVLNTEANVVRKFGVTDFPSCYLLFRNGSVSRVPVLMESRSFYTAYLQRLSGLTR
B: DVVMTQSHKFMSTSVGDRVSITCKASQDVSTAVAWYQQKSGQSPKLLIHSASYRYTGVPDRFTGSGSGTDFTFTISSVQAEDLAVYYCQQHYSIPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 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. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:05:33)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/7d9f7de811c0da2/tmp/folded.pdb (00:05:33)
[INFO] Main: Simulation completed successfully. (00:07:39)
|
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 |
|---|---|---|---|---|
| 35 | L | A | 1.3596 | |
| 36 | Y | A | 0.3522 | |
| 37 | S | A | -0.0932 | |
| 38 | P | A | -0.4225 | |
| 39 | S | A | -0.5256 | |
| 40 | D | A | -0.7027 | |
| 41 | P | A | -1.0592 | |
| 42 | L | A | 0.0000 | |
| 43 | T | A | 0.1716 | |
| 44 | L | A | 0.3323 | |
| 45 | L | A | 0.0000 | |
| 46 | Q | A | -1.0871 | |
| 47 | A | A | -1.5501 | |
| 48 | D | A | -2.1584 | |
| 49 | T | A | -1.3365 | |
| 50 | V | A | 0.0000 | |
| 51 | R | A | -1.6489 | |
| 52 | G | A | -1.1253 | |
| 53 | A | A | -0.8752 | |
| 54 | V | A | 0.0000 | |
| 55 | L | A | -1.1933 | |
| 56 | G | A | -1.1409 | |
| 57 | S | A | -1.1156 | |
| 58 | R | A | -1.7216 | |
| 59 | S | A | 0.0000 | |
| 60 | A | A | 0.0000 | |
| 61 | W | A | 0.0000 | |
| 62 | A | A | 0.0000 | |
| 63 | V | A | 0.0000 | |
| 64 | E | A | 0.0000 | |
| 65 | F | A | 0.0000 | |
| 66 | F | A | 0.0000 | |
| 67 | A | A | 0.0000 | |
| 68 | S | A | 0.8510 | |
| 69 | W | A | 1.3525 | |
| 70 | C | A | 0.0000 | |
| 71 | G | A | -0.0813 | |
| 72 | H | A | -0.4757 | |
| 73 | C | A | 0.0000 | |
| 74 | I | A | 1.4011 | |
| 75 | A | A | 0.2278 | |
| 76 | F | A | 0.0000 | |
| 77 | A | A | 0.0000 | |
| 78 | P | A | 0.0348 | |
| 79 | T | A | -0.5310 | |
| 80 | W | A | 0.0000 | |
| 81 | K | A | -0.9408 | |
| 82 | A | A | -0.9482 | |
| 83 | L | A | 0.0000 | |
| 84 | A | A | 0.0000 | |
| 85 | E | A | -2.5083 | |
| 86 | D | A | -1.7558 | |
| 87 | V | A | 0.0000 | |
| 88 | K | A | -1.7537 | |
| 89 | A | A | -1.2034 | |
| 90 | W | A | 0.0000 | |
| 91 | R | A | -1.0022 | |
| 92 | P | A | -0.9878 | |
| 93 | A | A | 0.0000 | |
| 94 | L | A | 0.0000 | |
| 95 | Y | A | -0.0248 | |
| 96 | L | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | A | A | 0.0000 | |
| 99 | L | A | 0.0000 | |
| 100 | D | A | -0.3036 | |
| 101 | C | A | -0.6882 | |
| 102 | A | A | -0.6302 | |
| 103 | E | A | -1.7137 | |
| 104 | E | A | -2.2316 | |
| 105 | T | A | -1.5193 | |
| 106 | N | A | 0.0000 | |
| 107 | S | A | -1.6097 | |
| 108 | A | A | -1.5596 | |
| 109 | V | A | 0.0000 | |
| 110 | C | A | 0.0000 | |
| 111 | R | A | -2.6668 | |
| 112 | D | A | -2.8256 | |
| 113 | F | A | 0.0000 | |
| 114 | N | A | -1.2487 | |
