| Chain sequence(s) |
A: GRSDAYTQVDNFLHAYARGGDELVNGHPSYTVDQAAEQILREQASWQKAPGDSVLTLSYSFLTKPNDFFNTPWKYVSDIYSLGKFSAFSAQQQAQAKLSLQSWSDVTNIHFVDAGQGDQGDLTFGNFSSSVGGAAFAFLPDVPDALKGQSWYLINSSYSANVNPANGNYGRQTLTHEIGHTLGLSHPGDYNAGEGDPTYADATYAEDTRAYSVMSYWEEQNTGQDFKGAYSSAPLLDDIAAIQKLYGANLTTRTGDTVYGFNSNTERDFYSATSSSSKLVFSVWDAGGNDTLDFSGFSQNQKINLNEKALSDVGGLKGNVSIAAGVTVENAIGGSGSDLLIGNDVANVLKGGAGNDILYGGLGADQLWGGAGADTFVYGDIAESSAAAPDTLRDFVSGQDKIDLSGLDAFVNGGLVLQYVDAFAGKAGQAILSYDAASKAGSLAIDFSGDAHADFAINLIGQATQADIVV
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 (00:05:09)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/90c6ccb77fe0e7c/tmp/folded.pdb (00:05:09)
[INFO] Main: Simulation completed successfully. (00:12:21)
|
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 | G | A | -1.0442 | |
| 2 | R | A | -2.0627 | |
| 3 | S | A | -1.7513 | |
| 4 | D | A | -2.4364 | |
| 5 | A | A | -1.3010 | |
| 6 | Y | A | -1.1716 | |
| 7 | T | A | -1.6873 | |
| 8 | Q | A | -1.5697 | |
| 9 | V | A | 0.0000 | |
| 10 | D | A | -1.5505 | |
| 11 | N | A | -1.8091 | |
| 12 | F | A | 0.0000 | |
| 13 | L | A | -0.5783 | |
| 14 | H | A | -1.1770 | |
| 15 | A | A | -0.5890 | |
| 16 | Y | A | -0.1540 | |
| 17 | A | A | -0.3699 | |
| 18 | R | A | -0.8306 | |
| 19 | G | A | -1.1387 | |
| 20 | G | A | -1.8027 | |
| 21 | D | A | -2.4833 | |
| 22 | E | A | -2.0542 | |
| 23 | L | A | 0.1664 | |
| 24 | V | A | 0.1796 | |
| 25 | N | A | -0.2754 | |
| 26 | G | A | -0.3957 | |
| 27 | H | A | -0.0980 | |
| 28 | P | A | -0.4131 | |
| 29 | S | A | 0.0000 | |
| 30 | Y | A | -0.3610 | |
| 31 | T | A | -0.5589 | |
| 32 | V | A | -0.8776 | |
| 33 | D | A | -2.4430 | |
| 34 | Q | A | -1.8847 | |
| 35 | A | A | -1.2441 | |
| 36 | A | A | 0.0000 | |
| 37 | E | A | -3.1395 | |
| 38 | Q | A | -1.7200 | |
| 39 | I | A | 0.0000 | |
| 40 | L | A | -1.9564 | |
| 41 | R | A | -2.3349 | |
| 42 | E | A | -3.0246 | |
| 43 | Q | A | -2.6315 | |
| 44 | A | A | 0.0000 | |
| 45 | S | A | -1.1736 | |
| 46 | W | A | -0.8544 | |
| 47 | Q | A | -1.4994 | |
| 48 | K | A | -1.8593 | |
| 49 | A | A | -1.3592 | |
| 50 | P | A | -1.4004 | |
| 51 | G | A | -1.5951 | |
| 52 | D | A | -2.2122 | |
| 53 | S | A | -1.1194 | |
| 54 | V | A | -0.7557 | |
| 55 | L | A | -0.7342 | |
| 56 | T | A | -0.5254 | |
| 57 | L | A | 0.0000 | |
| 58 | S | A | -0.9162 | |
| 59 | Y | A | 0.0000 | |
| 60 | S | A | 0.0000 | |
