| Chain sequence(s) |
A: GPLGGAGDGAPVGLDLDRLARDCDVVGGQLALHHQGTLTTWEFGTEEHAGGRPVHVGSAFPYGSSVTKAFTATAVLQLAGDGDLDLDRPVRELLPEAEAHPALAATLRQLLSHTAGLPSDHDDERAPSLRRWLTGFLALPVGPWPAPGSFSYSNVGYGIAGRVVEAVTGLTWSEAVRDFLLHHPLGTAITVLPTDPGSLPAGGLAGSAADLVRLGRLHLDEPGDPDLARLADPDALREMARPTAGADPFGLADGWGPGLGRFGPAGNRWLGHDGTLDGATCHLRIHPGRGTVVALTTNSPTGQALWDAVVDALRDADIDVGVHRPAPPPAIAAAAFADCTGTYRNGDLAVTVGIDGPYLVLELPGGARELAQPLAHRTFSSRGAGFFLGRFVTDADAVHALQYSGRTLLRE
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 (00:03:20)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/50d73f5a3710b5b/tmp/folded.pdb (00:03:20)
[INFO] Main: Simulation completed successfully. (00:07:26)
|
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 |
|---|---|---|---|---|
| 12 | G | A | -0.3663 | |
| 13 | P | A | 0.1300 | |
| 14 | L | A | 0.9798 | |
| 15 | G | A | -0.1150 | |
| 17 | G | A | -0.8123 | |
| 18 | A | A | -1.4009 | |
| 19 | G | A | -2.1672 | |
| 20 | D | A | -2.7954 | |
| 21 | G | A | -1.4815 | |
| 22 | A | A | -0.4114 | |
| 23 | P | A | -0.4663 | |
| 24 | V | A | 1.3404 | |
| 25 | G | A | 0.0088 | |
| 26 | L | A | -0.6261 | |
| 27 | D | A | -2.3301 | |
| 28 | L | A | 0.0000 | |
| 29 | D | A | -3.0866 | |
| 30 | R | A | -3.9812 | |
| 31 | L | A | -2.8354 | |
| 32 | A | A | 0.0000 | |
| 33 | R | A | -4.1349 | |
| 34 | D | A | -3.7381 | |
| 35 | C | A | -2.6193 | |
| 36 | D | A | -3.1478 | |
| 37 | V | A | 0.0000 | |
| 38 | V | A | -1.2573 | |
| 39 | G | A | 0.0000 | |
| 40 | G | A | 0.0000 | |
| 41 | Q | A | 0.0000 | |
| 42 | L | A | 0.0000 | |
| 43 | A | A | 0.0000 | |
| 44 | L | A | 0.0000 | |
| 45 | H | A | 0.0000 | |
| 46 | H | A | 0.0000 | |
| 47 | Q | A | -1.8516 | |
| 48 | G | A | -1.2629 | |
| 49 | T | A | -0.3255 | |
| 50 | L | A | 0.3810 | |
| 51 | T | A | 0.3385 | |
| 52 | T | A | 0.1519 | |
| 53 | W | A | -0.5634 | |
| 54 | E | A | -1.1426 | |
| 55 | F | A | 0.0000 | |
| 56 | G | A | -1.9535 | |
| 57 | T | A | -2.2236 | |
| 58 | E | A | -2.4600 | |
| 59 | E | A | -3.0856 | |
| 60 | H | A | -2.0249 | |
| 61 | A | A | -1.3540 | |
| 62 | G | A | -1.8000 | |
| 63 | G | A | -2.2520 | |
| 64 | R | A | -2.8989 | |
| 65 | P | A | -2.0747 | |
| 66 | V | A | 0.0000 | |
| 67 | H | A | -1.2150 | |
| 68 | V | A | 0.2715 | |
| 69 | G | A | -0.3024 | |
| 70 | S | A | 0.0000 | |
| 71 | A | A | -0.1541 | |
| 72 | F | A | 0.0000 | |
| 73 | P | A | -0.1019 | |
| 74 | Y | A | 0.0000 | |
| 75 | G | A | -0.1579 | |
| 76 | S | A | -0.0211 | |
| 77 | V | A | 0.0000 | |
| 78 | T | A | 0.0000 | |
