| Chain sequence(s) |
A: MARVSSLLSFCLTLLILFHGYAAQQGQQGQQFPNECQLDQLNALEPSHVLKSEAGRIEVWDHHAPQLRCSGVSFARYIIESKGLYLPSFFNTAKLSFVAKGRGLMGKVIPGCAETFQDSSEFQPRFEGQGQSQRFRDMHQKVEHIRSGDTIATTPGVAQWFYNDGQEPLVIVSVFDLASHQNQLDRNPRPFYLAGNNPQGQVWLQGREQQPQKNIFNGFGPEVIAQALKIDLQTAQQLQNQDDNRGNIVRVQGPFGVIRPPLRGQRPQEEEEEEGRHGRHGNGLEETICSARCTDNLDDPSRADVYKPQLGYISTLNSYDLPILRFIRLSALRGSIRQNAMVLPQWNANANAILYVTDGEAQIQIVNDNGNRVFDGQVSQGQLIAVPQGFSVVKRATSNRFQWVEFKTNANAQINTLAGRTSVLRGLPLEVITNGFQISPEEARRVKFNTLETTLTHSSGPASYGRPRVAAA
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage |
A: MARVSSLLSFCLTLLILFHGYAAQQ GQQGQQFPNECQLDQLNALEPSHVLKSEAGRIEVWDHHAPQLRCSGVSFARYIIESKGLYLPSFFNTAKLSFVAKGRGLMGKVIPGCAETFQDSSEFQPRFEGQGQSQRFRDMHQKVEHIRSGDTIATTPGVAQWFYNDGQEPLVIVSVFDLASHQNQLDRNPRPFYLAGNNPQGQVWLQGREQQPQKNIFNGFGPEVIAQALKIDLQTAQQLQNQDDNRGNIVRVQGPFGVIRPPLRGQRPQEEEEEEGRHGRHGNGLEETICSARCTDNLDDPSRADVYKPQLGYISTLNSYDLPILRFIRLSALRGSIRQNAMVLPQWNANANAILYVTDGEAQIQIVNDNGNRVFDGQVSQGQLIAVPQGFSVVKRATSNRFQWVEFKTNANAQINTLAGRTSVLRGLPLEVITNGFQISPEEARRVKFNTLETTLTHSSGPASYGRPRVAAA(Red indicates removed residues) |
| 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 A chain(s) selected (00:00:01)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:01)
[INFO] PDB: Running AlphaCutter (00:00:01)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:12)
[INFO] FoldX: Starting FoldX energy minimization (00:00:12)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:06:05)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/753bb7120c66eb4/tmp/folded.pdb (00:06:05)
[INFO] Main: Simulation completed successfully. (00:08:41)
|
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 |
|---|---|---|---|---|
| 26 | G | A | -1.4747 | |
| 27 | Q | A | -2.5468 | |
| 28 | Q | A | -2.7414 | |
| 29 | G | A | -2.2460 | |
| 30 | Q | A | -2.0843 | |
| 31 | Q | A | -1.6071 | |
| 32 | F | A | 0.4768 | |
| 33 | P | A | -0.5258 | |
| 34 | N | A | -1.3300 | |
| 35 | E | A | 0.0000 | |
| 36 | C | A | -0.8463 | |
| 37 | Q | A | -2.4216 | |
| 38 | L | A | 0.0000 | |
| 39 | D | A | -3.4545 | |
| 40 | Q | A | -3.1329 | |
| 41 | L | A | 0.0000 | |
| 42 | N | A | -2.0684 | |
| 43 | A | A | -1.1787 | |
| 44 | L | A | -1.2141 | |
| 45 | E | A | -2.2347 | |
| 46 | P | A | -1.0402 | |
| 47 | S | A | -0.6550 | |
| 48 | H | A | -0.2511 | |
| 49 | V | A | 0.2194 | |
| 50 | L | A | 0.0000 | |
| 51 | K | A | -2.2512 | |
| 52 | S | A | 0.0000 | |
| 53 | E | A | -2.2898 | |