| 115 | I | A | -0.3280 | |
| 116 | P | A | 0.2780 | |
| 117 | G | A | 0.1543 | |
| 118 | F | A | 0.2694 | |
| 119 | P | A | 0.1192 | |
| 120 | T | A | 0.1899 | |
| 121 | V | A | 0.0000 | |
| 122 | R | A | 0.0000 | |
| 123 | F | A | 0.0000 | |
| 124 | F | A | 0.0000 | |
| 125 | K | A | -1.2725 | |
| 126 | A | A | 0.0000 | |
| 127 | F | A | -0.4665 | |
| 128 | T | A | -1.2141 | |
| 129 | K | A | -2.2859 | |
| 130 | N | A | -2.2086 | |
| 131 | G | A | -1.6176 | |
| 132 | S | A | -0.7200 | |
| 133 | G | A | -0.5925 | |
| 134 | A | A | -0.0835 | |
| 135 | V | A | 0.2009 | |
| 136 | F | A | 0.0000 | |
| 137 | P | A | -0.0122 | |
| 138 | V | A | 0.0000 | |
| 139 | A | A | -0.3885 | |
| 140 | G | A | -0.8259 | |
| 141 | A | A | -1.2075 | |
| 142 | D | A | -2.0248 | |
| 143 | V | A | -1.3544 | |
| 144 | Q | A | -1.7952 | |
| 145 | T | A | -1.3805 | |
| 146 | L | A | 0.0000 | |
| 147 | R | A | 0.0000 | |
| 148 | E | A | -1.2823 | |
| 149 | R | A | -1.2673 | |
| 150 | L | A | 0.0000 | |
| 151 | I | A | 0.0000 | |
| 152 | D | A | -1.8399 | |
| 153 | A | A | -1.1765 | |
| 154 | L | A | 0.0000 | |
| 155 | E | A | -1.7498 | |
| 156 | S | A | -1.4072 | |
| 157 | H | A | 0.0000 | |
| 158 | H | A | -2.0525 | |
| 159 | D | A | -2.1901 | |
| 160 | T | A | -1.1678 | |
| 161 | W | A | -0.7950 | |
| 162 | P | A | 0.0000 | |
| 163 | P | A | -0.6579 | |
| 164 | A | A | -0.7026 | |
| 165 | C | A | -0.5032 | |
| 166 | P | A | -0.4419 | |
| 167 | P | A | -0.7587 | |
| 168 | L | A | 0.0000 | |
| 169 | E | A | -2.1724 | |
| 170 | P | A | -1.4520 | |
| 171 | A | A | 0.0000 | |
| 172 | K | A | -3.0655 | |
| 173 | L | A | -2.7290 | |
| 174 | E | A | -3.1395 | |
| 175 | E | A | -2.7275 | |
| 176 | I | A | 0.0000 | |
| 177 | D | A | -2.7126 | |
| 178 | G | A | -1.9676 | |
| 179 | F | A | 0.0000 | |
| 180 | F | A | -1.6566 | |
| 181 | A | A | -1.4980 | |
| 182 | R | A | -2.3352 | |
| 183 | N | A | -2.1756 | |
| 184 | N | A | -2.4887 | |
| 185 | E | A | -2.0824 | |
| 186 | E | A | -2.0505 | |
| 187 | Y | A | 0.0000 | |
| 188 | L | A | 0.0000 | |
| 189 | A | A | 0.0000 | |
| 190 | L | A | 0.0000 | |
| 191 | I | A | 0.0000 | |
| 192 | F | A | 0.0000 | |
| 193 | E | A | 0.0000 | |
| 194 | K | A | -1.7260 | |
| 195 | G | A | -1.3693 | |
| 196 | G | A | -0.9566 | |
| 197 | S | A | -0.6453 | |
| 198 | Y | A | -0.5203 | |
| 199 | L | A | -0.1826 | |
| 200 | G | A | 0.0000 | |
| 201 | R | A | 0.0000 | |
| 202 | E | A | 0.0000 | |
| 203 | V | A | 0.0000 | |
| 204 | A | A | 0.0000 | |
| 205 | L | A | 0.0000 | |
| 206 | D | A | 0.0000 | |
| 207 | L | A | 0.0000 | |
| 208 | S | A | -1.2944 | |
| 209 | Q | A | -2.3231 | |
| 210 | H | A | -2.3323 | |
| 211 | K | A | -2.9296 | |
