| Chain sequence(s) |
A: MDDVIARLAPLLRRHRVPGAQLALRWQGRTYTAEAGEESAGAGRPVTGGTAFPLGSLTKPFTATLAMMLAADGDLELDEPVSACLPGLRPGAGRVTLRQLLSHTAGLPANVEESAAGLTRRRWAEESAAAVHPPGSAFSYSNAGYLLVAHLVEDVTGMSWRAAVESFLLRPLGIEPLFAVGARRAAEQAGARPAADGHVVRPDGAALPIAEQSVTALEEPVAGLAGSAADLLAFAALHLPGHEGPGLLDGESAAEMRRDQLGGLPAGAFGLADGWGLGWSLYGTASGTWFGHDGTGDGAWCHLRVQPETGTAVALTTNGGNGAVLWEAVVAELRAAGVDVGHYPLGALTGGGTPLPAGSPAKDGCAGRYANGSWTCAVEASGGELYLSVGPGPRWRLRCFEDLRFTTEGSDAGSMPYVGRFLRDPGSGTVELVQITGRLARRHG
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] (00:00:01)
[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-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 (00:03:49)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/e43ed3c5200595b/tmp/folded.pdb (00:03:49)
[INFO] Main: Simulation completed successfully. (00:08:08)
|
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 | -1.3405 | |
| 2 | D | A | -2.5447 | |
| 3 | D | A | -2.6576 | |
| 4 | V | A | 0.0000 | |
| 5 | I | A | 0.0000 | |
| 6 | A | A | -1.6955 | |
| 7 | R | A | -2.0087 | |
| 8 | L | A | 0.0000 | |
| 9 | A | A | -1.3844 | |
| 10 | P | A | -1.8738 | |
| 11 | L | A | -1.8443 | |
| 12 | L | A | 0.0000 | |
| 13 | R | A | -3.4948 | |
| 14 | R | A | -3.3515 | |
| 15 | H | A | -2.3927 | |
| 16 | R | A | -3.5074 | |
| 17 | V | A | 0.0000 | |
| 18 | P | A | -0.8279 | |
| 19 | G | A | 0.0000 | |
| 20 | A | A | 0.0000 | |
| 21 | Q | A | 0.0000 | |
| 22 | L | A | 0.0000 | |
| 23 | A | A | 0.0000 | |
| 24 | L | A | 0.0000 | |
| 25 | R | A | -1.2630 | |
| 26 | W | A | -1.2919 | |
| 27 | Q | A | -2.0076 | |
| 28 | G | A | -2.0396 | |
| 29 | R | A | -2.4771 | |
| 30 | T | A | -1.2784 | |
| 31 | Y | A | -0.7286 | |
| 32 | T | A | -0.5377 | |
| 33 | A | A | -0.9199 | |
| 34 | E | A | -1.2962 | |
| 35 | A | A | 0.0000 | |
| 36 | G | A | -1.5500 | |
| 37 | E | A | -1.6332 | |
| 38 | E | A | 0.0000 | |
| 39 | S | A | 0.0000 | |
| 40 | A | A | -0.6046 | |
| 41 | G | A | -0.9316 | |
| 42 | A | A | -1.1252 | |
| 43 | G | A | -1.6813 | |
| 44 | R | A | -2.4513 | |
| 45 | P | A | -1.7475 | |
| 46 | V | A | 0.0000 | |
| 47 | T | A | -0.9439 | |
| 48 | G | A | -0.6495 | |
| 49 | G | A | -0.8002 | |
| 50 | T | A | 0.0000 | |
| 51 | A | A | 0.0000 | |
| 52 | F | A | 0.0000 | |
| 53 | P | A | 0.0000 | |
| 54 | L | A | 0.0000 | |
| 55 | G | A | 0.0000 | |
| 56 | S | A | -0.1515 | |
| 57 | L | A | 0.0000 | |
| 58 | T | A | 0.0000 | |
| 59 | K | A | 0.0000 | |
| 60 | P | A | 0.0000 | |
| 61 | F | A | 0.0000 | |
| 62 | T | A | 0.0000 | |
| 63 | A | A | 0.0000 | |
| 64 | T | A | 0.0000 | |
| 65 | L | A | 0.0000 | |
| 66 | A | A | 0.0000 | |
| 67 | M | A | 0.0000 | |
| 68 | M | A | -0.5773 | |
| 69 | L | A | -1.3259 | |
| 70 | A | A | -1.6576 | |
