| Chain sequence(s) |
A: MARAVGPERRLLAVYTGGTIGMRSELGVLVPGTGLAAILRTLPMFHDEEHARARGLSEDTLVLPPASRNQRILYTVLECQPLFDSSDMTIAEWVCLAQTIKRHYEQYHGFVVIHGTDTMAFAASMLSFMLENLQKTVILTGAQVPIHALWSDGRENLLGALLMAGQYVIPEVCLFFQNQLFRGNRATKVDARRFAAFCSPNLLPLATVGADITINRELVRKVDGKAGLVVHSSMEQDVGLLRLYPGIPAALVRAFLQPPLKGVVMETFGSGNGPTKPDLLQELRVATERGLVIVNCTHCLQGAVTTDYAAGMAMAGAGVISGFDMTSEAALAKLSYVLGQPGLSLDVRKELLTKDLRGEMTPPSVEERRPSLQGNTLGGGVSWLLSLSGSQEADALRNALVPSL
input PDB |
| Selected Chain(s) | A |
| 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 A 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 (00:09:36)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/c83181d3e77f1e5/tmp/folded.pdb (00:09:36)
[INFO] Main: Simulation completed successfully. (00:15:55)
|
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 | M | A | -0.1032 | |
| 2 | A | A | 0.1124 | |
| 3 | R | A | -1.0354 | |
| 4 | A | A | 0.0000 | |
| 5 | V | A | 1.0658 | |
| 6 | G | A | -0.1565 | |
| 7 | P | A | -1.1408 | |
| 8 | E | A | -1.2267 | |
| 9 | R | A | 0.0000 | |
| 10 | R | A | -1.2117 | |
| 11 | L | A | 0.0000 | |
| 12 | L | A | 0.0000 | |
| 13 | A | A | 0.0000 | |
| 14 | V | A | 0.0000 | |
| 15 | Y | A | 0.0000 | |
| 16 | T | A | 0.0000 | |
| 17 | G | A | 0.0000 | |
| 18 | G | A | 0.0000 | |
| 19 | T | A | -0.4452 | |
| 20 | I | A | 0.0000 | |
| 21 | G | A | 0.0000 | |
| 22 | M | A | 0.0000 | |
| 23 | R | A | -1.8193 | |
| 24 | S | A | -0.8626 | |
| 25 | E | A | -0.9981 | |
| 26 | L | A | 0.8711 | |
| 27 | G | A | 0.4298 | |
| 28 | V | A | 1.4487 | |
| 29 | L | A | 0.6492 | |
| 30 | V | A | -0.0047 | |
| 31 | P | A | -0.6662 | |
| 32 | G | A | 0.0000 | |
| 33 | T | A | -0.5716 | |
| 34 | G | A | -0.1737 | |
| 35 | L | A | 0.0000 | |
| 36 | A | A | -0.6517 | |
| 37 | A | A | -0.5011 | |
| 38 | I | A | 0.0381 | |
| 39 | L | A | 0.0000 | |
| 40 | R | A | -0.9342 | |
| 41 | T | A | -0.2876 | |
| 42 | L | A | -0.1617 | |
| 43 | P | A | -0.3325 | |
| 44 | M | A | -0.1579 | |
| 45 | F | A | 0.0000 | |
| 46 | H | A | 0.0000 | |
| 47 | D | A | -1.5520 | |
| 48 | E | A | -2.3117 | |
| 49 | E | A | -3.0981 | |
| 50 | H | A | -2.3704 | |
| 51 | A | A | 0.0000 | |
| 52 | R | A | -3.4164 | |
| 53 | A | A | -2.2277 | |
| 54 | R | A | -2.4800 | |
| 55 | G | A | -2.0978 | |
| 56 | L | A | -1.6458 | |
| 57 | S | A | -1.9697 | |
| 58 | E | A | -2.9797 | |
| 59 | D | A | -2.5800 | |
| 60 | T | A | 0.0000 | |
| 61 | L | A | 0.0000 | |
| 62 | V | A | 0.0000 | |
| 63 | L | A | 0.0000 | |
| 64 | P | A | -0.6797 | |
