| Chain sequence(s) |
A: STVPELLARQVTRAPDAVAVVDRDRVLTYRELDELAGRLSGRLIGRGVRRGDRVAVLLDRSADLVVTLLAIWKAGAAYVPVDAGYPAPRVAFMVADSGASRMVCSAATRDGVPEGIEAIVVTDAFEASAAGARPGDLAYVMYTSGSTGIPKGVAVPHRSVAELAGNPGWAVEPGDAVLMHAPYAFDASLFEIWVPLVSGGRVVIAEPGPVDARRLREAISSGVTRAHLTAGSFRAVAEESPESFAGLREVLTGGDVVPAHAVARVRSACPRVRIRHLYGPTETTLCATWHLLEPGDEIGPVLPIGRPLPGRRAQVLDASLRAVAPGVIGDLYLSGAGLADGYLRRAGLTAERFVADPSAPGARMYRTGDLAQWTADGALLFAGRADDQGSHH
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 (00:00:03)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:05:49)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/82ad4657857e151/tmp/folded.pdb (00:05:49)
[INFO] Main: Simulation completed successfully. (00:10:29)
|
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 |
|---|---|---|---|---|
| 9 | S | A | -1.9014 | |
| 10 | T | A | 0.0000 | |
| 11 | V | A | 0.0000 | |
| 12 | P | A | 0.0000 | |
| 13 | E | A | -2.4106 | |
| 14 | L | A | -1.3411 | |
| 15 | L | A | 0.0000 | |
| 16 | A | A | -1.9141 | |
| 17 | R | A | -2.4784 | |
| 18 | Q | A | -2.0049 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -2.0173 | |
| 21 | R | A | -2.5751 | |
| 22 | A | A | -1.9796 | |
| 23 | P | A | -2.4834 | |
| 24 | D | A | -2.5768 | |
| 25 | A | A | -1.5171 | |
| 26 | V | A | -0.4005 | |
| 27 | A | A | 0.0000 | |
| 28 | V | A | 0.0000 | |
| 29 | V | A | -0.6188 | |
| 30 | D | A | 0.0000 | |
| 31 | R | A | -3.3365 | |
| 32 | D | A | -3.2347 | |
| 33 | R | A | -2.6644 | |
| 34 | V | A | -0.5575 | |
| 35 | L | A | 0.0000 | |
| 36 | T | A | -1.3793 | |
| 37 | Y | A | 0.0000 | |
| 38 | R | A | -3.1226 | |
| 39 | E | A | -2.5096 | |
| 40 | L | A | 0.0000 | |
| 41 | D | A | -2.2131 | |
| 42 | E | A | -2.6147 | |
| 43 | L | A | -1.6422 | |
| 44 | A | A | 0.0000 | |
| 45 | G | A | -1.9101 | |
| 46 | R | A | -2.4349 | |
| 47 | L | A | 0.0000 | |
| 48 | S | A | 0.0000 | |
| 49 | G | A | 0.0000 | |
| 50 | R | A | -1.1208 | |
| 51 | L | A | 0.0000 | |
| 52 | I | A | -1.1889 | |
| 53 | G | A | -1.2897 | |
| 54 | R | A | -1.8224 | |
| 55 | G | A | -1.5434 | |
| 56 | V | A | 0.0000 | |
| 57 | R | A | -2.6215 | |
| 58 | R | A | -2.1425 | |
| 59 | G | A | -1.5812 | |
| 60 | D | A | -1.8576 | |
| 61 | R | A | -1.2710 | |
| 62 | V | A | 0.0000 | |
| 63 | A | A | 0.0000 | |
| 64 | V | A | 0.0000 | |
| 65 | L | A | 0.0000 | |
| 66 | L | A | 0.0000 | |
| 67 | D | A | -2.2965 | |
| 68 | R | A | -1.7793 | |
| 69 | S | A | -1.6902 | |