| 54 | A | A | 0.0000 | |
| 55 | G | A | -1.9909 | |
| 56 | R | A | -1.6026 | |
| 57 | I | A | 0.0000 | |
| 58 | E | A | 0.0000 | |
| 59 | V | A | 0.0000 | |
| 60 | W | A | 0.0000 | |
| 61 | D | A | -1.3175 | |
| 62 | H | A | 0.0000 | |
| 63 | H | A | -1.6374 | |
| 64 | A | A | -0.9682 | |
| 65 | P | A | -0.8593 | |
| 66 | Q | A | 0.0000 | |
| 67 | L | A | 0.0000 | |
| 68 | R | A | -0.7643 | |
| 69 | C | A | 0.0000 | |
| 70 | S | A | 0.0000 | |
| 71 | G | A | 0.0000 | |
| 72 | V | A | 0.0000 | |
| 73 | S | A | 0.0000 | |
| 74 | F | A | 0.0000 | |
| 75 | A | A | 0.0000 | |
| 76 | R | A | -0.1663 | |
| 77 | Y | A | 0.0000 | |
| 78 | I | A | -0.7962 | |
| 79 | I | A | 0.0000 | |
| 80 | E | A | -3.1064 | |
| 81 | S | A | -2.7173 | |
| 82 | K | A | -2.6751 | |
| 83 | G | A | 0.0000 | |
| 84 | L | A | -0.7896 | |
| 85 | Y | A | 0.0000 | |
| 86 | L | A | 0.3288 | |
| 87 | P | A | 0.5730 | |
| 88 | S | A | 0.0000 | |
| 89 | F | A | 0.6863 | |
| 90 | F | A | 0.0000 | |
| 91 | N | A | 0.0000 | |
| 92 | T | A | 0.0000 | |
| 93 | A | A | 0.0000 | |
| 94 | K | A | 0.0000 | |
| 95 | L | A | 0.0000 | |
| 96 | S | A | 0.0000 | |
| 97 | F | A | 0.0000 | |
| 98 | V | A | 0.0000 | |
| 99 | A | A | -1.0588 | |
| 100 | K | A | -1.8372 | |
| 101 | G | A | -2.3060 | |
| 102 | R | A | -2.5255 | |
| 103 | G | A | 0.0000 | |
| 104 | L | A | 0.0000 | |
| 105 | M | A | 0.0000 | |
| 106 | G | A | 0.0000 | |
| 107 | K | A | 0.1374 | |
| 108 | V | A | 0.7846 | |
| 109 | I | A | 0.7405 | |
| 110 | P | A | -0.2060 | |
| 111 | G | A | -0.9066 | |
| 112 | C | A | -0.9866 | |
| 113 | A | A | -1.2149 | |
| 114 | E | A | -2.1329 | |
| 115 | T | A | -1.4051 | |
| 116 | F | A | -1.6222 | |
| 117 | Q | A | -2.1626 | |
| 118 | D | A | -2.1945 | |
| 119 | S | A | -1.9785 | |
| 120 | S | A | -2.1543 | |
| 121 | E | A | -1.6861 | |
| 122 | F | A | -0.2348 | |
| 123 | Q | A | -1.1352 | |
| 124 | P | A | -1.0939 | |
| 125 | R | A | -1.7167 | |
| 126 | F | A | -0.3009 | |
| 127 | E | A | -1.9036 | |
| 128 | G | A | -2.0392 | |
| 129 | Q | A | -2.3337 | |
| 130 | G | A | -2.1398 | |
| 131 | Q | A | -2.4453 | |
| 132 | S | A | -2.1297 | |
| 133 | Q | A | -2.4460 | |
| 134 | R | A | -3.1611 | |
| 135 | F | A | -2.6389 | |
| 136 | R | A | -3.4483 | |
| 137 | D | A | -3.0292 | |
| 138 | M | A | -1.8266 | |
| 139 | H | A | -1.5276 | |
| 140 | Q | A | -1.3590 | |
| 141 | K | A | -2.1799 | |
| 142 | V | A | 0.0000 | |
| 143 | E | A | -1.1801 | |