| 71 | A | A | -1.8400 | |
| 72 | D | A | -2.6331 | |
| 73 | G | A | -2.4933 | |
| 74 | D | A | -2.7514 | |
| 75 | L | A | 0.0000 | |
| 76 | E | A | -3.4726 | |
| 77 | L | A | -2.2699 | |
| 78 | D | A | -3.2112 | |
| 79 | E | A | -3.4226 | |
| 80 | P | A | -2.3491 | |
| 81 | V | A | 0.0000 | |
| 82 | S | A | -1.2007 | |
| 83 | A | A | -0.8408 | |
| 84 | C | A | -0.6526 | |
| 85 | L | A | 0.0000 | |
| 86 | P | A | -0.7447 | |
| 87 | G | A | -1.5591 | |
| 88 | L | A | 0.0000 | |
| 89 | R | A | -2.5957 | |
| 90 | P | A | -1.6674 | |
| 91 | G | A | -1.3145 | |
| 92 | A | A | 0.0000 | |
| 93 | G | A | 0.0000 | |
| 94 | R | A | -2.4973 | |
| 95 | V | A | 0.0000 | |
| 96 | T | A | -2.0922 | |
| 97 | L | A | 0.0000 | |
| 98 | R | A | -1.4419 | |
| 99 | Q | A | -0.7625 | |
| 100 | L | A | 0.0000 | |
| 101 | L | A | 0.0000 | |
| 102 | S | A | 0.0000 | |
| 103 | H | A | 0.0000 | |
| 104 | T | A | 0.0000 | |
| 105 | A | A | 0.0000 | |
| 106 | G | A | 0.0000 | |
| 107 | L | A | 0.0000 | |
| 108 | P | A | -0.2726 | |
| 109 | A | A | 0.0000 | |
| 110 | N | A | -0.9306 | |
| 111 | V | A | 0.0000 | |
| 112 | E | A | -1.6078 | |
| 113 | E | A | -2.2845 | |
| 114 | S | A | -1.2445 | |
| 115 | A | A | 0.0000 | |
| 116 | A | A | -0.7878 | |
| 117 | G | A | -0.5911 | |
| 118 | L | A | -0.3830 | |
| 119 | T | A | -0.6401 | |
| 120 | R | A | -1.2542 | |
| 121 | R | A | -2.0368 | |
| 122 | R | A | -2.2218 | |
| 123 | W | A | 0.0000 | |
| 124 | A | A | 0.0000 | |
| 125 | E | A | -2.5133 | |
| 126 | E | A | -2.7785 | |
| 127 | S | A | -1.6387 | |
| 128 | A | A | 0.0000 | |
| 129 | A | A | -0.6460 | |
| 130 | A | A | -0.3511 | |
| 131 | V | A | 0.1845 | |
| 132 | H | A | 0.0000 | |
| 133 | P | A | -0.3167 | |
| 134 | P | A | -0.6740 | |
| 135 | G | A | -0.4273 | |
| 136 | S | A | -0.3144 | |
| 137 | A | A | 0.0000 | |
| 138 | F | A | 0.0000 | |
| 139 | S | A | 0.0000 | |
| 140 | Y | A | 0.0000 | |
| 141 | S | A | 0.0000 | |
| 142 | N | A | -0.3987 | |
| 143 | A | A | 0.0000 | |
| 144 | G | A | 0.0000 | |
| 145 | Y | A | 0.0000 | |
| 146 | L | A | 0.0000 | |
| 147 | L | A | 0.0000 | |
| 148 | V | A | 0.0000 | |
| 149 | A | A | 0.0000 | |
| 150 | H | A | 0.0000 | |
| 151 | L | A | 0.0000 | |
| 152 | V | A | 0.0000 | |
| 153 | E | A | -0.8369 | |
| 154 | D | A | -0.9070 | |
| 155 | V | A | -0.4591 | |
| 156 | T | A | -0.4913 | |
| 157 | G | A | -0.5780 | |
| 158 | M | A | -0.2935 | |
| 159 | S | A | -0.5766 | |
| 160 | W | A | 0.0000 | |
| 161 | R | A | -0.8127 | |
| 162 | A | A | -0.4613 | |
| 163 | A | A | 0.0000 | |
| 164 | V | A | 0.0000 | |
| 165 | E | A | -1.4252 | |
| 166 | S | A | -0.6377 | |
| 167 | F | A | 0.1316 | |
| 168 | L | A | 0.0000 | |
| 169 | L | A | 0.0000 | |
| 170 | R | A | -2.4975 | |