| 79 | K | A | 0.0000 | |
| 80 | A | A | 0.0000 | |
| 81 | F | A | 0.0000 | |
| 82 | T | A | 0.0000 | |
| 83 | A | A | 0.0000 | |
| 84 | T | A | 0.0000 | |
| 85 | A | A | 0.0000 | |
| 86 | V | A | 0.0000 | |
| 87 | L | A | 0.0000 | |
| 88 | Q | A | -1.1598 | |
| 89 | L | A | 0.0000 | |
| 90 | A | A | -2.0350 | |
| 91 | G | A | -2.4440 | |
| 92 | D | A | -2.8896 | |
| 93 | G | A | -2.4943 | |
| 94 | D | A | -2.7511 | |
| 95 | L | A | 0.0000 | |
| 96 | D | A | -2.6010 | |
| 97 | L | A | 0.0000 | |
| 98 | D | A | -2.9410 | |
| 99 | R | A | -3.3783 | |
| 100 | P | A | -2.2969 | |
| 101 | V | A | 0.0000 | |
| 102 | R | A | -2.6485 | |
| 103 | E | A | -2.9326 | |
| 104 | L | A | -1.5435 | |
| 105 | L | A | 0.0000 | |
| 106 | P | A | -1.7637 | |
| 107 | E | A | -1.6593 | |
| 108 | A | A | -1.5762 | |
| 109 | E | A | -1.6996 | |
| 110 | A | A | -0.8271 | |
| 130 | H | A | -0.6091 | |
| 131 | P | A | -0.2940 | |
| 132 | A | A | 0.0000 | |
| 133 | L | A | 0.0000 | |
| 134 | A | A | -1.0680 | |
| 135 | A | A | 0.0000 | |
| 136 | T | A | -1.8558 | |
| 137 | L | A | 0.0000 | |
| 138 | R | A | -1.3946 | |
| 139 | Q | A | -1.0620 | |
| 140 | L | A | 0.0000 | |
| 141 | L | A | 0.0000 | |
| 142 | S | A | 0.0000 | |
| 143 | H | A | 0.0000 | |
| 144 | T | A | 0.0000 | |
| 145 | A | A | 0.0000 | |
| 146 | G | A | -0.2938 | |
| 147 | L | A | 0.0000 | |
| 148 | P | A | 0.0000 | |
| 149 | S | A | 0.0000 | |
| 150 | D | A | -1.8638 | |
| 151 | H | A | -2.0797 | |
| 152 | D | A | -3.4185 | |
| 153 | D | A | -3.4944 | |
| 154 | E | A | -3.6811 | |
| 155 | R | A | -3.5295 | |
| 156 | A | A | 0.0000 | |
| 157 | P | A | -1.7980 | |
| 158 | S | A | -1.5735 | |
| 159 | L | A | 0.0000 | |
| 160 | R | A | -1.8655 | |
| 161 | R | A | -2.6216 | |
| 162 | W | A | 0.0000 | |
| 163 | L | A | 0.0000 | |
| 164 | T | A | -1.0072 | |
| 165 | G | A | -0.8223 | |
| 166 | F | A | 0.0000 | |
| 167 | L | A | 0.1050 | |
| 168 | A | A | 0.4769 | |
| 169 | L | A | 0.8077 | |
| 170 | P | A | 0.5645 | |
| 171 | V | A | 1.0570 | |
| 172 | G | A | -0.1503 | |
| 173 | P | A | -0.6159 | |
| 174 | W | A | 0.1585 | |
| 175 | P | A | 0.0000 | |
| 176 | A | A | -0.1649 | |
| 177 | P | A | -0.4819 | |
| 178 | G | A | -0.8324 | |
| 179 | S | A | -0.8666 | |
| 180 | F | A | 0.0000 | |
| 181 | S | A | 0.0000 | |
| 182 | Y | A | 0.0000 | |
| 183 | S | A | 0.0000 | |
| 184 | N | A | -0.8311 | |
| 185 | V | A | 0.0000 | |
| 186 | G | A | 0.0000 | |
| 187 | Y | A | 0.0000 | |
| 188 | G | A | 0.0000 | |
| 189 | I | A | 0.0000 | |