| 61 | F | A | 0.0000 | |
| 62 | L | A | 0.0000 | |
| 63 | T | A | -1.5365 | |
| 64 | K | A | -2.1895 | |
| 65 | P | A | -2.1084 | |
| 66 | N | A | -2.0797 | |
| 67 | D | A | -2.4375 | |
| 68 | F | A | 0.0000 | |
| 69 | F | A | 0.0000 | |
| 70 | N | A | -2.1930 | |
| 71 | T | A | -0.9654 | |
| 72 | P | A | 0.0000 | |
| 73 | W | A | 0.2738 | |
| 74 | K | A | -1.3601 | |
| 75 | Y | A | -0.7671 | |
| 76 | V | A | -0.1672 | |
| 77 | S | A | -0.6281 | |
| 78 | D | A | -1.4292 | |
| 79 | I | A | 0.0000 | |
| 80 | Y | A | 0.9902 | |
| 81 | S | A | -0.0410 | |
| 82 | L | A | 0.0000 | |
| 83 | G | A | -1.3298 | |
| 84 | K | A | -2.0999 | |
| 85 | F | A | -1.3017 | |
| 86 | S | A | -0.7961 | |
| 87 | A | A | -0.5251 | |
| 88 | F | A | 0.0000 | |
| 89 | S | A | -0.5984 | |
| 90 | A | A | -0.8680 | |
| 91 | Q | A | -1.6521 | |
| 92 | Q | A | 0.0000 | |
| 93 | Q | A | -1.1516 | |
| 94 | A | A | -0.8167 | |
| 95 | Q | A | -1.1545 | |
| 96 | A | A | 0.0000 | |
| 97 | K | A | -1.1022 | |
| 98 | L | A | -0.4957 | |
| 99 | S | A | 0.0000 | |
| 100 | L | A | 0.0000 | |
| 101 | Q | A | -0.6102 | |
| 102 | S | A | 0.0000 | |
| 103 | W | A | 0.0000 | |
| 104 | S | A | -0.5527 | |
| 105 | D | A | 0.0000 | |
| 106 | V | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | N | A | -0.5784 | |
| 109 | I | A | 0.0000 | |
| 110 | H | A | -0.7031 | |
| 111 | F | A | -0.2874 | |
| 112 | V | A | -0.1796 | |
| 113 | D | A | -1.4707 | |
| 114 | A | A | -1.6115 | |
| 115 | G | A | -1.6085 | |
| 116 | Q | A | -2.3482 | |
| 117 | G | A | -2.3041 | |
| 118 | D | A | -3.2750 | |
| 119 | Q | A | -2.7425 | |
| 120 | G | A | 0.0000 | |
| 121 | D | A | -2.4302 | |
| 122 | L | A | 0.0000 | |
| 123 | T | A | 0.0000 | |
| 124 | F | A | 0.0000 | |
| 125 | G | A | 0.0000 | |
| 126 | N | A | 0.0000 | |
| 127 | F | A | 0.0000 | |
| 128 | S | A | -0.7899 | |
| 129 | S | A | -0.5696 | |
| 130 | S | A | -0.2699 | |
| 131 | V | A | -0.0935 | |
| 132 | G | A | -0.5462 | |
| 133 | G | A | -0.1536 | |
| 134 | A | A | 0.0211 | |
| 135 | A | A | 0.1024 | |
| 136 | F | A | 0.2378 | |
| 137 | A | A | 0.2317 | |
| 138 | F | A | 0.1240 | |
| 139 | L | A | -0.5537 | |
| 140 | P | A | 0.0000 | |
| 141 | D | A | -2.3829 | |
| 142 | V | A | -1.1895 | |
| 143 | P | A | -1.4733 | |
| 144 | D | A | -2.3947 | |
| 145 | A | A | -1.4013 | |
| 146 | L | A | 0.0000 | |
| 147 | K | A | -2.0611 | |
