| Chain sequence(s) |
A: MSDITVTNWAGNITYTAKELLRPHSLDALRALVADSARVRVLGSGHSFNEIAEPGDGGVLLSLAGLPSVVDVDTAARTVRVGGGVRYAELARVVHARGLALPNMASLPHISVAGSVATGTHGSGVGNGSLASMVREVELVTADGSTVVIARGDERFGGAVTSLGALGVVTSLTLDLEPAYEMEQHVFTELPLAGLDPATFETVMAAAYSVSLFTDWRAPGFRQVWLKRRTDRPLDVFPYAAPAAEKMHPIPGMPAVNCTEQFGVPGPWHERLPHFRAEFTPSSGAELQSEYLMPREHALAALHAMDAIRETLAPVLQTCEIRTVAADAQWLSPAYGRDTVAAHFTWVEDTAAVLPVVRRLEEALVPFAARPHWGKVFTVPAGELRALYPRLADFGALAKALDPAGKFTNAFVRGVLAG
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. (00:00:03)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:03:30)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/1a0c8eed769624c/tmp/folded.pdb (00:03:30)
[INFO] Main: Simulation completed successfully. (00:06:41)
|
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 |
|---|---|---|---|---|
| 1 | M | A | 0.2252 | |
| 2 | S | A | -0.8152 | |
| 3 | D | A | -2.2074 | |
| 4 | I | A | -0.8803 | |
| 5 | T | A | -0.7668 | |
| 6 | V | A | 0.0000 | |
| 7 | T | A | 0.0080 | |
| 8 | N | A | 0.0000 | |
| 9 | W | A | -0.2164 | |
| 10 | A | A | 0.0000 | |
| 11 | G | A | -0.5197 | |
| 12 | N | A | -0.6679 | |
| 13 | I | A | -0.1921 | |
| 14 | T | A | -0.2516 | |
| 15 | Y | A | 0.0000 | |
| 16 | T | A | -1.2940 | |
| 17 | A | A | -1.8274 | |
| 18 | K | A | -2.8779 | |
| 19 | E | A | -2.4403 | |
| 20 | L | A | -1.0885 | |
| 21 | L | A | -0.8858 | |
| 22 | R | A | -1.7826 | |
| 23 | P | A | 0.0000 | |
| 24 | H | A | -1.5551 | |
| 25 | S | A | -1.1213 | |
| 26 | L | A | -0.6108 | |
| 27 | D | A | -1.7989 | |
| 28 | A | A | -1.1524 | |
| 29 | L | A | 0.0000 | |
| 30 | R | A | -1.4913 | |
| 31 | A | A | -1.2179 | |
| 32 | L | A | -0.9058 | |
| 33 | V | A | 0.0000 | |
| 34 | A | A | -1.6584 | |
| 35 | D | A | -2.0767 | |
| 36 | S | A | 0.0000 | |
| 37 | A | A | -0.6474 | |
| 38 | R | A | -1.0196 | |
| 39 | V | A | 0.0000 | |
| 40 | R | A | 0.0000 | |
| 41 | V | A | 0.4709 | |
| 42 | L | A | 0.0000 | |
| 43 | G | A | -0.5042 | |
| 44 | S | A | -0.4580 | |
| 45 | G | A | -0.1874 | |
| 46 | H | A | -0.3019 | |
| 47 | S | A | -0.3803 | |
| 48 | F | A | 0.0000 | |
| 49 | N | A | 0.0000 | |
| 50 | E | A | -1.2105 | |
| 51 | I | A | 0.0000 | |
| 52 | A | A | 0.0000 | |
| 53 | E | A | -0.8171 | |
| 54 | P | A | 0.0000 | |
| 55 | G | A | -1.3750 | |
| 56 | D | A | -2.3310 | |
| 57 | G | A | -1.6022 | |
| 58 | G | A | -1.0086 | |
| 59 | V | A | -0.5260 | |
| 60 | L | A | 0.0000 | |
| 61 | L | A | 0.0000 | |
| 62 | S | A | 0.0000 | |
| 63 | L | A | 0.0000 | |
| 64 | A | A | -0.7453 | |
| 65 | G | A | -1.0981 | |
| 66 | L | A | -0.5706 | |