| 144 | H | A | -1.0159 | |
| 145 | I | A | 0.0000 | |
| 146 | R | A | -2.5907 | |
| 147 | S | A | -1.6760 | |
| 148 | G | A | 0.0000 | |
| 149 | D | A | 0.0000 | |
| 150 | T | A | 0.0000 | |
| 151 | I | A | 0.0000 | |
| 152 | A | A | 0.0000 | |
| 153 | T | A | 0.0000 | |
| 154 | T | A | 0.1290 | |
| 155 | P | A | -0.3311 | |
| 156 | G | A | -0.0066 | |
| 157 | V | A | 0.0000 | |
| 158 | A | A | 0.0000 | |
| 159 | Q | A | 0.0000 | |
| 160 | W | A | 0.4110 | |
| 161 | F | A | 0.0000 | |
| 162 | Y | A | 0.0000 | |
| 163 | N | A | 0.0000 | |
| 164 | D | A | -1.9078 | |
| 165 | G | A | -2.3918 | |
| 166 | Q | A | -2.7287 | |
| 167 | E | A | -3.0167 | |
| 168 | P | A | -2.2415 | |
| 169 | L | A | 0.0000 | |
| 170 | V | A | -1.0209 | |
| 171 | I | A | 0.0000 | |
| 172 | V | A | 0.0000 | |
| 173 | S | A | 0.0000 | |
| 174 | V | A | 0.0000 | |
| 175 | F | A | 0.0000 | |
| 176 | D | A | 0.0000 | |
| 177 | L | A | 0.0000 | |
| 178 | A | A | -0.6957 | |
| 179 | S | A | -1.1880 | |
| 180 | H | A | -1.5820 | |
| 181 | Q | A | -0.8077 | |
| 182 | N | A | -0.9739 | |
| 183 | Q | A | -1.2047 | |
| 184 | L | A | 0.1031 | |
| 185 | D | A | -0.9643 | |
| 186 | R | A | -1.5092 | |
| 187 | N | A | -0.9076 | |
| 188 | P | A | 0.0000 | |
| 189 | R | A | -0.1300 | |
| 190 | P | A | 0.0000 | |
| 191 | F | A | 0.8188 | |
| 192 | Y | A | 0.0000 | |
| 193 | L | A | 0.8903 | |
| 194 | A | A | 0.4166 | |
| 195 | G | A | 0.0000 | |
| 196 | N | A | 0.0000 | |
| 197 | N | A | 0.0000 | |
| 198 | P | A | -1.8395 | |
| 199 | Q | A | -1.2287 | |
| 200 | G | A | 0.0000 | |
| 201 | Q | A | -1.3526 | |
| 202 | V | A | -0.8516 | |
| 203 | W | A | 0.0000 | |
| 204 | L | A | 0.0000 | |
| 205 | Q | A | -2.1515 | |
| 206 | G | A | -2.2612 | |
| 207 | R | A | -3.2957 | |
| 208 | E | A | -3.6214 | |
| 209 | Q | A | -3.1008 | |
| 210 | Q | A | -2.8408 | |
| 211 | P | A | -1.7121 | |
| 212 | Q | A | -1.0528 | |
| 213 | K | A | -1.2541 | |
| 214 | N | A | 0.0000 | |
| 215 | I | A | 1.0416 | |
| 216 | F | A | 0.7024 | |
| 217 | N | A | -0.3398 | |
| 218 | G | A | 0.2283 | |
| 219 | F | A | 1.2949 | |
| 220 | G | A | 0.2128 | |
| 221 | P | A | -0.8328 | |
| 222 | E | A | -1.2919 | |
| 223 | V | A | 0.8136 | |
| 224 | I | A | 0.0000 | |
| 225 | A | A | 0.0000 | |
| 226 | Q | A | -1.4047 | |
| 227 | A | A | -0.2929 | |
| 228 | L | A | -0.2561 | |
| 229 | K | A | -1.4683 | |
| 230 | I | A | -1.2235 | |
| 231 | D | A | -2.2508 | |