| 212 | G | A | -2.0119 | |
| 213 | V | A | 0.0000 | |
| 214 | A | A | -0.7763 | |
| 215 | V | A | 0.0000 | |
| 216 | R | A | 0.0000 | |
| 217 | R | A | 0.0000 | |
| 218 | V | A | 0.0000 | |
| 219 | L | A | -1.2637 | |
| 220 | N | A | -1.6585 | |
| 221 | T | A | -1.0679 | |
| 222 | E | A | -1.8137 | |
| 223 | A | A | -1.9527 | |
| 224 | N | A | -2.8222 | |
| 225 | V | A | 0.0000 | |
| 226 | V | A | -2.0959 | |
| 227 | R | A | -3.3117 | |
| 228 | K | A | -2.8847 | |
| 229 | F | A | -1.3835 | |
| 230 | G | A | -1.8241 | |
| 231 | V | A | 0.0000 | |
| 232 | T | A | -0.9251 | |
| 233 | D | A | -1.2058 | |
| 234 | F | A | -0.7483 | |
| 235 | P | A | -0.5890 | |
| 236 | S | A | 0.0000 | |
| 237 | C | A | 0.0000 | |
| 238 | Y | A | 0.1783 | |
| 239 | L | A | 0.0000 | |
| 240 | L | A | 0.0000 | |
| 241 | F | A | -0.5738 | |
| 242 | R | A | -1.9069 | |
| 243 | N | A | -1.7940 | |
| 244 | G | A | -0.9157 | |
| 245 | S | A | -0.0703 | |
| 246 | V | A | 1.0000 | |
| 247 | S | A | 0.2944 | |
| 248 | R | A | -0.3420 | |
| 249 | V | A | 0.0000 | |
| 250 | P | A | 0.2086 | |
| 251 | V | A | 1.2287 | |
| 252 | L | A | 2.0336 | |
| 253 | M | A | 1.4382 | |
| 254 | E | A | 0.1340 | |
| 255 | S | A | 0.1805 | |
| 256 | R | A | -0.0940 | |
| 257 | S | A | 0.0388 | |
| 258 | F | A | 0.8665 | |
| 259 | Y | A | 0.0000 | |
| 260 | T | A | -0.2913 | |
| 261 | A | A | -0.3011 | |
| 262 | Y | A | -0.1791 | |
| 263 | L | A | 0.0000 | |
| 264 | Q | A | -1.4681 | |
| 265 | R | A | -2.0378 | |
| 266 | L | A | -1.1342 | |
| 267 | S | A | -0.9385 | |
| 268 | G | A | -1.0543 | |
| 269 | L | A | -1.7221 | |
| 270 | T | A | -1.8327 | |
| 271 | R | A | -2.6756 | |
| 1 | D | B | -1.0729 | |
| 2 | V | B | 0.1009 | |
| 3 | V | B | 1.3594 | |
| 4 | M | B | 0.0000 | |
| 5 | T | B | -0.1124 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -1.2101 | |
| 8 | H | B | -1.7126 | |
| 9 | K | B | -1.9078 | |
| 10 | F | B | -0.6586 | |
| 11 | M | B | -0.3925 | |
| 12 | S | B | -0.4048 | |
| 13 | T | B | 0.0000 | |
| 14 | S | B | -0.6648 | |
| 15 | V | B | 0.2460 | |
| 16 | G | B | -1.0621 | |
| 17 | D | B | -2.4810 | |
| 18 | R | B | -2.7225 | |
| 19 | V | B | 0.0000 | |
| 20 | S | B | -0.4954 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8522 | |
| 23 | C | B | 0.0000 | |
| 24 | K | B | -1.9349 | |
| 25 | A | B | 0.0000 | |
| 26 | S | B | -1.1989 | |
| 27 | Q | B | -2.3281 | |
| 28 | D | B | -2.7729 | |
| 29 | V | B | 0.0000 | |
| 30 | S | B | -0.8985 | |
| 31 | T | B | -0.5035 | |
| 32 | A | B | 0.0000 | |
| 33 | V | B | 0.0000 | |
| 34 | A | B | 0.0000 | |
| 35 | W | B | 0.0000 | |
| 36 | Y | B | -0.0287 | |
| 37 | Q | B | 0.0000 | |
| 38 | Q | B | -1.3603 | |