| 70 | A | A | 0.0000 | |
| 71 | D | A | -1.2681 | |
| 72 | L | A | 0.0000 | |
| 73 | V | A | 0.0000 | |
| 74 | V | A | 0.0000 | |
| 75 | T | A | 0.0000 | |
| 76 | L | A | 0.0000 | |
| 77 | L | A | 0.0000 | |
| 78 | A | A | 0.0000 | |
| 79 | I | A | 0.0000 | |
| 80 | W | A | 0.0000 | |
| 81 | K | A | -0.8832 | |
| 82 | A | A | 0.0000 | |
| 83 | G | A | 0.0000 | |
| 84 | A | A | 0.0000 | |
| 85 | A | A | 0.0000 | |
| 86 | Y | A | 0.0000 | |
| 87 | V | A | 0.0000 | |
| 88 | P | A | 0.0000 | |
| 89 | V | A | 0.0000 | |
| 90 | D | A | -0.9537 | |
| 91 | A | A | -1.1233 | |
| 92 | G | A | -0.8452 | |
| 93 | Y | A | -0.5363 | |
| 94 | P | A | -0.6252 | |
| 95 | A | A | -0.3551 | |
| 96 | P | A | -0.4346 | |
| 97 | R | A | -0.6698 | |
| 98 | V | A | 0.0000 | |
| 99 | A | A | -0.2200 | |
| 100 | F | A | 0.2717 | |
| 101 | M | A | 0.0000 | |
| 102 | V | A | 0.0000 | |
| 103 | A | A | 0.1191 | |
| 104 | D | A | -0.3040 | |
| 105 | S | A | 0.0000 | |
| 106 | G | A | -0.6707 | |
| 107 | A | A | 0.0000 | |
| 108 | S | A | -0.6703 | |
| 109 | R | A | -0.8812 | |
| 110 | M | A | 0.0000 | |
| 111 | V | A | 0.0000 | |
| 112 | C | A | 0.0000 | |
| 113 | S | A | -1.4038 | |
| 114 | A | A | -1.0985 | |
| 115 | A | A | -1.0814 | |
| 116 | T | A | -1.8062 | |
| 117 | R | A | -2.7008 | |
| 118 | D | A | -2.9575 | |
| 119 | G | A | -1.9268 | |
| 120 | V | A | -1.5214 | |
| 121 | P | A | -1.4860 | |
| 122 | E | A | -2.2051 | |
| 123 | G | A | -1.3483 | |
| 124 | I | A | -0.7779 | |
| 125 | E | A | -0.9412 | |
| 126 | A | A | -1.0053 | |
| 127 | I | A | 0.0000 | |
| 128 | V | A | 0.0000 | |
| 129 | V | A | -0.7871 | |
| 130 | T | A | -0.9893 | |
| 131 | D | A | -1.7508 | |
| 134 | A | A | -0.3361 | |
| 135 | F | A | -0.3317 | |
| 136 | E | A | -1.8112 | |
| 137 | A | A | -1.6796 | |
| 138 | S | A | -1.0618 | |
| 139 | A | A | -0.5649 | |
| 140 | A | A | -0.6854 | |
| 141 | G | A | -0.9987 | |
| 142 | A | A | -1.7774 | |
| 143 | R | A | -2.8223 | |
| 144 | P | A | -2.3071 | |
| 145 | G | A | -1.8619 | |
| 146 | D | A | -1.6955 | |
| 147 | L | A | -1.1206 | |
| 148 | A | A | 0.0000 | |
| 149 | Y | A | 0.0000 | |
| 150 | V | A | 0.0000 | |
| 151 | M | A | 0.0000 | |
| 152 | Y | A | 0.0000 | |
| 153 | T | A | 0.2347 | |
| 154 | S | A | 0.1432 | |
| 155 | G | A | -0.4289 | |
| 156 | S | A | -1.0130 | |
| 157 | T | A | -0.1124 | |
| 158 | G | A | 0.2783 | |
| 159 | I | A | 1.6011 | |
| 160 | P | A | 0.6264 | |