| 171 | P | A | -1.2352 | |
| 172 | L | A | -1.0374 | |
| 173 | G | A | -1.6131 | |
| 174 | I | A | 0.0000 | |
| 175 | E | A | -2.5776 | |
| 176 | P | A | -1.6426 | |
| 177 | L | A | 0.0000 | |
| 178 | F | A | 0.0000 | |
| 179 | A | A | 0.0000 | |
| 180 | V | A | -0.2479 | |
| 181 | G | A | -1.1907 | |
| 182 | A | A | -1.5278 | |
| 183 | R | A | -2.8134 | |
| 184 | R | A | -3.3411 | |
| 185 | A | A | -2.1616 | |
| 186 | A | A | -2.3090 | |
| 187 | E | A | -3.3228 | |
| 188 | Q | A | -2.6741 | |
| 189 | A | A | -1.1984 | |
| 190 | G | A | -1.0413 | |
| 191 | A | A | -1.4504 | |
| 192 | R | A | -1.2004 | |
| 193 | P | A | -1.0636 | |
| 194 | A | A | -0.7807 | |
| 195 | A | A | 0.0000 | |
| 196 | D | A | 0.0000 | |
| 197 | G | A | 0.0000 | |
| 198 | H | A | 0.0000 | |
| 199 | V | A | 1.3352 | |
| 200 | V | A | -0.4544 | |
| 201 | R | A | -2.1900 | |
| 202 | P | A | -2.3480 | |
| 203 | D | A | -2.6283 | |
| 204 | G | A | -1.8188 | |
| 205 | A | A | -0.8659 | |
| 206 | A | A | -0.0101 | |
| 207 | L | A | 1.2646 | |
| 208 | P | A | 0.5731 | |
| 209 | I | A | 0.1811 | |
| 210 | A | A | -1.0825 | |
| 211 | E | A | -2.1977 | |
| 212 | Q | A | -1.1454 | |
| 213 | S | A | -0.6336 | |
| 214 | V | A | -0.2080 | |
| 215 | T | A | -0.2310 | |
| 216 | A | A | -0.0221 | |
| 217 | L | A | 0.0000 | |
| 218 | E | A | -0.3545 | |
| 219 | E | A | 0.0000 | |
| 220 | P | A | 0.0000 | |
| 221 | V | A | 0.0000 | |
| 222 | A | A | -0.0634 | |
| 223 | G | A | 0.0000 | |
| 224 | L | A | 0.0000 | |
| 225 | A | A | 0.0000 | |
| 226 | G | A | 0.0000 | |
| 227 | S | A | 0.0000 | |
| 228 | A | A | 0.0000 | |
| 229 | A | A | -0.1835 | |
| 230 | D | A | -0.5413 | |
| 231 | L | A | 0.0000 | |
| 232 | L | A | 0.0000 | |
| 233 | A | A | -0.1504 | |
| 234 | F | A | 0.0000 | |
| 235 | A | A | 0.0000 | |
| 236 | A | A | -0.5420 | |
| 237 | L | A | 0.0000 | |
| 238 | H | A | 0.0000 | |
| 239 | L | A | 0.0000 | |
| 240 | P | A | -1.2008 | |
| 241 | G | A | -1.3377 | |
| 242 | H | A | -1.6851 | |
| 243 | E | A | -2.3574 | |
| 244 | G | A | -1.4381 | |
| 245 | P | A | -0.8319 | |
| 246 | G | A | -1.0976 | |
| 247 | L | A | -0.1756 | |
| 248 | L | A | 0.0000 | |
| 249 | D | A | -1.9206 | |
| 250 | G | A | -1.9907 | |
| 251 | E | A | -2.4709 | |
| 252 | S | A | -1.7084 | |
| 253 | A | A | 0.0000 | |
| 254 | A | A | -1.6744 | |
| 255 | E | A | -1.9488 | |
| 256 | M | A | 0.0000 | |
| 257 | R | A | -1.8353 | |
| 258 | R | A | -3.0878 | |
| 259 | D | A | -3.2064 | |
| 260 | Q | A | -1.9010 | |
| 261 | L | A | 0.0000 | |
| 262 | G | A | -1.2939 | |
| 263 | G | A | -0.6508 | |
| 264 | L | A | -0.2796 | |
| 265 | P | A | -0.2864 | |
| 266 | A | A | 0.0000 | |
| 267 | G | A | -0.4674 | |
| 268 | A | A | 0.0000 | |