| 65 | P | A | -1.1776 | |
| 66 | A | A | -0.8619 | |
| 67 | S | A | -1.7390 | |
| 68 | R | A | -2.7460 | |
| 69 | N | A | -2.6470 | |
| 70 | Q | A | -1.7337 | |
| 71 | R | A | -1.5329 | |
| 72 | I | A | 0.0000 | |
| 73 | L | A | 0.0000 | |
| 74 | Y | A | 0.0000 | |
| 75 | T | A | -0.6963 | |
| 76 | V | A | -0.1339 | |
| 77 | L | A | -0.0795 | |
| 78 | E | A | -0.4747 | |
| 79 | C | A | -0.5043 | |
| 80 | Q | A | -1.2453 | |
| 81 | P | A | -0.9777 | |
| 82 | L | A | -0.5200 | |
| 83 | F | A | -0.9161 | |
| 84 | D | A | -1.7760 | |
| 85 | S | A | 0.0000 | |
| 86 | S | A | -1.8756 | |
| 87 | D | A | -2.4111 | |
| 88 | M | A | 0.0000 | |
| 89 | T | A | -0.5820 | |
| 90 | I | A | 0.0186 | |
| 91 | A | A | 0.0227 | |
| 92 | E | A | -0.2453 | |
| 93 | W | A | 0.0000 | |
| 94 | V | A | 0.3053 | |
| 95 | C | A | 0.3908 | |
| 96 | L | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | Q | A | -1.2107 | |
| 99 | T | A | 0.0000 | |
| 100 | I | A | 0.0000 | |
| 101 | K | A | -2.3364 | |
| 102 | R | A | -3.0497 | |
| 103 | H | A | -2.3841 | |
| 104 | Y | A | 0.0000 | |
| 105 | E | A | -2.8997 | |
| 106 | Q | A | -2.4680 | |
| 107 | Y | A | 0.0000 | |
| 108 | H | A | -1.3687 | |
| 109 | G | A | 0.0000 | |
| 110 | F | A | 0.0000 | |
| 111 | V | A | 0.0000 | |
| 112 | V | A | 0.0000 | |
| 113 | I | A | 0.0000 | |
| 114 | H | A | 0.0000 | |
| 115 | G | A | 0.0000 | |
| 116 | T | A | 0.0000 | |
| 117 | D | A | -2.2276 | |
| 118 | T | A | -1.2541 | |
| 119 | M | A | 0.0000 | |
| 120 | A | A | 0.0000 | |
| 121 | F | A | 0.1171 | |
| 122 | A | A | 0.0000 | |
| 123 | A | A | 0.0000 | |
| 124 | S | A | 0.0000 | |
| 125 | M | A | 0.0000 | |
| 126 | L | A | 0.0000 | |
| 127 | S | A | 0.0000 | |
| 128 | F | A | 0.0000 | |
| 129 | M | A | 0.0000 | |
| 130 | L | A | 0.0000 | |
| 131 | E | A | -0.2117 | |
| 132 | N | A | -1.1786 | |
| 133 | L | A | 0.0000 | |
| 134 | Q | A | -1.4226 | |
| 135 | K | A | -0.4714 | |
| 136 | T | A | 0.0000 | |
| 137 | V | A | 0.0000 | |
| 138 | I | A | 0.0000 | |
| 139 | L | A | 0.0000 | |
| 140 | T | A | 0.0000 | |
| 141 | G | A | 0.0000 | |
| 142 | A | A | 0.0000 | |
| 143 | Q | A | -0.6637 | |
| 144 | V | A | 0.4231 | |
| 145 | P | A | 0.0000 | |
| 146 | I | A | 0.0000 | |
| 147 | H | A | -0.0949 | |
| 148 | A | A | 0.7124 | |
| 149 | L | A | 2.0586 | |
| 150 | W | A | 1.8977 | |
| 151 | S | A | 0.7449 | |
| 152 | D | A | 0.0000 | |
| 153 | G | A | 0.0000 | |
| 154 | R | A | -0.9566 | |
| 155 | E | A | -2.1340 | |