| 161 | K | A | 0.0000 | |
| 162 | G | A | 0.0000 | |
| 163 | V | A | 0.0000 | |
| 164 | A | A | 0.0000 | |
| 165 | V | A | 0.0000 | |
| 166 | P | A | 0.0000 | |
| 167 | H | A | 0.0000 | |
| 168 | R | A | -2.6730 | |
| 169 | S | A | 0.0000 | |
| 170 | V | A | 0.0000 | |
| 171 | A | A | 0.0000 | |
| 172 | E | A | -1.8644 | |
| 173 | L | A | 0.0000 | |
| 174 | A | A | 0.0000 | |
| 175 | G | A | -0.7858 | |
| 176 | N | A | -0.8377 | |
| 177 | P | A | -0.5771 | |
| 178 | G | A | -0.3115 | |
| 179 | W | A | 0.0000 | |
| 180 | A | A | -0.4843 | |
| 181 | V | A | -1.0896 | |
| 182 | E | A | -2.0296 | |
| 183 | P | A | -1.3294 | |
| 184 | G | A | -1.2170 | |
| 185 | D | A | 0.0000 | |
| 186 | A | A | 0.0000 | |
| 187 | V | A | 0.0000 | |
| 188 | L | A | 0.0000 | |
| 189 | M | A | 0.0000 | |
| 190 | H | A | -0.5499 | |
| 191 | A | A | 0.1137 | |
| 192 | P | A | -0.1072 | |
| 193 | Y | A | 0.0000 | |
| 194 | A | A | 0.0000 | |
| 195 | F | A | 1.3107 | |
| 196 | D | A | 0.5341 | |
| 197 | A | A | 0.2557 | |
| 198 | S | A | 0.0000 | |
| 199 | L | A | 0.0000 | |
| 200 | F | A | 0.0000 | |
| 201 | E | A | 0.0000 | |
| 202 | I | A | 0.0000 | |
| 203 | W | A | 0.0000 | |
| 204 | V | A | 0.0000 | |
| 205 | P | A | 0.0000 | |
| 206 | L | A | 0.0000 | |
| 207 | V | A | 0.0000 | |
| 208 | S | A | -1.0037 | |
| 209 | G | A | 0.0000 | |
| 210 | G | A | 0.0000 | |
| 211 | R | A | -0.7505 | |
| 212 | V | A | 0.0000 | |
| 213 | V | A | -0.2534 | |
| 214 | I | A | 0.0000 | |
| 215 | A | A | 0.0000 | |
| 216 | E | A | -2.4944 | |
| 217 | P | A | -1.6283 | |
| 218 | G | A | -1.1936 | |
| 219 | P | A | -1.1541 | |
| 220 | V | A | -1.7212 | |
| 221 | D | A | -2.5185 | |
| 222 | A | A | -2.8753 | |
| 223 | R | A | -3.4422 | |
| 224 | R | A | -3.2865 | |
| 225 | L | A | 0.0000 | |
| 226 | R | A | -3.3816 | |
| 227 | E | A | -3.1736 | |
| 228 | A | A | -1.9238 | |
| 229 | I | A | -1.5427 | |
| 230 | S | A | -1.4034 | |
| 231 | S | A | -1.0165 | |
| 232 | G | A | -0.7569 | |
| 233 | V | A | 0.0000 | |
| 234 | T | A | -0.6059 | |
| 235 | R | A | 0.0000 | |
| 236 | A | A | 0.0000 | |
| 237 | H | A | 0.0000 | |
| 238 | L | A | 0.0000 | |
| 239 | T | A | -0.6652 | |
| 240 | A | A | 0.0000 | |
| 241 | G | A | -1.0019 | |
| 242 | S | A | -0.8706 | |
| 243 | F | A | 0.0000 | |
| 244 | R | A | -1.5257 | |
| 245 | A | A | -1.4851 | |
| 246 | V | A | 0.0000 | |
| 247 | A | A | 0.0000 | |
| 248 | E | A | -2.2990 | |