| 67 | P | A | -0.2197 | |
| 68 | S | A | -0.3385 | |
| 69 | V | A | 0.0221 | |
| 70 | V | A | -0.5786 | |
| 71 | D | A | -1.9872 | |
| 72 | V | A | -1.7248 | |
| 73 | D | A | -2.2712 | |
| 74 | T | A | -1.5782 | |
| 75 | A | A | -0.6394 | |
| 76 | A | A | -0.8560 | |
| 77 | R | A | -1.7214 | |
| 78 | T | A | -1.6436 | |
| 79 | V | A | 0.0000 | |
| 80 | R | A | -1.7228 | |
| 81 | V | A | 0.0000 | |
| 82 | G | A | -0.4776 | |
| 83 | G | A | 0.0000 | |
| 84 | G | A | -0.6204 | |
| 85 | V | A | 0.0000 | |
| 86 | R | A | -1.3264 | |
| 87 | Y | A | 0.0000 | |
| 88 | A | A | -1.2688 | |
| 89 | E | A | -1.1992 | |
| 90 | L | A | 0.0000 | |
| 91 | A | A | 0.0000 | |
| 92 | R | A | -2.3000 | |
| 93 | V | A | 0.0000 | |
| 94 | V | A | 0.0000 | |
| 95 | H | A | -1.6503 | |
| 96 | A | A | -1.3887 | |
| 97 | R | A | -2.2068 | |
| 98 | G | A | -1.3970 | |
| 99 | L | A | 0.0000 | |
| 100 | A | A | 0.0000 | |
| 101 | L | A | 0.0000 | |
| 102 | P | A | -0.2487 | |
| 103 | N | A | 0.0000 | |
| 104 | M | A | 0.0000 | |
| 105 | A | A | 0.0000 | |
| 106 | S | A | 0.0449 | |
| 107 | L | A | 0.1680 | |
| 108 | P | A | 0.0000 | |
| 109 | H | A | -0.6069 | |
| 110 | I | A | -0.3898 | |
| 111 | S | A | 0.0000 | |
| 112 | V | A | 0.0000 | |
| 113 | A | A | -0.2690 | |
| 114 | G | A | -0.4258 | |
| 115 | S | A | 0.0000 | |
| 116 | V | A | 0.0000 | |
| 117 | A | A | -0.0712 | |
| 118 | T | A | 0.0000 | |
| 119 | G | A | 0.0000 | |
| 120 | T | A | -0.0527 | |
| 121 | H | A | 0.0000 | |
| 122 | G | A | 0.0000 | |
| 123 | S | A | 0.0000 | |
| 124 | G | A | 0.0000 | |
| 125 | V | A | -0.1934 | |
| 126 | G | A | -0.3543 | |
| 127 | N | A | 0.0000 | |
| 128 | G | A | -0.3024 | |
| 129 | S | A | 0.0000 | |
| 130 | L | A | 0.0000 | |
| 131 | A | A | 0.0000 | |
| 132 | S | A | -0.3973 | |
| 133 | M | A | 0.0000 | |
| 134 | V | A | 0.0000 | |
| 135 | R | A | -1.9000 | |
| 136 | E | A | -1.2829 | |
| 137 | V | A | 0.0000 | |
| 138 | E | A | 0.3297 | |
| 139 | L | A | 0.0000 | |
| 140 | V | A | 0.0000 | |
| 141 | T | A | 0.0000 | |
| 142 | A | A | -1.2475 | |
| 143 | D | A | -2.1545 | |
| 144 | G | A | 0.0000 | |
| 145 | S | A | -0.9057 | |
| 146 | T | A | 0.0088 | |
| 147 | V | A | 0.8553 | |
| 148 | V | A | 1.1671 | |
| 149 | I | A | 0.0000 | |
| 150 | A | A | -1.4775 | |
| 151 | R | A | -2.6630 | |
| 152 | G | A | -2.1909 | |
| 153 | D | A | -2.2712 | |
| 154 | E | A | -2.7443 | |
| 155 | R | A | -2.1435 | |
| 156 | F | A | 0.0000 | |
| 157 | G | A | -1.3076 | |
| 158 | G | A | 0.0000 | |
| 159 | A | A | 0.0000 | |
| 160 | V | A | 0.0000 | |