| 156 | N | A | 0.0000 | |
| 157 | L | A | 0.0000 | |
| 158 | L | A | -0.2899 | |
| 159 | G | A | -0.6157 | |
| 160 | A | A | 0.0000 | |
| 161 | L | A | 0.0000 | |
| 162 | L | A | 0.3035 | |
| 163 | M | A | 0.0000 | |
| 164 | A | A | 0.0000 | |
| 165 | G | A | 0.0000 | |
| 166 | Q | A | -0.3333 | |
| 167 | Y | A | 0.0000 | |
| 168 | V | A | 0.2451 | |
| 169 | I | A | 0.0000 | |
| 170 | P | A | -0.3927 | |
| 171 | E | A | 0.0000 | |
| 172 | V | A | 0.0000 | |
| 173 | C | A | 0.0000 | |
| 174 | L | A | 0.0000 | |
| 175 | F | A | 0.0000 | |
| 176 | F | A | 0.0000 | |
| 177 | Q | A | -1.3839 | |
| 178 | N | A | -1.4757 | |
| 179 | Q | A | -0.6578 | |
| 180 | L | A | 0.0000 | |
| 181 | F | A | 0.0000 | |
| 182 | R | A | 0.0000 | |
| 183 | G | A | 0.0000 | |
| 184 | N | A | 0.0000 | |
| 185 | R | A | 0.0000 | |
| 186 | A | A | 0.0000 | |
| 187 | T | A | 0.1039 | |
| 188 | K | A | -0.1947 | |
| 189 | V | A | 0.5585 | |
| 190 | D | A | -0.7258 | |
| 191 | A | A | -1.4231 | |
| 192 | R | A | -2.4169 | |
| 193 | R | A | -2.2281 | |
| 194 | F | A | -0.5060 | |
| 195 | A | A | -0.6430 | |
| 196 | A | A | 0.0000 | |
| 197 | F | A | 0.0000 | |
| 198 | C | A | 0.4583 | |
| 199 | S | A | 0.3923 | |
| 200 | P | A | 0.1751 | |
| 201 | N | A | -0.1533 | |
| 202 | L | A | 0.6599 | |
| 203 | L | A | 1.4946 | |
| 204 | P | A | 0.5462 | |
| 205 | L | A | 0.0000 | |
| 206 | A | A | 0.0000 | |
| 207 | T | A | -0.4421 | |
| 208 | V | A | -0.6336 | |
| 209 | G | A | -0.9864 | |
| 210 | A | A | -0.8648 | |
| 211 | D | A | -1.6185 | |
| 212 | I | A | -0.5059 | |
| 213 | T | A | -0.6514 | |
| 214 | I | A | 0.0000 | |
| 215 | N | A | -1.4584 | |
| 216 | R | A | -2.8012 | |
| 217 | E | A | -2.8206 | |
| 218 | L | A | -1.3118 | |
| 219 | V | A | -1.3068 | |
| 220 | R | A | -1.7804 | |
| 221 | K | A | -2.4016 | |
| 222 | V | A | -1.8042 | |
| 223 | D | A | -2.8684 | |
| 224 | G | A | -2.4171 | |
| 225 | K | A | -2.5918 | |
| 226 | A | A | -1.5850 | |
| 227 | G | A | -1.0905 | |
| 228 | L | A | 0.0000 | |
| 229 | V | A | 0.5867 | |
| 230 | V | A | 0.1398 | |
| 231 | H | A | -0.0076 | |
| 232 | S | A | -0.0192 | |
| 233 | S | A | -0.4941 | |
| 234 | M | A | 0.0000 | |
| 235 | E | A | -1.1405 | |
| 236 | Q | A | -1.6626 | |
| 237 | D | A | -1.4903 | |
| 238 | V | A | -0.6327 | |
| 239 | G | A | 0.0144 | |
| 240 | L | A | 0.1507 | |
| 241 | L | A | 0.0000 | |
| 242 | R | A | -1.5953 | |
| 243 | L | A | 0.0000 | |
| 244 | Y | A | 0.2853 | |
| 245 | P | A | 0.0421 | |