| 249 | E | A | -2.6039 | |
| 250 | S | A | -2.0640 | |
| 251 | P | A | 0.0000 | |
| 252 | E | A | -2.4222 | |
| 253 | S | A | 0.0000 | |
| 254 | F | A | 0.0000 | |
| 255 | A | A | -1.4342 | |
| 256 | G | A | -1.4154 | |
| 257 | L | A | 0.0000 | |
| 258 | R | A | -1.6897 | |
| 259 | E | A | 0.0000 | |
| 260 | V | A | 0.0000 | |
| 261 | L | A | 0.0000 | |
| 262 | T | A | 0.0000 | |
| 263 | G | A | -0.5114 | |
| 264 | G | A | -1.0855 | |
| 265 | D | A | -1.3610 | |
| 266 | V | A | 0.4632 | |
| 267 | V | A | 0.0000 | |
| 268 | P | A | -0.1865 | |
| 269 | A | A | -0.3989 | |
| 270 | H | A | -1.2566 | |
| 271 | A | A | 0.0000 | |
| 272 | V | A | 0.0000 | |
| 273 | A | A | -1.3770 | |
| 274 | R | A | -1.7743 | |
| 275 | V | A | 0.0000 | |
| 276 | R | A | 0.0000 | |
| 277 | S | A | -1.4263 | |
| 278 | A | A | -1.1252 | |
| 279 | C | A | 0.0000 | |
| 280 | P | A | -2.2112 | |
| 281 | R | A | -3.0893 | |
| 282 | V | A | 0.0000 | |
| 283 | R | A | -2.1774 | |
| 284 | I | A | 0.0000 | |
| 285 | R | A | 0.0000 | |
| 286 | H | A | 0.0000 | |
| 287 | L | A | 0.0000 | |
| 288 | Y | A | -0.2342 | |
| 289 | G | A | -0.2002 | |
| 290 | P | A | -0.3456 | |
| 291 | T | A | 0.0960 | |
| 292 | E | A | 0.0000 | |
| 293 | T | A | 0.0000 | |
| 294 | T | A | 0.0000 | |
| 295 | L | A | 0.0000 | |
| 296 | C | A | 0.0000 | |
| 297 | A | A | 0.0000 | |
| 298 | T | A | 0.0000 | |
| 299 | W | A | -0.2757 | |
| 300 | H | A | -0.3147 | |
| 301 | L | A | -0.2987 | |
| 302 | L | A | 0.0000 | |
| 303 | E | A | -3.1500 | |
| 304 | P | A | -3.0784 | |
| 305 | G | A | -2.9174 | |
| 306 | D | A | -3.7225 | |
| 307 | E | A | -3.1603 | |
| 308 | I | A | -1.3272 | |
| 309 | G | A | -0.7077 | |
| 310 | P | A | -0.1346 | |
| 311 | V | A | 0.9269 | |
| 312 | L | A | 0.0000 | |
| 313 | P | A | 0.3118 | |
| 314 | I | A | 0.0000 | |
| 315 | G | A | 0.0000 | |
| 316 | R | A | -1.5555 | |
| 317 | P | A | -1.2834 | |
| 318 | L | A | 0.0000 | |
| 319 | P | A | -1.0299 | |
| 320 | G | A | -1.0817 | |
| 321 | R | A | 0.0000 | |
| 322 | R | A | -1.5300 | |
| 323 | A | A | -0.9013 | |
| 324 | Q | A | -0.7943 | |
| 325 | V | A | 0.0000 | |
| 326 | L | A | 0.0000 | |
| 327 | D | A | -0.5065 | |
| 328 | A | A | -0.3551 | |
| 329 | S | A | -0.2222 | |
| 330 | L | A | 0.1744 | |
| 331 | R | A | -1.3392 | |
| 332 | A | A | -0.6088 | |
| 333 | V | A | 0.1753 | |
| 334 | A | A | 0.2358 | |
| 335 | P | A | -0.0209 | |
| 336 | G | A | 0.4451 | |