| 190 | A | A | 0.0000 | |
| 191 | G | A | 0.0000 | |
| 192 | R | A | -0.3476 | |
| 193 | V | A | 0.0000 | |
| 194 | V | A | 0.0000 | |
| 195 | E | A | -0.4259 | |
| 196 | A | A | -0.0609 | |
| 197 | V | A | -0.1332 | |
| 198 | T | A | -0.2962 | |
| 199 | G | A | -0.3418 | |
| 200 | L | A | -0.3938 | |
| 201 | T | A | -0.7767 | |
| 202 | W | A | 0.0000 | |
| 203 | S | A | -1.3752 | |
| 204 | E | A | -2.3769 | |
| 205 | A | A | 0.0000 | |
| 206 | V | A | 0.0000 | |
| 207 | R | A | -3.2696 | |
| 208 | D | A | -2.9679 | |
| 209 | F | A | -1.0943 | |
| 210 | L | A | 0.0000 | |
| 211 | L | A | 0.0000 | |
| 212 | H | A | -2.1085 | |
| 213 | P | A | -1.6753 | |
| 214 | L | A | 0.0000 | |
| 215 | G | A | -1.1548 | |
| 216 | T | A | -0.9040 | |
| 217 | A | A | -0.5053 | |
| 218 | I | A | 0.0000 | |
| 219 | T | A | 0.0208 | |
| 220 | V | A | 0.1692 | |
| 221 | L | A | 0.5270 | |
| 222 | P | A | 0.0164 | |
| 223 | T | A | -0.4330 | |
| 224 | D | A | -1.7251 | |
| 225 | P | A | -1.4739 | |
| 226 | G | A | 0.0000 | |
| 227 | S | A | -1.1036 | |
| 228 | L | A | 0.0000 | |
| 229 | P | A | 0.0000 | |
| 230 | A | A | 0.0000 | |
| 231 | G | A | -0.0538 | |
| 232 | G | A | 0.0000 | |
| 233 | L | A | 0.0000 | |
| 234 | A | A | 0.0000 | |
| 235 | G | A | 0.0000 | |
| 236 | S | A | 0.0000 | |
| 237 | A | A | 0.0000 | |
| 238 | A | A | 0.1202 | |
| 239 | D | A | -0.3465 | |
| 240 | L | A | 0.0000 | |
| 241 | V | A | 0.0000 | |
| 242 | R | A | -0.4888 | |
| 243 | L | A | 0.0000 | |
| 244 | G | A | 0.0000 | |
| 245 | R | A | -1.0816 | |
| 246 | L | A | 0.0000 | |
| 247 | H | A | 0.0000 | |
| 248 | L | A | 0.0000 | |
| 249 | D | A | -3.1587 | |
| 250 | E | A | -3.3353 | |
| 251 | P | A | -2.2553 | |
| 252 | G | A | -1.9741 | |
| 253 | D | A | -1.9037 | |
| 254 | P | A | -2.0321 | |
| 255 | D | A | -2.6374 | |
| 256 | L | A | 0.0000 | |
| 257 | A | A | -2.3072 | |
| 258 | R | A | -2.5498 | |
| 259 | L | A | -1.2447 | |
| 260 | A | A | 0.0000 | |
| 261 | D | A | -2.2573 | |
| 262 | P | A | -2.4301 | |
| 263 | D | A | -2.4290 | |
| 264 | A | A | 0.0000 | |
| 265 | L | A | 0.0000 | |
| 266 | R | A | -1.9371 | |
| 267 | E | A | -1.6722 | |
| 268 | M | A | 0.0000 | |
| 269 | A | A | -1.2643 | |
| 270 | R | A | -2.2052 | |
| 271 | P | A | -1.5887 | |
| 272 | T | A | -1.1112 | |
| 273 | A | A | -0.8034 | |
| 274 | G | A | -1.0695 | |
| 275 | A | A | 0.0000 | |
| 276 | D | A | -2.0196 | |
| 277 | P | A | 0.0000 | |
| 278 | F | A | -0.3157 | |
| 279 | G | A | 0.0000 | |