| 161 | T | A | 0.0000 | |
| 162 | S | A | 0.0000 | |
| 163 | L | A | 0.0000 | |
| 164 | G | A | 0.0051 | |
| 165 | A | A | 0.0000 | |
| 166 | L | A | 0.0000 | |
| 167 | G | A | 0.0000 | |
| 168 | V | A | 0.0000 | |
| 169 | V | A | 0.3048 | |
| 170 | T | A | 0.0814 | |
| 171 | S | A | 0.0000 | |
| 172 | L | A | 0.0000 | |
| 173 | T | A | -1.1153 | |
| 174 | L | A | 0.0000 | |
| 175 | D | A | -1.2716 | |
| 176 | L | A | 0.0000 | |
| 177 | E | A | -0.8003 | |
| 178 | P | A | -0.8808 | |
| 179 | A | A | -0.8789 | |
| 180 | Y | A | 0.0000 | |
| 181 | E | A | -1.6824 | |
| 182 | M | A | 0.0000 | |
| 183 | E | A | -0.1944 | |
| 184 | Q | A | 0.0000 | |
| 185 | H | A | 0.3146 | |
| 186 | V | A | 0.0000 | |
| 187 | F | A | -0.2604 | |
| 188 | T | A | -0.8076 | |
| 189 | E | A | -1.7680 | |
| 190 | L | A | 0.0000 | |
| 191 | P | A | -0.7499 | |
| 192 | L | A | 0.0000 | |
| 193 | A | A | -0.5808 | |
| 194 | G | A | -0.9437 | |
| 195 | L | A | 0.0000 | |
| 196 | D | A | -1.8618 | |
| 197 | P | A | -1.6659 | |
| 198 | A | A | -1.1175 | |
| 199 | T | A | -1.1323 | |
| 200 | F | A | 0.0000 | |
| 201 | E | A | -2.0449 | |
| 202 | T | A | -1.0322 | |
| 203 | V | A | 0.0000 | |
| 204 | M | A | 0.0000 | |
| 205 | A | A | -0.3771 | |
| 206 | A | A | -0.2604 | |
| 207 | A | A | -0.3895 | |
| 208 | Y | A | -0.0657 | |
| 209 | S | A | 0.0000 | |
| 210 | V | A | 0.0000 | |
| 211 | S | A | 0.0000 | |
| 212 | L | A | 0.0000 | |
| 213 | F | A | 0.0000 | |
| 214 | T | A | 0.0000 | |
| 215 | D | A | -1.0298 | |
| 216 | W | A | 0.0000 | |
| 217 | R | A | -2.5554 | |
| 218 | A | A | -1.5584 | |
| 219 | P | A | -1.1364 | |
| 220 | G | A | 0.0000 | |
| 221 | F | A | 0.0000 | |
| 222 | R | A | -1.1845 | |
| 223 | Q | A | 0.0000 | |
| 224 | V | A | 0.0000 | |
| 225 | W | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | K | A | 0.0000 | |
| 228 | R | A | -1.0055 | |
| 229 | R | A | 0.0000 | |
| 230 | T | A | -1.9169 | |
| 231 | D | A | -2.9235 | |
| 232 | R | A | -2.9113 | |
| 233 | P | A | -1.5906 | |
| 234 | L | A | -0.7978 | |
| 235 | D | A | -0.9932 | |
| 236 | V | A | 0.9650 | |
| 237 | F | A | 0.0000 | |
| 238 | P | A | 0.2048 | |
| 239 | Y | A | 0.2281 | |
| 240 | A | A | -0.4439 | |
| 241 | A | A | -0.3672 | |
| 242 | P | A | -0.3146 | |
| 243 | A | A | -0.5355 | |
| 244 | A | A | -0.6498 | |
| 245 | E | A | -1.6942 | |
| 246 | K | A | -0.7665 | |
| 247 | M | A | -0.2524 | |
| 248 | H | A | 0.0000 | |
| 249 | P | A | 0.0000 | |
| 250 | I | A | -0.0303 | |
| 251 | P | A | -0.3496 | |
| 252 | G | A | -0.3686 | |
| 253 | M | A | 0.3289 | |