| 39 | K | B | -1.7998 | |
| 40 | S | B | -1.4039 | |
| 41 | G | B | -1.4261 | |
| 42 | Q | B | -2.1290 | |
| 43 | S | B | -1.5614 | |
| 44 | P | B | -1.4508 | |
| 45 | K | B | -1.6709 | |
| 46 | L | B | -0.3736 | |
| 47 | L | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | H | B | 0.0010 | |
| 50 | S | B | 0.0000 | |
| 51 | A | B | 0.0000 | |
| 52 | S | B | -0.2202 | |
| 53 | Y | B | 0.1400 | |
| 54 | R | B | -0.6020 | |
| 55 | Y | B | 0.2851 | |
| 56 | T | B | -0.0160 | |
| 57 | G | B | -0.5728 | |
| 58 | V | B | -0.5973 | |
| 59 | P | B | -1.1265 | |
| 60 | D | B | -2.1662 | |
| 61 | R | B | -1.6059 | |
| 62 | F | B | 0.0000 | |
| 63 | T | B | -0.6288 | |
| 64 | G | B | 0.0000 | |
| 65 | S | B | -0.5525 | |
| 66 | G | B | -1.0010 | |
| 67 | S | B | -1.0122 | |
| 68 | G | B | -1.6852 | |
| 69 | T | B | -2.1606 | |
| 70 | D | B | -2.3695 | |
| 71 | F | B | 0.0000 | |
| 72 | T | B | -0.6797 | |
| 73 | F | B | 0.0000 | |
| 74 | T | B | -0.5688 | |
| 75 | I | B | 0.0000 | |
| 76 | S | B | -1.8277 | |
| 77 | S | B | -1.6640 | |
| 78 | V | B | 0.0000 | |
| 79 | Q | B | -0.7784 | |
| 80 | A | B | -0.5565 | |
| 81 | E | B | -1.7188 | |
| 82 | D | B | 0.0000 | |
| 83 | L | B | -0.2752 | |
| 84 | A | B | 0.0000 | |
| 85 | V | B | -0.2564 | |
| 86 | Y | B | 0.0000 | |
| 87 | Y | B | 0.6119 | |
| 88 | C | B | 0.0000 | |
| 89 | Q | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | H | B | 0.6048 | |
| 92 | Y | B | 0.2331 | |
| 93 | S | B | 0.5681 | |
| 94 | I | B | 1.1582 | |
| 95 | P | B | 0.9581 | |
| 96 | L | B | 1.7028 | |
| 97 | T | B | 1.7153 | |
| 98 | F | B | 2.5323 | |
| 99 | G | B | 0.0000 | |
| 100 | A | B | 0.2819 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | K | B | -0.6648 | |
| 104 | L | B | 0.0000 | |
| 105 | E | B | 0.0000 | |
| 106 | L | B | -0.4657 | |
| 107 | K | B | -1.8629 | |
| 108 | R | B | -1.9050 | |
| 109 | A | B | -1.5193 | |
| 110 | D | B | -2.4347 | |
| 111 | A | B | -1.4106 | |
| 112 | A | B | -0.7938 | |
| 113 | P | B | 0.0000 | |
| 114 | T | B | -0.2185 | |
| 115 | V | B | 0.0000 | |
| 116 | S | B | 0.5074 | |
| 117 | I | B | 1.0101 | |
| 118 | F | B | 1.4730 | |
| 119 | P | B | 0.4838 | |
| 120 | P | B | 0.0000 | |
| 121 | S | B | -0.6748 | |
| 122 | S | B | -1.2788 | |
| 123 | E | B | -2.1942 | |
| 124 | Q | B | -1.5694 | |
| 125 | L | B | -1.4866 | |
| 126 | T | B | -1.1431 | |
| 127 | S | B | -1.1064 | |
| 128 | G | B | -1.4007 | |
| 129 | G | B | -1.2879 | |
| 130 | A | B | 0.0000 | |
| 131 | S | B | 0.0599 | |
| 132 | V | B | 0.0000 | |
| 133 | V | B | 1.1411 | |
| 134 | C | B | 0.0000 | |
| 135 | F | B | 0.9325 | |
| 136 | L | B | 0.0000 | |
| 137 | N | B | -0.6029 | |
| 138 | N | B | -1.2989 | |