| 280 | L | A | -0.0756 | |
| 281 | A | A | 0.0000 | |
| 282 | D | A | -1.5326 | |
| 283 | G | A | 0.0000 | |
| 284 | W | A | 0.0000 | |
| 285 | G | A | 0.0000 | |
| 286 | P | A | 0.0000 | |
| 287 | G | A | 0.0000 | |
| 288 | L | A | 0.0000 | |
| 289 | G | A | 0.0000 | |
| 290 | R | A | -1.0227 | |
| 291 | F | A | 0.0000 | |
| 292 | G | A | 0.0000 | |
| 293 | P | A | -1.1243 | |
| 294 | A | A | -0.6946 | |
| 295 | G | A | -0.8410 | |
| 296 | N | A | -1.1763 | |
| 297 | R | A | -1.5436 | |
| 298 | W | A | 0.0000 | |
| 299 | L | A | 0.0000 | |
| 300 | G | A | 0.0000 | |
| 301 | H | A | 0.0000 | |
| 302 | D | A | -0.2175 | |
| 303 | G | A | 0.0000 | |
| 304 | T | A | 0.0009 | |
| 305 | L | A | 0.4705 | |
| 306 | D | A | -1.2561 | |
| 307 | G | A | -0.8030 | |
| 308 | A | A | -0.5163 | |
| 309 | T | A | 0.0000 | |
| 310 | C | A | 0.0000 | |
| 311 | H | A | 0.0000 | |
| 312 | L | A | 0.0000 | |
| 313 | R | A | 0.0000 | |
| 314 | I | A | 0.0000 | |
| 315 | H | A | -1.1920 | |
| 316 | P | A | -1.6564 | |
| 317 | G | A | -1.7969 | |
| 318 | R | A | -1.9999 | |
| 319 | G | A | -1.9831 | |
| 320 | T | A | 0.0000 | |
| 321 | V | A | 0.0000 | |
| 322 | V | A | 0.0000 | |
| 323 | A | A | 0.0000 | |
| 324 | L | A | 0.0000 | |
| 325 | T | A | 0.0000 | |
| 326 | T | A | 0.0000 | |
| 327 | N | A | -1.0113 | |
| 328 | S | A | 0.0000 | |
| 329 | P | A | -0.6918 | |
| 330 | T | A | -0.6890 | |
| 331 | G | A | 0.0000 | |
| 332 | Q | A | -0.6499 | |
| 333 | A | A | -0.8107 | |
| 334 | L | A | 0.0000 | |
| 335 | W | A | 0.0000 | |
| 336 | D | A | -1.1229 | |
| 337 | A | A | -1.2847 | |
| 338 | V | A | 0.0000 | |
| 339 | V | A | -1.8727 | |
| 340 | D | A | -3.1448 | |
| 341 | A | A | -2.6018 | |
| 342 | L | A | 0.0000 | |
| 343 | R | A | -4.4190 | |
| 344 | D | A | -3.8465 | |
| 345 | A | A | -2.9414 | |
| 346 | D | A | -3.9610 | |
| 347 | I | A | 0.0000 | |
| 348 | D | A | -3.2225 | |
| 349 | V | A | 0.0000 | |
| 350 | G | A | 0.0000 | |
| 351 | V | A | -0.9140 | |
| 352 | H | A | -1.0574 | |
| 353 | R | A | -1.8433 | |
| 354 | P | A | -0.9412 | |
| 355 | A | A | -0.5846 | |
| 356 | P | A | -0.4994 | |
| 357 | P | A | -0.4328 | |
| 358 | P | A | -0.2395 | |
| 359 | A | A | 0.1008 | |
| 360 | I | A | 0.5128 | |
| 361 | A | A | 0.3743 | |
| 362 | A | A | 0.0000 | |
| 363 | A | A | 0.1027 | |
| 364 | A | A | -0.1947 | |
| 365 | F | A | 0.0000 | |
| 366 | A | A | -0.4436 | |
| 367 | D | A | -1.2633 | |
| 368 | C | A | 0.0000 | |
| 369 | T | A | -0.4261 | |
| 370 | G | A | -0.8653 | |