| 269 | F | A | -0.2315 | |
| 270 | G | A | -0.0725 | |
| 271 | L | A | -0.1138 | |
| 272 | A | A | 0.0000 | |
| 273 | D | A | -2.0620 | |
| 274 | G | A | 0.0000 | |
| 275 | W | A | 0.0000 | |
| 276 | G | A | 0.0000 | |
| 277 | L | A | 0.0000 | |
| 278 | G | A | 0.0000 | |
| 279 | W | A | 0.0000 | |
| 280 | S | A | 0.0000 | |
| 281 | L | A | 0.0000 | |
| 282 | Y | A | 0.0000 | |
| 283 | G | A | -1.0876 | |
| 284 | T | A | -0.5034 | |
| 285 | A | A | -0.3124 | |
| 286 | S | A | -0.7088 | |
| 287 | G | A | -0.8317 | |
| 288 | T | A | -0.8795 | |
| 289 | W | A | 0.0000 | |
| 290 | F | A | 0.0000 | |
| 291 | G | A | 0.0000 | |
| 292 | H | A | 0.0000 | |
| 293 | D | A | -0.2908 | |
| 294 | G | A | 0.0000 | |
| 295 | T | A | -0.2928 | |
| 296 | G | A | -0.4212 | |
| 297 | D | A | -0.6727 | |
| 298 | G | A | 0.2932 | |
| 299 | A | A | 0.0000 | |
| 300 | W | A | -0.0378 | |
| 301 | C | A | 0.0000 | |
| 302 | H | A | 0.0000 | |
| 303 | L | A | 0.0000 | |
| 304 | R | A | 0.0000 | |
| 305 | V | A | 0.0000 | |
| 306 | Q | A | 0.0000 | |
| 307 | P | A | -1.0167 | |
| 308 | E | A | -1.9703 | |
| 309 | T | A | -1.3081 | |
| 310 | G | A | 0.0000 | |
| 311 | T | A | 0.0000 | |
| 312 | A | A | 0.0000 | |
| 313 | V | A | 0.0000 | |
| 314 | A | A | 0.0000 | |
| 315 | L | A | 0.0000 | |
| 316 | T | A | 0.0000 | |
| 317 | T | A | 0.0000 | |
| 318 | N | A | 0.0000 | |
| 319 | G | A | 0.0000 | |
| 320 | G | A | 0.0012 | |
| 321 | N | A | 0.0000 | |
| 322 | G | A | 0.0000 | |
| 323 | A | A | 0.0000 | |
| 324 | V | A | 0.2922 | |
| 325 | L | A | 0.0000 | |
| 326 | W | A | 0.0000 | |
| 327 | E | A | -0.4257 | |
| 328 | A | A | -0.6709 | |
| 329 | V | A | 0.0000 | |
| 330 | V | A | 0.0000 | |
| 331 | A | A | -0.8129 | |
| 332 | E | A | -1.4319 | |
| 333 | L | A | 0.0000 | |
| 334 | R | A | -1.5259 | |
| 335 | A | A | -0.8700 | |
| 336 | A | A | -0.8919 | |
| 337 | G | A | -1.0108 | |
| 338 | V | A | 0.0000 | |
| 339 | D | A | -1.1274 | |
| 340 | V | A | 0.0000 | |
| 341 | G | A | 0.0000 | |
| 342 | H | A | -0.5238 | |
| 343 | Y | A | 0.0000 | |
| 344 | P | A | -0.0175 | |
| 345 | L | A | 0.3639 | |
| 346 | G | A | 0.3017 | |
| 347 | A | A | 0.1315 | |
| 348 | L | A | -0.0488 | |
| 349 | T | A | -0.4872 | |
| 350 | G | A | -0.7214 | |
| 351 | G | A | -0.8573 | |
| 352 | G | A | -1.3830 | |
| 353 | T | A | -1.1101 | |
| 354 | P | A | -1.1973 | |
| 355 | L | A | -1.0658 | |
| 356 | P | A | -0.7692 | |
| 357 | A | A | -0.7664 | |
| 358 | G | A | -1.1317 | |
| 359 | S | A | -1.0265 | |
| 360 | P | A | -1.0518 | |
| 361 | A | A | -1.3516 | |
| 362 | K | A | 0.0000 | |
| 363 | D | A | -2.1016 | |
| 364 | G | A | -1.4573 | |
| 365 | C | A | 0.0000 | |
| 366 | A | A | -1.5993 | |
| 367 | G | A | -1.9849 | |