| 246 | G | A | -0.5538 | |
| 247 | I | A | 0.0000 | |
| 248 | P | A | -0.6183 | |
| 249 | A | A | -1.1699 | |
| 250 | A | A | -0.4058 | |
| 251 | L | A | 0.3206 | |
| 252 | V | A | 0.0000 | |
| 253 | R | A | -1.5730 | |
| 254 | A | A | -0.3893 | |
| 255 | F | A | 0.2548 | |
| 256 | L | A | 0.0000 | |
| 257 | Q | A | -1.1927 | |
| 258 | P | A | -0.9437 | |
| 259 | P | A | -0.9413 | |
| 260 | L | A | -0.8693 | |
| 261 | K | A | -1.5021 | |
| 262 | G | A | 0.0000 | |
| 263 | V | A | 0.0000 | |
| 264 | V | A | 0.0000 | |
| 265 | M | A | 0.0000 | |
| 266 | E | A | 0.0000 | |
| 267 | T | A | 0.0000 | |
| 268 | F | A | -0.0038 | |
| 269 | G | A | -0.2417 | |
| 270 | S | A | -0.4665 | |
| 271 | G | A | 0.0000 | |
| 272 | N | A | -0.1825 | |
| 273 | G | A | 0.0000 | |
| 274 | P | A | -0.7676 | |
| 275 | T | A | -1.1397 | |
| 276 | K | A | -2.5512 | |
| 277 | P | A | -2.1736 | |
| 278 | D | A | -3.0612 | |
| 279 | L | A | 0.0000 | |
| 280 | L | A | -1.7042 | |
| 281 | Q | A | -2.3735 | |
| 282 | E | A | -1.7740 | |
| 283 | L | A | 0.0000 | |
| 284 | R | A | -2.2618 | |
| 285 | V | A | -1.1764 | |
| 286 | A | A | 0.0000 | |
| 287 | T | A | -1.7963 | |
| 288 | E | A | -2.5675 | |
| 289 | R | A | -2.3755 | |
| 290 | G | A | -1.6073 | |
| 291 | L | A | 0.0000 | |
| 292 | V | A | 0.0000 | |
| 293 | I | A | 0.0000 | |
| 294 | V | A | 0.0000 | |
| 295 | N | A | 0.0000 | |
| 296 | C | A | 0.0000 | |
| 297 | T | A | 0.0000 | |
| 298 | H | A | -0.8871 | |
| 299 | C | A | -0.0179 | |
| 300 | L | A | 0.6140 | |
| 301 | Q | A | -0.8855 | |
| 302 | G | A | -0.7165 | |
| 303 | A | A | -0.2904 | |
| 304 | V | A | 0.0000 | |
| 305 | T | A | -0.7859 | |
| 306 | T | A | -0.9195 | |
| 307 | D | A | -1.5801 | |
| 308 | Y | A | 0.1593 | |
| 309 | A | A | 0.2462 | |
| 310 | A | A | -0.0386 | |
| 311 | G | A | 0.0000 | |
| 312 | M | A | 0.2072 | |
| 313 | A | A | 0.0289 | |
| 314 | M | A | 0.0000 | |
| 315 | A | A | -0.1772 | |
| 316 | G | A | -0.4330 | |
| 317 | A | A | 0.0000 | |
| 318 | G | A | -0.8038 | |
| 319 | V | A | 0.0000 | |
| 320 | I | A | 0.0000 | |
| 321 | S | A | 0.0316 | |
| 322 | G | A | 0.0000 | |
| 323 | F | A | 0.2122 | |
| 324 | D | A | 0.0000 | |
| 325 | M | A | 0.0000 | |
| 326 | T | A | -0.0902 | |
| 327 | S | A | 0.0612 | |
| 328 | E | A | 0.0543 | |
| 329 | A | A | 0.0000 | |
| 330 | A | A | 0.0000 | |
| 331 | L | A | 0.3054 | |
| 332 | A | A | 0.0000 | |
| 333 | K | A | 0.0000 | |
| 334 | L | A | 0.0000 | |
| 335 | S | A | 0.0000 | |