| 232 | L | A | -1.4994 | |
| 233 | Q | A | -2.0082 | |
| 234 | T | A | -1.2465 | |
| 235 | A | A | 0.0000 | |
| 236 | Q | A | -2.0453 | |
| 237 | Q | A | -2.0254 | |
| 238 | L | A | -0.5431 | |
| 239 | Q | A | 0.0000 | |
| 240 | N | A | -2.1050 | |
| 241 | Q | A | -2.7846 | |
| 242 | D | A | -3.1804 | |
| 243 | D | A | -2.6419 | |
| 244 | N | A | -2.8353 | |
| 245 | R | A | -2.6078 | |
| 246 | G | A | 0.0000 | |
| 247 | N | A | 0.0000 | |
| 248 | I | A | 0.0000 | |
| 249 | V | A | 0.0000 | |
| 250 | R | A | -2.8879 | |
| 251 | V | A | -1.5716 | |
| 252 | Q | A | -1.8957 | |
| 253 | G | A | -1.3061 | |
| 254 | P | A | -0.6764 | |
| 255 | F | A | -0.2868 | |
| 256 | G | A | -0.2520 | |
| 257 | V | A | -0.1772 | |
| 258 | I | A | -0.9729 | |
| 259 | R | A | -0.9470 | |
| 260 | P | A | -0.8160 | |
| 261 | P | A | -0.3407 | |
| 262 | L | A | -0.1226 | |
| 263 | R | A | -2.0221 | |
| 264 | G | A | -1.9367 | |
| 265 | Q | A | -2.5568 | |
| 266 | R | A | -3.6981 | |
| 267 | P | A | -3.4099 | |
| 268 | Q | A | -4.4772 | |
| 269 | E | A | -5.3735 | |
| 270 | E | A | -6.0419 | |
| 271 | E | A | -6.0914 | |
| 272 | E | A | -6.0270 | |
| 273 | E | A | -6.2386 | |
| 274 | E | A | -5.7910 | |
| 275 | G | A | -5.1182 | |
| 276 | R | A | -5.2594 | |
| 277 | H | A | -4.1703 | |
| 278 | G | A | -3.7454 | |
| 279 | R | A | -3.8897 | |
| 280 | H | A | -2.9225 | |
| 281 | G | A | -2.2208 | |
| 282 | N | A | -2.6368 | |
| 283 | G | A | -1.3569 | |
| 284 | L | A | -0.1915 | |
| 285 | E | A | -2.1557 | |
| 286 | E | A | -2.5445 | |
| 287 | T | A | -1.2553 | |
| 288 | I | A | -0.2533 | |
| 289 | C | A | -0.6776 | |
| 290 | S | A | -1.2207 | |
| 291 | A | A | -0.8360 | |
| 292 | R | A | -1.5140 | |
| 293 | C | A | -0.5619 | |
| 294 | T | A | -0.4794 | |
| 295 | D | A | 0.0000 | |
| 296 | N | A | -0.9738 | |
| 297 | L | A | 0.0000 | |
| 298 | D | A | -1.4483 | |
| 299 | D | A | -1.5731 | |
| 300 | P | A | -1.1285 | |
| 301 | S | A | -1.1528 | |
| 302 | R | A | -1.8638 | |
| 303 | A | A | -1.3869 | |
| 304 | D | A | -1.6940 | |
| 305 | V | A | -0.3174 | |
| 306 | Y | A | 0.3078 | |
| 307 | K | A | -0.2094 | |
| 308 | P | A | -0.8279 | |
| 309 | Q | A | -1.7580 | |
| 310 | L | A | 0.0000 | |
| 311 | G | A | 0.0000 | |
| 312 | Y | A | 0.0000 | |
| 313 | I | A | 0.0000 | |
| 314 | S | A | 0.0000 | |
| 315 | T | A | -0.8003 | |
| 316 | L | A | 0.0000 | |
| 317 | N | A | -0.8666 | |
| 318 | S | A | 0.0000 | |