| 368 | R | A | -2.7239 | |
| 369 | Y | A | 0.0000 | |
| 370 | A | A | -0.9356 | |
| 371 | N | A | 0.0000 | |
| 372 | G | A | -0.4329 | |
| 373 | S | A | -0.7654 | |
| 374 | W | A | -0.3124 | |
| 375 | T | A | -0.6272 | |
| 376 | C | A | 0.0000 | |
| 377 | A | A | -1.5752 | |
| 378 | V | A | 0.0000 | |
| 379 | E | A | -2.5350 | |
| 380 | A | A | -1.6627 | |
| 381 | S | A | -1.1935 | |
| 382 | G | A | -0.8750 | |
| 383 | G | A | -1.2073 | |
| 384 | E | A | -1.5558 | |
| 385 | L | A | 0.0000 | |
| 386 | Y | A | 0.0000 | |
| 387 | L | A | 0.0000 | |
| 388 | S | A | -1.5113 | |
| 389 | V | A | -0.4327 | |
| 390 | G | A | -0.5422 | |
| 391 | P | A | -0.7786 | |
| 392 | G | A | -0.8937 | |
| 393 | P | A | -1.4870 | |
| 394 | R | A | -2.6100 | |
| 395 | W | A | -2.0696 | |
| 396 | R | A | -2.5192 | |
| 397 | L | A | 0.0000 | |
| 398 | R | A | -1.6627 | |
| 399 | C | A | 0.0000 | |
| 400 | F | A | 0.0000 | |
| 401 | E | A | -2.6503 | |
| 402 | D | A | -2.4264 | |
| 403 | L | A | 0.0000 | |
| 404 | R | A | -1.3603 | |
| 405 | F | A | 0.0000 | |
| 406 | T | A | 0.0000 | |
| 407 | T | A | 0.0000 | |
| 408 | E | A | -2.2385 | |
| 409 | G | A | -1.9601 | |
| 410 | S | A | -1.9040 | |
| 411 | D | A | -2.4673 | |
| 412 | A | A | -1.7328 | |
| 413 | G | A | -1.2661 | |
| 414 | S | A | -0.9267 | |
| 415 | M | A | -0.0362 | |
| 416 | P | A | -0.3053 | |
| 417 | Y | A | 0.3114 | |
| 418 | V | A | 0.0000 | |
| 419 | G | A | 0.0000 | |
| 420 | R | A | -0.6125 | |
| 421 | F | A | 0.0000 | |
| 422 | L | A | -0.9530 | |
| 423 | R | A | -1.8151 | |
| 424 | D | A | -1.7970 | |
| 425 | P | A | -1.3174 | |
| 426 | G | A | -1.1571 | |
| 427 | S | A | -1.1467 | |
| 428 | G | A | -1.3148 | |
| 429 | T | A | -1.3638 | |
| 430 | V | A | 0.0000 | |
| 431 | E | A | -1.6112 | |
| 432 | L | A | -1.0011 | |
| 433 | V | A | 0.0000 | |
| 434 | Q | A | 0.0000 | |
| 435 | I | A | 0.0000 | |
| 436 | T | A | 0.0542 | |
| 437 | G | A | 0.0000 | |
| 438 | R | A | -0.3543 | |
| 439 | L | A | 0.0000 | |
| 440 | A | A | 0.0000 | |
| 441 | R | A | -1.2827 | |
| 442 | R | A | -1.9743 | |
| 443 | H | A | -2.1414 | |
| 444 | G | A | -1.4485 |
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 | -0.3727 | 2.6701 | View | CSV | PDB |
| 4.5 | -0.4306 | 2.6154 | View | CSV | PDB |
| 5.0 | -0.5031 | 2.5479 | View | CSV | PDB |
| 5.5 | -0.582 | 2.477 | View | CSV | PDB |
| 6.0 | -0.6594 | 2.4119 | View | CSV | PDB |
| 6.5 | -0.728 | 2.361 | View | CSV | PDB |
| 7.0 | -0.7832 | 2.3273 | View | CSV | PDB |
| 7.5 | -0.8257 | 2.3053 | View | CSV | PDB |
| 8.0 | -0.8586 | 2.2892 | View | CSV | PDB |
| 8.5 | -0.8832 | 2.2771 | View | CSV | PDB |
| 9.0 | -0.8994 | 2.2694 | 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