| 254 | P | A | 0.4250 | |
| 255 | A | A | 0.3750 | |
| 256 | V | A | 1.5473 | |
| 257 | N | A | 0.3709 | |
| 258 | C | A | 0.0000 | |
| 259 | T | A | 0.0000 | |
| 260 | E | A | -0.2491 | |
| 261 | Q | A | 0.0000 | |
| 262 | F | A | 1.5451 | |
| 263 | G | A | 0.9168 | |
| 264 | V | A | 1.0396 | |
| 265 | P | A | -0.1382 | |
| 266 | G | A | -0.6409 | |
| 267 | P | A | -0.8249 | |
| 268 | W | A | 0.0000 | |
| 269 | H | A | -1.0211 | |
| 270 | E | A | -1.1301 | |
| 271 | R | A | 0.0000 | |
| 272 | L | A | 0.0000 | |
| 273 | P | A | 0.0000 | |
| 274 | H | A | 0.0000 | |
| 275 | F | A | -0.1216 | |
| 276 | R | A | -0.8611 | |
| 277 | A | A | -1.2581 | |
| 278 | E | A | -1.7862 | |
| 279 | F | A | -0.4194 | |
| 280 | T | A | -0.5395 | |
| 281 | P | A | -0.3636 | |
| 282 | S | A | -0.2855 | |
| 283 | S | A | -0.4058 | |
| 284 | G | A | -0.4445 | |
| 285 | A | A | -0.6381 | |
| 286 | E | A | -0.8839 | |
| 287 | L | A | 0.0000 | |
| 288 | Q | A | -0.3035 | |
| 289 | S | A | 0.0000 | |
| 290 | E | A | 0.0000 | |
| 291 | Y | A | 0.0000 | |
| 292 | L | A | 0.0000 | |
| 293 | M | A | 0.0000 | |
| 294 | P | A | 0.0000 | |
| 295 | R | A | -1.6164 | |
| 296 | E | A | -2.2006 | |
| 297 | H | A | -1.1554 | |
| 298 | A | A | 0.0000 | |
| 299 | L | A | -0.7160 | |
| 300 | A | A | -0.4914 | |
| 301 | A | A | 0.0000 | |
| 302 | L | A | 0.0000 | |
| 303 | H | A | -0.7782 | |
| 304 | A | A | -0.5407 | |
| 305 | M | A | 0.0000 | |
| 306 | D | A | -1.0758 | |
| 307 | A | A | -0.5398 | |
| 308 | I | A | -0.8572 | |
| 309 | R | A | -1.8359 | |
| 310 | E | A | -2.4091 | |
| 311 | T | A | -1.5084 | |
| 312 | L | A | 0.0000 | |
| 313 | A | A | 0.0000 | |
| 314 | P | A | -0.9024 | |
| 315 | V | A | 0.0000 | |
| 316 | L | A | 0.0000 | |
| 317 | Q | A | -0.2661 | |
| 318 | T | A | 0.0000 | |
| 319 | C | A | 0.0000 | |
| 320 | E | A | 0.0000 | |
| 321 | I | A | 0.0000 | |
| 322 | R | A | 0.0000 | |
| 323 | T | A | 0.0000 | |
| 324 | V | A | 0.0000 | |
| 325 | A | A | -0.5434 | |
| 326 | A | A | -0.6429 | |
| 327 | D | A | 0.0000 | |
| 328 | A | A | -0.1111 | |
| 329 | Q | A | 0.0000 | |
| 330 | W | A | 0.0000 | |
| 331 | L | A | 0.0000 | |
| 332 | S | A | 0.0000 | |
| 333 | P | A | 0.0000 | |
| 334 | A | A | 0.0000 | |
| 335 | Y | A | -0.4271 | |
| 336 | G | A | -0.8246 | |
| 337 | R | A | -1.1002 | |
| 338 | D | A | -1.4453 | |
| 339 | T | A | 0.0000 | |
| 340 | V | A | 0.0000 | |
| 341 | A | A | 0.0000 | |
| 342 | A | A | 0.0000 | |
| 343 | H | A | 0.0000 | |
| 344 | F | A | 0.0000 | |
| 345 | T | A | 0.0000 | |
| 346 | W | A | 0.0000 | |