| 148 | G | A | 0.0000 | |
| 149 | Q | A | 0.0000 | |
| 150 | S | A | 0.0000 | |
| 151 | W | A | 0.0000 | |
| 152 | Y | A | 0.0000 | |
| 153 | L | A | 0.0000 | |
| 154 | I | A | 0.3124 | |
| 155 | N | A | -0.5264 | |
| 156 | S | A | -0.3802 | |
| 157 | S | A | -0.2733 | |
| 158 | Y | A | 0.1347 | |
| 159 | S | A | -0.0546 | |
| 160 | A | A | 0.1642 | |
| 161 | N | A | 0.0000 | |
| 162 | V | A | 0.0899 | |
| 163 | N | A | -1.3318 | |
| 164 | P | A | 0.0000 | |
| 165 | A | A | -1.0112 | |
| 166 | N | A | -1.5408 | |
| 167 | G | A | -0.8867 | |
| 168 | N | A | -0.4601 | |
| 169 | Y | A | 0.6905 | |
| 170 | G | A | 0.0000 | |
| 171 | R | A | 0.0000 | |
| 172 | Q | A | 0.0000 | |
| 173 | T | A | 0.0000 | |
| 174 | L | A | 0.0000 | |
| 175 | T | A | 0.0000 | |
| 176 | H | A | 0.0000 | |
| 177 | E | A | 0.0000 | |
| 178 | I | A | 0.0000 | |
| 179 | G | A | 0.0000 | |
| 180 | H | A | 0.0000 | |
| 181 | T | A | 0.0000 | |
| 182 | L | A | 0.0000 | |
| 183 | G | A | 0.0000 | |
| 184 | L | A | 0.0000 | |
| 185 | S | A | 0.0000 | |
| 186 | H | A | -0.3343 | |
| 187 | P | A | 0.0000 | |
| 188 | G | A | -0.8213 | |
| 189 | D | A | -2.0988 | |
| 190 | Y | A | -1.1729 | |
| 191 | N | A | -1.7238 | |
| 192 | A | A | -2.1209 | |
| 193 | G | A | -2.3646 | |
| 194 | E | A | -2.7031 | |
| 195 | G | A | -2.3895 | |
| 196 | D | A | -2.6209 | |
| 197 | P | A | -1.8107 | |
| 198 | T | A | -0.7935 | |
| 199 | Y | A | -0.1957 | |
| 200 | A | A | -0.5210 | |
| 201 | D | A | -1.3119 | |
| 202 | A | A | -0.6433 | |
| 203 | T | A | -0.4615 | |
| 204 | Y | A | 0.0000 | |
| 205 | A | A | 0.0000 | |
| 206 | E | A | 0.0000 | |
| 207 | D | A | 0.0000 | |
| 208 | T | A | 0.0000 | |
| 209 | R | A | -0.3441 | |
| 210 | A | A | 0.0000 | |
| 211 | Y | A | 0.0000 | |
| 212 | S | A | 0.0000 | |
| 213 | V | A | 0.0000 | |
| 214 | M | A | 0.0000 | |
| 215 | S | A | 0.0000 | |
| 216 | Y | A | 1.0626 | |
| 217 | W | A | -0.0325 | |
| 218 | E | A | -1.3102 | |
| 219 | E | A | 0.0000 | |
| 220 | Q | A | -1.9848 | |
| 221 | N | A | -1.5307 | |
| 222 | T | A | -0.9039 | |
| 223 | G | A | -1.1754 | |
| 224 | Q | A | 0.0000 | |
| 225 | D | A | -2.2321 | |
| 226 | F | A | 0.0000 | |
| 227 | K | A | -2.4733 | |
| 228 | G | A | -1.5654 | |
| 229 | A | A | 0.0000 | |
| 230 | Y | A | -0.3270 | |
| 231 | S | A | 0.0000 | |
| 232 | S | A | 0.0000 | |
| 233 | A | A | 0.0000 | |