| 371 | T | A | -1.1114 | |
| 372 | Y | A | 0.0000 | |
| 373 | R | A | -1.4817 | |
| 374 | N | A | 0.0000 | |
| 375 | G | A | -1.0296 | |
| 376 | D | A | -2.2244 | |
| 377 | L | A | -0.9372 | |
| 378 | A | A | -1.0044 | |
| 379 | V | A | 0.0000 | |
| 380 | T | A | -1.0513 | |
| 381 | V | A | 0.0000 | |
| 382 | G | A | -0.3798 | |
| 383 | I | A | -0.2410 | |
| 384 | D | A | -1.6094 | |
| 385 | G | A | -1.1716 | |
| 386 | P | A | -0.5991 | |
| 387 | Y | A | -0.5626 | |
| 388 | L | A | 0.0000 | |
| 389 | V | A | 0.0000 | |
| 390 | L | A | 0.0000 | |
| 391 | E | A | -2.0471 | |
| 392 | L | A | -1.2417 | |
| 393 | P | A | -1.1115 | |
| 394 | G | A | -1.0392 | |
| 395 | G | A | -1.3491 | |
| 396 | A | A | -1.6064 | |
| 397 | R | A | -2.5736 | |
| 398 | E | A | -1.7823 | |
| 399 | L | A | -1.1796 | |
| 400 | A | A | 0.0000 | |
| 401 | Q | A | -0.6638 | |
| 402 | P | A | 0.0000 | |
| 403 | L | A | 0.0000 | |
| 404 | A | A | -0.5248 | |
| 405 | H | A | -1.2168 | |
| 406 | R | A | -0.9587 | |
| 407 | T | A | 0.0000 | |
| 408 | F | A | 0.0000 | |
| 409 | S | A | -0.3070 | |
| 410 | S | A | 0.0000 | |
| 411 | R | A | -1.8606 | |
| 412 | G | A | -1.1470 | |
| 413 | A | A | -0.3502 | |
| 414 | G | A | -0.4193 | |
| 415 | F | A | 0.9267 | |
| 416 | L | A | 0.0000 | |
| 417 | G | A | 0.0000 | |
| 418 | R | A | -0.7043 | |
| 419 | F | A | 0.0000 | |
| 420 | V | A | -0.6379 | |
| 421 | T | A | -1.4877 | |
| 422 | D | A | -2.3839 | |
| 423 | A | A | -1.3266 | |
| 426 | D | A | -2.3822 | |
| 427 | A | A | -1.5558 | |
| 428 | V | A | 0.0000 | |
| 429 | H | A | -1.4540 | |
| 430 | A | A | 0.0000 | |
| 431 | L | A | 0.0000 | |
| 432 | Q | A | 0.0000 | |
| 433 | Y | A | 0.0882 | |
| 434 | S | A | 0.1162 | |
| 435 | G | A | 0.0000 | |
| 436 | R | A | -0.3489 | |
| 437 | T | A | -0.3004 | |
| 438 | L | A | 0.0000 | |
| 439 | L | A | -0.8525 | |
| 440 | R | A | -1.8006 | |
| 441 | E | A | -2.3619 |
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 | -0.2007 | 2.9823 | View | CSV | PDB |
| 4.5 | -0.2766 | 2.9823 | View | CSV | PDB |
| 5.0 | -0.3708 | 2.9823 | View | CSV | PDB |
| 5.5 | -0.4716 | 2.9823 | View | CSV | PDB |
| 6.0 | -0.5703 | 2.9823 | View | CSV | PDB |
| 6.5 | -0.6625 | 2.9823 | View | CSV | PDB |
| 7.0 | -0.748 | 2.9823 | View | CSV | PDB |
| 7.5 | -0.828 | 2.9823 | View | CSV | PDB |
| 8.0 | -0.9031 | 2.9823 | View | CSV | PDB |
| 8.5 | -0.9701 | 2.9823 | View | CSV | PDB |
| 9.0 | -1.0227 | 2.9823 | 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