| 319 | Y | A | 0.3776 | |
| 320 | D | A | -0.6614 | |
| 321 | L | A | 0.0000 | |
| 322 | P | A | -0.5298 | |
| 323 | I | A | -0.3432 | |
| 324 | L | A | 0.0000 | |
| 325 | R | A | -1.4741 | |
| 326 | F | A | 0.4315 | |
| 327 | I | A | 0.0000 | |
| 328 | R | A | -2.1476 | |
| 329 | L | A | 0.0000 | |
| 330 | S | A | 0.0000 | |
| 331 | A | A | 0.0000 | |
| 332 | L | A | 0.0000 | |
| 333 | R | A | 0.0000 | |
| 334 | G | A | 0.0000 | |
| 335 | S | A | 0.0000 | |
| 336 | I | A | 0.0000 | |
| 337 | R | A | -3.4782 | |
| 338 | Q | A | -3.6396 | |
| 339 | N | A | -2.6734 | |
| 340 | A | A | 0.0000 | |
| 341 | M | A | -1.1152 | |
| 342 | V | A | 0.0000 | |
| 343 | L | A | 0.0000 | |
| 344 | P | A | 0.2613 | |
| 345 | Q | A | 0.0000 | |
| 346 | W | A | -0.1163 | |
| 347 | N | A | 0.0000 | |
| 348 | A | A | -0.7574 | |
| 349 | N | A | -0.9766 | |
| 350 | A | A | 0.0000 | |
| 351 | N | A | -0.8009 | |
| 352 | A | A | 0.0000 | |
| 353 | I | A | 0.0000 | |
| 354 | L | A | 0.0000 | |
| 355 | Y | A | 0.0000 | |
| 356 | V | A | 0.0000 | |
| 357 | T | A | 0.0000 | |
| 358 | D | A | -2.2065 | |
| 359 | G | A | -2.2951 | |
| 360 | E | A | -2.5005 | |
| 361 | A | A | 0.0000 | |
| 362 | Q | A | -1.8025 | |
| 363 | I | A | 0.0000 | |
| 364 | Q | A | -1.5248 | |
| 365 | I | A | 0.0000 | |
| 366 | V | A | -2.0494 | |
| 367 | N | A | 0.0000 | |
| 368 | D | A | -3.4308 | |
| 369 | N | A | -3.3145 | |
| 370 | G | A | -2.5797 | |
| 371 | N | A | -3.5110 | |
| 372 | R | A | -3.6984 | |
| 373 | V | A | 0.0000 | |
| 374 | F | A | 0.0000 | |
| 375 | D | A | -2.8399 | |
| 376 | G | A | -1.8910 | |
| 377 | Q | A | -2.2271 | |
| 378 | V | A | 0.0000 | |
| 379 | S | A | -1.6107 | |
| 380 | Q | A | -2.0753 | |
| 381 | G | A | -1.3880 | |
| 382 | Q | A | -1.5901 | |
| 383 | L | A | 0.0000 | |
| 384 | I | A | 0.0000 | |
| 385 | A | A | 0.0000 | |
| 386 | V | A | 0.0000 | |
| 387 | P | A | 0.0000 | |
| 388 | Q | A | -1.5745 | |
| 389 | G | A | -1.2121 | |
| 390 | F | A | 0.0000 | |
| 391 | S | A | -0.5332 | |
| 392 | V | A | 0.0000 | |
| 393 | V | A | -0.0709 | |
| 394 | K | A | 0.0000 | |
| 395 | R | A | -2.0132 | |
| 396 | A | A | 0.0000 | |
| 397 | T | A | -2.1007 | |
| 398 | S | A | -2.4596 | |
| 399 | N | A | -3.1591 | |
| 400 | R | A | -3.3690 | |
| 401 | F | A | 0.0000 | |
| 402 | Q | A | -1.3347 | |
| 403 | W | A | 0.0000 | |
| 404 | V | A | 0.0000 | |
| 405 | E | A | 0.0000 | |
| 406 | F | A | 0.0000 | |