| 234 | P | A | 0.0000 | |
| 235 | L | A | 0.0000 | |
| 236 | L | A | 0.0000 | |
| 237 | D | A | -0.3634 | |
| 238 | D | A | 0.0000 | |
| 239 | I | A | 0.0000 | |
| 240 | A | A | -0.8422 | |
| 241 | A | A | 0.0000 | |
| 242 | I | A | 0.0000 | |
| 243 | Q | A | -1.7204 | |
| 244 | K | A | -2.0291 | |
| 245 | L | A | -0.8553 | |
| 246 | Y | A | -0.4730 | |
| 247 | G | A | -0.7225 | |
| 248 | A | A | -0.3355 | |
| 249 | N | A | 0.1615 | |
| 250 | L | A | 1.2477 | |
| 251 | T | A | 0.3879 | |
| 252 | T | A | 0.0000 | |
| 253 | R | A | -0.6989 | |
| 254 | T | A | -0.8559 | |
| 255 | G | A | -1.7743 | |
| 256 | D | A | -2.7977 | |
| 257 | T | A | 0.0000 | |
| 258 | V | A | -0.9317 | |
| 259 | Y | A | 0.0000 | |
| 260 | G | A | 0.0000 | |
| 261 | F | A | -0.6207 | |
| 262 | N | A | -1.4726 | |
| 263 | S | A | -1.5045 | |
| 264 | N | A | -2.1942 | |
| 265 | T | A | -1.8504 | |
| 266 | E | A | -2.4174 | |
| 267 | R | A | -1.6382 | |
| 268 | D | A | -1.4117 | |
| 269 | F | A | 0.0000 | |
| 270 | Y | A | 0.0000 | |
| 271 | S | A | -1.0494 | |
| 272 | A | A | 0.0000 | |
| 273 | T | A | -0.5217 | |
| 274 | S | A | -0.4862 | |
| 275 | S | A | -0.7414 | |
| 276 | S | A | -0.7468 | |
| 277 | S | A | -1.0357 | |
| 278 | K | A | -1.8568 | |
| 279 | L | A | 0.0000 | |
| 280 | V | A | 0.0000 | |
| 281 | F | A | 0.0000 | |
| 282 | S | A | 0.0000 | |
| 283 | V | A | 0.0000 | |
| 284 | W | A | 0.0000 | |
| 285 | D | A | 0.0000 | |
| 286 | A | A | -0.0652 | |
| 287 | G | A | -0.8841 | |
| 288 | G | A | -1.9246 | |
| 289 | N | A | -2.1459 | |
| 290 | D | A | 0.0000 | |
| 291 | T | A | -0.3773 | |
| 292 | L | A | 0.0000 | |
| 293 | D | A | 0.0000 | |
| 294 | F | A | 0.0000 | |
| 295 | S | A | -0.3724 | |
| 296 | G | A | -0.6579 | |
| 297 | F | A | 0.0000 | |
| 298 | S | A | -1.0450 | |
| 299 | Q | A | -1.5993 | |
| 300 | N | A | -2.0740 | |
| 301 | Q | A | 0.0000 | |
| 302 | K | A | -1.4035 | |
| 303 | I | A | 0.0000 | |
| 304 | N | A | 0.0000 | |
| 305 | L | A | 0.0000 | |
| 306 | N | A | -1.7116 | |
| 307 | E | A | -2.4714 | |
| 308 | K | A | -1.9348 | |
| 309 | A | A | -1.0315 | |
| 310 | L | A | -0.6225 | |
| 311 | S | A | 0.0000 | |
| 312 | D | A | -1.2231 | |
| 313 | V | A | 0.0000 | |
| 314 | G | A | 0.0000 | |
| 315 | G | A | -1.5147 | |
| 316 | L | A | 0.0000 | |
| 317 | K | A | -1.8859 | |
| 318 | G | A | 0.0000 | |
| 319 | N | A | 0.0000 | |