| 337 | V | A | 1.6087 | |
| 338 | I | A | 2.0035 | |
| 339 | G | A | 0.0000 | |
| 340 | D | A | -0.7313 | |
| 341 | L | A | 0.0000 | |
| 342 | Y | A | 0.0000 | |
| 343 | L | A | 0.0000 | |
| 344 | S | A | 0.0000 | |
| 345 | G | A | -0.9803 | |
| 346 | A | A | -1.0169 | |
| 347 | G | A | 0.0000 | |
| 348 | L | A | -0.7920 | |
| 349 | A | A | 0.0000 | |
| 350 | D | A | -1.7612 | |
| 351 | G | A | 0.0000 | |
| 352 | Y | A | 0.0000 | |
| 353 | L | A | -1.0757 | |
| 354 | R | A | -1.9971 | |
| 355 | R | A | -1.2435 | |
| 356 | A | A | -1.0942 | |
| 357 | G | A | -1.0614 | |
| 358 | L | A | -0.8076 | |
| 359 | T | A | -1.0833 | |
| 360 | A | A | -0.9005 | |
| 361 | E | A | -1.7768 | |
| 362 | R | A | -1.3734 | |
| 363 | F | A | 0.0000 | |
| 364 | V | A | -0.5462 | |
| 365 | A | A | -0.4460 | |
| 366 | D | A | 0.0000 | |
| 367 | P | A | -0.4817 | |
| 368 | S | A | -0.4812 | |
| 369 | A | A | -0.5300 | |
| 370 | P | A | -0.6349 | |
| 371 | G | A | -0.7521 | |
| 372 | A | A | -0.6555 | |
| 373 | R | A | -0.8256 | |
| 374 | M | A | 0.0000 | |
| 375 | Y | A | 0.0000 | |
| 376 | R | A | -1.4189 | |
| 377 | T | A | -0.9482 | |
| 378 | G | A | -1.5043 | |
| 379 | D | A | -1.5055 | |
| 380 | L | A | -0.3116 | |
| 381 | A | A | 0.0000 | |
| 382 | Q | A | 0.8837 | |
| 383 | W | A | 0.0088 | |
| 384 | T | A | -0.5667 | |
| 385 | A | A | -0.9978 | |
| 386 | D | A | -1.8461 | |
| 387 | G | A | -1.3112 | |
| 388 | A | A | -1.0309 | |
| 389 | L | A | 0.0000 | |
| 390 | L | A | 0.6780 | |
| 391 | F | A | 1.0510 | |
| 392 | A | A | 0.1022 | |
| 393 | G | A | -1.2929 | |
| 394 | R | A | -2.7930 | |
| 395 | A | A | -2.4101 | |
| 396 | D | A | -3.3705 | |
| 397 | D | A | -3.6949 | |
| 398 | Q | A | -2.9127 | |
| 399 | G | A | -2.3151 | |
| 400 | S | A | -2.1823 | |
| 401 | H | A | -2.2112 | |
| 402 | H | A | -1.6897 |
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 | -0.4424 | 3.5903 | View | CSV | PDB |
| 4.5 | -0.507 | 3.5493 | View | CSV | PDB |
| 5.0 | -0.5875 | 3.5219 | View | CSV | PDB |
| 5.5 | -0.6738 | 3.4898 | View | CSV | PDB |
| 6.0 | -0.7569 | 3.4533 | View | CSV | PDB |
| 6.5 | -0.8302 | 3.4146 | View | CSV | PDB |
| 7.0 | -0.8909 | 3.3752 | View | CSV | PDB |
| 7.5 | -0.9416 | 3.3364 | View | CSV | PDB |
| 8.0 | -0.9853 | 3.3002 | View | CSV | PDB |
| 8.5 | -1.0218 | 3.2693 | View | CSV | PDB |
| 9.0 | -1.048 | 3.2449 | 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