| Chain sequence(s) |
A: MGSSHHHHHHHENLYFQGKAAVIGLGVEGKKAVNSLLSHGWEVYATDLNSNVDLSDLELPMISMNLVSGGETVSIVSDNLTVDLGFSNSSAIEECDAIAISPSMYGGAFADKLLEKGKLLSNVVTKHKDIFTIGITGTNGKTTSVHMLKSILENAGKKVLVGGNGGGGFSGYYDLILEASNDDYDILLVEVCDMTLDFCNYCFDFDMVGLTNIGNDHMDVHKTIANYKNTLVRFFEGKTVFTAFNQDFNADFKEVASKAIPFFEYDEKLQVWGRFNALNAGLVAAIATELKIPKDIIMESLADFKAVEGRMNVYKINNASIFVGKTDNSDALTSVLNENDFYALFIGTPRANEEHRLSILDEAVKYNPEVIVLFPGLDDTVDMGLYRLNRLGYEGRIEVANSLDEIIALIAEFSHEDALFIGGNGQEAIIEIQERIRLLSENL
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] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:11:06)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/47d406db02c8bc4/tmp/folded.pdb (00:11:06)
[INFO] Main: Simulation completed successfully. (00:20:05)
|
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 | 0.7463 | |
| 2 | G | A | -0.2506 | |
| 3 | S | A | -0.6913 | |
| 4 | S | A | -1.2258 | |
| 5 | H | A | -2.1332 | |
| 6 | H | A | -2.4816 | |
| 7 | H | A | -2.7314 | |
| 8 | H | A | -2.8299 | |
| 9 | H | A | -2.9860 | |
| 10 | H | A | -3.1670 | |
| 11 | H | A | -2.9762 | |
| 12 | E | A | -2.7067 | |
| 13 | N | A | -1.4373 | |
| 14 | L | A | 1.1846 | |
| 15 | Y | A | 1.7991 | |
| 16 | F | A | 2.1100 | |
| 17 | Q | A | -0.2299 | |
| 18 | G | A | 0.0000 | |
| 19 | K | A | -1.8075 | |
| 20 | A | A | 0.0000 | |
| 21 | A | A | 0.0000 | |
| 22 | V | A | 0.0000 | |
| 23 | I | A | 0.0000 | |
| 24 | G | A | 0.1903 | |
| 25 | L | A | 0.0000 | |
| 26 | G | A | -0.0872 | |
| 27 | V | A | 0.6976 | |
| 28 | E | A | 0.0000 | |
| 29 | G | A | 0.0000 | |
| 30 | K | A | 0.0000 | |
| 31 | K | A | -0.7113 | |
| 32 | A | A | 0.0000 | |
| 33 | V | A | 0.0000 | |
| 34 | N | A | -1.0318 | |
| 35 | S | A | 0.0000 | |
| 36 | L | A | 0.0000 | |
| 37 | L | A | -0.6276 | |
| 38 | S | A | -0.6428 | |
| 39 | H | A | -0.4439 | |
| 40 | G | A | -0.5264 | |
| 41 | W | A | 0.0000 | |
| 42 | E | A | -2.0395 | |
| 43 | V | A | 0.0000 | |
| 44 | Y | A | 0.0000 | |
| 45 | A | A | 0.0000 | |
| 46 | T | A | 0.0000 | |
| 47 | D | A | 0.0000 | |
| 48 | L | A | 0.9527 | |
| 49 | N | A | -1.2336 | |
| 50 | S | A | -1.3563 | |
| 51 | N | A | -1.9993 | |
| 52 | V | A | -1.4211 | |
| 53 | D | A | -2.2597 | |
| 54 | L | A | -1.4466 | |
| 55 | S | A | -1.6941 | |
| 56 | D | A | -2.4070 | |
| 57 | L | A | 0.0000 | |
| 58 | E | A | -1.9796 | |
| 59 | L | A | -0.0447 | |
| 60 | P | A | 0.6254 | |