| 320 | V | A | 0.0000 | |
| 321 | S | A | 0.0000 | |
| 322 | I | A | 0.0000 | |
| 323 | A | A | 0.0000 | |
| 324 | A | A | -1.1924 | |
| 325 | G | A | -1.0547 | |
| 326 | V | A | 0.0000 | |
| 327 | T | A | -0.9998 | |
| 328 | V | A | 0.0000 | |
| 329 | E | A | 0.0000 | |
| 330 | N | A | -0.1830 | |
| 331 | A | A | 0.0000 | |
| 332 | I | A | 0.1445 | |
| 333 | G | A | 0.0000 | |
| 334 | G | A | 0.0000 | |
| 335 | S | A | -1.0192 | |
| 336 | G | A | -1.3476 | |
| 337 | S | A | -1.3960 | |
| 338 | D | A | 0.0000 | |
| 339 | L | A | 0.0000 | |
| 340 | L | A | 0.0000 | |
| 341 | I | A | 0.0000 | |
| 342 | G | A | 0.0000 | |
| 343 | N | A | 0.0000 | |
| 344 | D | A | -1.0988 | |
| 345 | V | A | -0.2512 | |
| 346 | A | A | -0.0597 | |
| 347 | N | A | 0.0000 | |
| 348 | V | A | 0.2001 | |
| 349 | L | A | 0.0000 | |
| 350 | K | A | -0.4391 | |
| 351 | G | A | 0.0000 | |
| 352 | G | A | -0.6978 | |
| 353 | A | A | -0.7262 | |
| 354 | G | A | -1.1876 | |
| 355 | N | A | -1.7777 | |
| 356 | D | A | 0.0000 | |
| 357 | I | A | -0.2316 | |
| 358 | L | A | 0.0000 | |
| 359 | Y | A | 0.3976 | |
| 360 | G | A | 0.0000 | |
| 361 | G | A | 0.0000 | |
| 362 | L | A | 0.4440 | |
| 363 | G | A | 0.0250 | |
| 364 | A | A | 0.0797 | |
| 365 | D | A | 0.0000 | |
| 366 | Q | A | -0.2307 | |
| 367 | L | A | 0.0000 | |
| 368 | W | A | -0.1327 | |
| 369 | G | A | 0.0000 | |
| 370 | G | A | -0.4831 | |
| 371 | A | A | -0.4608 | |
| 372 | G | A | -0.9657 | |
| 373 | A | A | -1.0015 | |
| 374 | D | A | 0.0000 | |
| 375 | T | A | -0.4159 | |
| 376 | F | A | 0.0000 | |
| 377 | V | A | 0.0000 | |
| 378 | Y | A | 0.0000 | |
| 379 | G | A | -0.6826 | |
| 380 | D | A | -0.9884 | |
| 381 | I | A | -0.3089 | |
| 382 | A | A | 0.1117 | |
| 383 | E | A | 0.0000 | |
| 384 | S | A | 0.0000 | |
| 385 | S | A | 0.0302 | |
| 386 | A | A | -0.2613 | |
| 387 | A | A | -0.0446 | |
| 388 | A | A | -0.0437 | |
| 389 | P | A | -0.1957 | |
| 390 | D | A | 0.0000 | |
| 391 | T | A | -0.2584 | |
| 392 | L | A | 0.0000 | |
| 393 | R | A | -0.4270 | |
| 394 | D | A | -0.2073 | |
| 395 | F | A | 0.0000 | |
| 396 | V | A | 0.8689 | |
| 397 | S | A | -0.2973 | |
| 398 | G | A | -0.7410 | |
| 399 | Q | A | -1.3152 | |
| 400 | D | A | 0.0000 | |
| 401 | K | A | -0.4853 | |
| 402 | I | A | 0.0000 | |
| 403 | D | A | 0.0000 | |
| 404 | L | A | 0.0000 | |
| 405 | S | A | -0.1121 | |
| 406 | G | A | -0.4688 | |