| 407 | K | A | 0.0000 | |
| 408 | T | A | -0.9345 | |
| 409 | N | A | -1.5157 | |
| 410 | A | A | 0.0000 | |
| 411 | N | A | -1.1939 | |
| 412 | A | A | -1.1622 | |
| 413 | Q | A | -1.0486 | |
| 414 | I | A | 0.0191 | |
| 415 | N | A | -0.0038 | |
| 416 | T | A | 0.0000 | |
| 417 | L | A | 0.5444 | |
| 418 | A | A | 0.2766 | |
| 419 | G | A | 0.0000 | |
| 420 | R | A | -1.4516 | |
| 421 | T | A | -0.6643 | |
| 422 | S | A | 0.0000 | |
| 423 | V | A | 0.6909 | |
| 424 | L | A | 0.9166 | |
| 425 | R | A | -0.1966 | |
| 426 | G | A | -0.2509 | |
| 427 | L | A | 0.4079 | |
| 428 | P | A | -0.2266 | |
| 429 | L | A | -1.0658 | |
| 430 | E | A | -1.7508 | |
| 431 | V | A | -0.0482 | |
| 432 | I | A | 0.0000 | |
| 433 | T | A | -1.4435 | |
| 434 | N | A | -1.5105 | |
| 435 | G | A | -0.5144 | |
| 436 | F | A | 0.4022 | |
| 437 | Q | A | -1.0385 | |
| 438 | I | A | -0.8932 | |
| 439 | S | A | -1.8981 | |
| 440 | P | A | -2.6284 | |
| 441 | E | A | -3.4010 | |
| 442 | E | A | -2.7969 | |
| 443 | A | A | 0.0000 | |
| 444 | R | A | -3.4922 | |
| 445 | R | A | -3.1249 | |
| 446 | V | A | -0.6673 | |
| 447 | K | A | -0.7856 | |
| 448 | F | A | -0.5009 | |
| 449 | N | A | -1.2800 | |
| 450 | T | A | -0.2967 | |
| 451 | L | A | 0.4450 | |
| 452 | E | A | -0.5214 | |
| 453 | T | A | -0.5800 | |
| 454 | T | A | -0.2948 | |
| 455 | L | A | 0.0000 | |
| 456 | T | A | -0.8149 | |
| 457 | H | A | -1.9403 | |
| 458 | S | A | -1.2984 | |
| 459 | S | A | -0.9165 | |
| 460 | G | A | -0.8583 | |
| 461 | P | A | -0.3795 | |
| 462 | A | A | -0.1309 | |
| 463 | S | A | 0.2081 | |
| 464 | Y | A | 0.4976 | |
| 465 | G | A | -1.1439 | |
| 466 | R | A | -2.1031 | |
| 467 | P | A | -1.4894 | |
| 468 | R | A | -1.6413 | |
| 469 | V | A | 0.5702 | |
| 470 | A | A | 0.3991 | |
| 471 | A | A | 0.3322 | |
| 472 | A | A | 0.3337 |
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 | -0.6876 | 4.1213 | View | CSV | PDB |
| 4.5 | -0.7549 | 4.1213 | View | CSV | PDB |
| 5.0 | -0.8392 | 4.1213 | View | CSV | PDB |
| 5.5 | -0.9273 | 4.1213 | View | CSV | PDB |
| 6.0 | -1.0062 | 4.1213 | View | CSV | PDB |
| 6.5 | -1.0659 | 4.1213 | View | CSV | PDB |
| 7.0 | -1.1036 | 4.1213 | View | CSV | PDB |
| 7.5 | -1.1251 | 4.1213 | View | CSV | PDB |
| 8.0 | -1.1369 | 4.1213 | View | CSV | PDB |
| 8.5 | -1.1413 | 4.1213 | View | CSV | PDB |
| 9.0 | -1.138 | 4.1213 | 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