| 336 | Y | A | 0.0000 | |
| 337 | V | A | 0.0000 | |
| 338 | L | A | 0.0000 | |
| 339 | G | A | -0.6603 | |
| 340 | Q | A | -0.4513 | |
| 341 | P | A | -0.4829 | |
| 342 | G | A | -0.2835 | |
| 343 | L | A | 0.0596 | |
| 344 | S | A | -0.3508 | |
| 345 | L | A | -0.3796 | |
| 346 | D | A | -1.6658 | |
| 347 | V | A | -0.4858 | |
| 348 | R | A | -0.7483 | |
| 349 | K | A | -1.5637 | |
| 350 | E | A | -2.2344 | |
| 351 | L | A | -1.1283 | |
| 352 | L | A | 0.0000 | |
| 353 | T | A | -1.2633 | |
| 354 | K | A | -1.7658 | |
| 355 | D | A | -1.1591 | |
| 356 | L | A | -0.5430 | |
| 357 | R | A | -0.6697 | |
| 358 | G | A | 0.0000 | |
| 359 | E | A | 0.0000 | |
| 360 | M | A | 0.0000 | |
| 361 | T | A | -0.4077 | |
| 362 | P | A | -0.6742 | |
| 363 | P | A | -1.1821 | |
| 364 | S | A | -1.2150 | |
| 365 | V | A | -0.6511 | |
| 366 | E | A | -2.8842 | |
| 367 | E | A | -3.6959 | |
| 368 | R | A | -3.7798 | |
| 369 | R | A | -3.6360 | |
| 370 | P | A | -2.1884 | |
| 371 | S | A | -1.1751 | |
| 372 | L | A | 0.3407 | |
| 373 | Q | A | -0.9125 | |
| 374 | G | A | -0.9224 | |
| 375 | N | A | -0.6197 | |
| 376 | T | A | 0.0981 | |
| 377 | L | A | 1.3108 | |
| 378 | G | A | 0.6111 | |
| 379 | G | A | 0.3858 | |
| 380 | G | A | 1.0211 | |
| 381 | V | A | 1.8949 | |
| 382 | S | A | 1.4324 | |
| 383 | W | A | 1.9936 | |
| 384 | L | A | 2.0083 | |
| 385 | L | A | 2.2783 | |
| 386 | S | A | 1.2401 | |
| 387 | L | A | 0.5005 | |
| 388 | S | A | -0.3153 | |
| 389 | G | A | -1.3029 | |
| 390 | S | A | -1.5913 | |
| 391 | Q | A | -2.5437 | |
| 392 | E | A | -2.5541 | |
| 393 | A | A | -2.0418 | |
| 394 | D | A | -2.7405 | |
| 395 | A | A | -1.8801 | |
| 396 | L | A | -0.9706 | |
| 397 | R | A | -1.9099 | |
| 398 | N | A | -1.2286 | |
| 399 | A | A | 0.1303 | |
| 400 | L | A | 1.3873 | |
| 401 | V | A | 1.7628 | |
| 402 | P | A | 0.6944 | |
| 403 | S | A | 0.6668 | |
| 404 | L | A | 1.6336 |
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 | -0.2776 | 4.1324 | View | CSV | PDB |
| 4.5 | -0.3284 | 4.1378 | View | CSV | PDB |
| 5.0 | -0.3921 | 4.1495 | View | CSV | PDB |
| 5.5 | -0.4596 | 4.1668 | View | CSV | PDB |
| 6.0 | -0.5222 | 4.183 | View | CSV | PDB |
| 6.5 | -0.5726 | 4.1929 | View | CSV | PDB |
| 7.0 | -0.6079 | 4.1971 | View | CSV | PDB |
| 7.5 | -0.6306 | 4.1986 | View | CSV | PDB |
| 8.0 | -0.6449 | 4.1991 | View | CSV | PDB |
| 8.5 | -0.6521 | 4.1993 | View | CSV | PDB |
| 9.0 | -0.6517 | 4.1994 | 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