| 347 | V | A | -0.4506 | |
| 348 | E | A | -1.8047 | |
| 349 | D | A | -1.4896 | |
| 350 | T | A | -0.6581 | |
| 351 | A | A | -0.2847 | |
| 352 | A | A | -0.2618 | |
| 353 | V | A | 0.0000 | |
| 354 | L | A | 0.1300 | |
| 355 | P | A | -0.6149 | |
| 356 | V | A | 0.0000 | |
| 357 | V | A | 0.0000 | |
| 358 | R | A | -1.9495 | |
| 359 | R | A | -2.7810 | |
| 360 | L | A | 0.0000 | |
| 361 | E | A | 0.0000 | |
| 362 | E | A | -2.0980 | |
| 363 | A | A | -0.9694 | |
| 364 | L | A | 0.0000 | |
| 365 | V | A | 0.9632 | |
| 366 | P | A | 0.3870 | |
| 367 | F | A | 0.3402 | |
| 368 | A | A | 0.6229 | |
| 369 | A | A | 0.3630 | |
| 370 | R | A | 0.0000 | |
| 371 | P | A | 0.0000 | |
| 372 | H | A | 0.0000 | |
| 373 | W | A | 0.0000 | |
| 374 | G | A | 0.0000 | |
| 375 | K | A | 0.0000 | |
| 376 | V | A | 0.0000 | |
| 377 | F | A | 0.3253 | |
| 378 | T | A | -0.0850 | |
| 379 | V | A | -0.4167 | |
| 380 | P | A | -0.7220 | |
| 381 | A | A | -1.0099 | |
| 382 | G | A | -1.3153 | |
| 383 | E | A | -1.8095 | |
| 384 | L | A | 0.0000 | |
| 385 | R | A | -1.1090 | |
| 386 | A | A | -0.8051 | |
| 387 | L | A | -0.3824 | |
| 388 | Y | A | 0.0000 | |
| 389 | P | A | -0.9443 | |
| 390 | R | A | -1.6916 | |
| 391 | L | A | -0.9560 | |
| 392 | A | A | -1.0896 | |
| 393 | D | A | -2.1308 | |
| 394 | F | A | 0.0000 | |
| 395 | G | A | -1.0918 | |
| 396 | A | A | -1.0998 | |
| 397 | L | A | 0.0000 | |
| 398 | A | A | 0.0000 | |
| 399 | K | A | -1.8941 | |
| 400 | A | A | -0.7495 | |
| 401 | L | A | -0.5251 | |
| 402 | D | A | 0.0000 | |
| 403 | P | A | -0.8990 | |
| 404 | A | A | -0.5053 | |
| 405 | G | A | -0.8716 | |
| 406 | K | A | -0.6143 | |
| 407 | F | A | 0.0000 | |
| 408 | T | A | -0.6720 | |
| 409 | N | A | 0.0000 | |
| 410 | A | A | -0.8582 | |
| 411 | F | A | 0.0000 | |
| 412 | V | A | 0.0000 | |
| 413 | R | A | -1.7995 | |
| 414 | G | A | -1.0657 | |
| 415 | V | A | 0.0000 | |
| 416 | L | A | -0.5714 | |
| 417 | A | A | -0.7406 | |
| 418 | G | A | -0.6818 |
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 | -0.1123 | 4.4276 | View | CSV | PDB |
| 4.5 | -0.1755 | 4.349 | View | CSV | PDB |
| 5.0 | -0.2493 | 4.2518 | View | CSV | PDB |
| 5.5 | -0.3248 | 4.1562 | View | CSV | PDB |
| 6.0 | -0.3945 | 4.0775 | View | CSV | PDB |
| 6.5 | -0.4521 | 4.0283 | View | CSV | PDB |
| 7.0 | -0.4956 | 4.013 | View | CSV | PDB |
| 7.5 | -0.5278 | 4.021 | View | CSV | PDB |
| 8.0 | -0.5516 | 4.0397 | View | CSV | PDB |
| 8.5 | -0.5674 | 4.0622 | View | CSV | PDB |
| 9.0 | -0.5743 | 4.0859 | 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