| 407 | L | A | 0.0000 | |
| 408 | D | A | -1.3466 | |
| 409 | A | A | 0.0000 | |
| 410 | F | A | 0.5869 | |
| 411 | V | A | 0.4350 | |
| 412 | N | A | -1.1070 | |
| 413 | G | A | -0.8068 | |
| 414 | G | A | -0.1936 | |
| 415 | L | A | 0.7446 | |
| 416 | V | A | 1.8591 | |
| 417 | L | A | 0.8795 | |
| 418 | Q | A | -0.4965 | |
| 419 | Y | A | -0.0871 | |
| 420 | V | A | -0.3501 | |
| 421 | D | A | -1.3173 | |
| 422 | A | A | -0.4710 | |
| 423 | F | A | -0.4797 | |
| 424 | A | A | -0.7354 | |
| 425 | G | A | -1.5291 | |
| 426 | K | A | -2.3526 | |
| 427 | A | A | -1.0507 | |
| 428 | G | A | 0.0000 | |
| 429 | Q | A | 0.0000 | |
| 430 | A | A | 0.0000 | |
| 431 | I | A | -0.0513 | |
| 432 | L | A | 0.0728 | |
| 433 | S | A | -0.3343 | |
| 434 | Y | A | -0.3993 | |
| 435 | D | A | -1.5902 | |
| 436 | A | A | -1.1972 | |
| 437 | A | A | -0.8112 | |
| 438 | S | A | -1.1782 | |
| 439 | K | A | -2.0134 | |
| 440 | A | A | -1.1793 | |
| 441 | G | A | -0.6242 | |
| 442 | S | A | -0.1880 | |
| 443 | L | A | 0.0000 | |
| 444 | A | A | -0.2493 | |
| 445 | I | A | 0.0000 | |
| 446 | D | A | 0.0000 | |
| 447 | F | A | 0.0000 | |
| 448 | S | A | -1.4122 | |
| 449 | G | A | -2.0699 | |
| 450 | D | A | -2.5993 | |
| 451 | A | A | -1.6786 | |
| 452 | H | A | -1.8069 | |
| 453 | A | A | -1.1156 | |
| 454 | D | A | -1.3188 | |
| 455 | F | A | 0.0000 | |
| 456 | A | A | -0.2184 | |
| 457 | I | A | 0.0000 | |
| 458 | N | A | -0.4576 | |
| 459 | L | A | 0.0000 | |
| 460 | I | A | -0.2379 | |
| 461 | G | A | -0.5913 | |
| 462 | Q | A | -0.7711 | |
| 463 | A | A | -0.2726 | |
| 464 | T | A | -0.5933 | |
| 465 | Q | A | -1.0256 | |
| 466 | A | A | -0.7162 | |
| 467 | D | A | 0.0000 | |
| 468 | I | A | 0.0000 | |
| 469 | V | A | 0.3574 | |
| 470 | V | A | 1.1237 |
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 | -0.248 | 2.2048 | View | CSV | PDB |
| 4.5 | -0.3027 | 2.0427 | View | CSV | PDB |
| 5.0 | -0.3664 | 2.0427 | View | CSV | PDB |
| 5.5 | -0.4301 | 2.0427 | View | CSV | PDB |
| 6.0 | -0.4855 | 2.0427 | View | CSV | PDB |
| 6.5 | -0.5273 | 2.0427 | View | CSV | PDB |
| 7.0 | -0.5572 | 2.0427 | View | CSV | PDB |
| 7.5 | -0.5796 | 2.0427 | View | CSV | PDB |
| 8.0 | -0.5967 | 2.0427 | View | CSV | PDB |
| 8.5 | -0.6062 | 2.0427 | View | CSV | PDB |
| 9.0 | -0.6041 | 2.0637 | 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