| 139 | F | B | 0.0000 | |
| 140 | Y | B | -1.9638 | |
| 141 | P | B | -1.9780 | |
| 142 | K | B | -1.8849 | |
| 143 | D | B | -2.4783 | |
| 144 | I | B | -1.6833 | |
| 145 | N | B | -1.8348 | |
| 146 | V | B | 0.0000 | |
| 147 | K | B | -1.8824 | |
| 148 | W | B | 0.0000 | |
| 149 | K | B | -2.2269 | |
| 150 | I | B | 0.0000 | |
| 151 | D | B | -2.4056 | |
| 152 | G | B | -1.7885 | |
| 153 | S | B | -2.1072 | |
| 154 | E | B | -3.1556 | |
| 155 | R | B | -2.6532 | |
| 156 | Q | B | -2.3811 | |
| 157 | N | B | -1.9012 | |
| 158 | G | B | -0.5832 | |
| 159 | V | B | 0.0728 | |
| 160 | L | B | 1.0854 | |
| 161 | N | B | 0.4405 | |
| 162 | S | B | 0.5028 | |
| 163 | W | B | 0.3608 | |
| 164 | T | B | -0.8243 | |
| 165 | D | B | -1.9947 | |
| 166 | Q | B | -1.8468 | |
| 167 | D | B | -2.3419 | |
| 168 | S | B | -1.8530 | |
| 169 | K | B | -2.3529 | |
| 170 | D | B | -1.8528 | |
| 171 | S | B | 0.0000 | |
| 172 | T | B | 0.0000 | |
| 173 | Y | B | 0.0000 | |
| 174 | S | B | -0.6438 | |
| 175 | M | B | 0.0000 | |
| 176 | S | B | 0.5542 | |
| 177 | S | B | 0.0000 | |
| 178 | T | B | 0.8453 | |
| 179 | L | B | 0.0000 | |
| 180 | T | B | 0.0049 | |
| 181 | L | B | 0.0000 | |
| 182 | T | B | -1.7107 | |
| 183 | K | B | -2.5838 | |
| 184 | D | B | -3.4828 | |
| 185 | E | B | -3.0437 | |
| 186 | Y | B | 0.0000 | |
| 187 | E | B | -3.6550 | |
| 188 | R | B | -3.8207 | |
| 189 | H | B | -3.1189 | |
| 190 | N | B | -2.7010 | |
| 191 | S | B | -1.8046 | |
| 192 | Y | B | 0.0000 | |
| 193 | T | B | -1.0370 | |
| 194 | C | B | 0.0000 | |
| 195 | E | B | -0.8099 | |
| 196 | A | B | 0.0000 | |
| 197 | T | B | -1.0567 | |
| 198 | H | B | 0.0000 | |
| 199 | K | B | -2.3804 | |
| 200 | T | B | -1.3670 | |
| 201 | S | B | -0.7627 | |
| 202 | T | B | -0.6067 | |
| 203 | S | B | -0.3826 | |
| 204 | P | B | -0.4443 | |
| 205 | I | B | 0.3546 | |
| 206 | V | B | 0.3024 | |
| 207 | K | B | -0.2373 | |
| 208 | S | B | -0.2310 | |
| 209 | F | B | -0.7938 | |
| 210 | N | B | -2.0695 | |
| 211 | R | B | -2.2954 | |
| 212 | N | B | -2.5012 | |
| 213 | E | B | -2.4614 | |
| 214 | C | B | -0.8427 |
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 | -0.5452 | 5.0285 | View | CSV | PDB |
| 4.5 | -0.6083 | 5.0302 | View | CSV | PDB |
| 5.0 | -0.6818 | 5.0344 | View | CSV | PDB |
| 5.5 | -0.7545 | 5.0411 | View | CSV | PDB |
| 6.0 | -0.8152 | 5.0482 | View | CSV | PDB |
| 6.5 | -0.8551 | 5.053 | View | CSV | PDB |
| 7.0 | -0.8741 | 5.0552 | View | CSV | PDB |
| 7.5 | -0.8791 | 5.056 | View | CSV | PDB |
| 8.0 | -0.8752 | 5.0562 | View | CSV | PDB |
| 8.5 | -0.8622 | 5.0563 | View | CSV | PDB |
| 9.0 | -0.8377 | 5.0562 | 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