| 61 | M | A | 1.9092 | |
| 62 | I | A | 2.1493 | |
| 63 | S | A | 0.7686 | |
| 64 | M | A | 1.0293 | |
| 65 | N | A | 0.5245 | |
| 66 | L | A | 1.9983 | |
| 67 | V | A | 2.1754 | |
| 68 | S | A | 0.3700 | |
| 69 | G | A | -0.6007 | |
| 70 | G | A | -1.4021 | |
| 71 | E | A | -2.4053 | |
| 72 | T | A | -0.8474 | |
| 73 | V | A | 0.4437 | |
| 74 | S | A | 1.1491 | |
| 75 | I | A | 0.0000 | |
| 76 | V | A | 0.6814 | |
| 77 | S | A | -0.1663 | |
| 78 | D | A | -1.7017 | |
| 79 | N | A | -1.6477 | |
| 80 | L | A | 0.0000 | |
| 81 | T | A | -0.3064 | |
| 82 | V | A | 0.0000 | |
| 83 | D | A | 0.0000 | |
| 84 | L | A | 0.0000 | |
| 85 | G | A | -0.1725 | |
| 86 | F | A | 0.5818 | |
| 87 | S | A | 0.1669 | |
| 88 | N | A | -0.9382 | |
| 89 | S | A | -1.2886 | |
| 90 | S | A | -1.6241 | |
| 91 | A | A | -1.6036 | |
| 92 | I | A | 0.0000 | |
| 93 | E | A | -3.4430 | |
| 94 | E | A | -3.1798 | |
| 95 | C | A | -2.6590 | |
| 96 | D | A | -2.8015 | |
| 97 | A | A | 0.0000 | |
| 98 | I | A | 0.0000 | |
| 99 | A | A | 0.0000 | |
| 100 | I | A | 0.0000 | |
| 101 | S | A | 0.1739 | |
| 102 | P | A | 0.0000 | |
| 103 | S | A | -0.0660 | |
| 104 | M | A | 0.1511 | |
| 105 | Y | A | -0.0219 | |
| 106 | G | A | -0.6819 | |
| 107 | G | A | -0.4446 | |
| 108 | A | A | -0.3194 | |
| 109 | F | A | 0.5616 | |
| 110 | A | A | 0.0000 | |
| 111 | D | A | -2.6936 | |
| 112 | K | A | -2.8217 | |
| 113 | L | A | -2.2714 | |
| 114 | L | A | -2.4983 | |
| 115 | E | A | -3.8015 | |
| 116 | K | A | -3.7432 | |
| 117 | G | A | -3.3886 | |
| 118 | K | A | -2.5369 | |
| 119 | L | A | 0.0000 | |
| 120 | L | A | 0.0000 | |
| 121 | S | A | 0.0000 | |
| 122 | N | A | -0.6133 | |
| 123 | V | A | -0.2642 | |
| 124 | V | A | 0.0655 | |
| 125 | T | A | -1.1820 | |
| 126 | K | A | -2.8301 | |
| 127 | H | A | 0.0000 | |
| 128 | K | A | -2.3716 | |
| 129 | D | A | -2.7788 | |
| 130 | I | A | -1.8962 | |
| 131 | F | A | -0.7512 | |
| 132 | T | A | 0.0000 | |
| 133 | I | A | 0.0000 | |
| 134 | G | A | 0.0000 | |
| 135 | I | A | 0.0000 | |
| 136 | T | A | 0.0000 | |
| 137 | G | A | 0.0000 | |
| 138 | T | A | 0.0000 | |
| 139 | N | A | -0.5008 | |
| 140 | G | A | -0.2022 | |
| 141 | K | A | -0.3529 | |
| 142 | T | A | -0.2872 | |
| 143 | T | A | 0.0000 | |
| 144 | S | A | 0.0000 | |
| 145 | V | A | 0.0000 | |
| 146 | H | A | -0.6061 | |
| 147 | M | A | 0.0000 | |
| 148 | L | A | 0.0000 | |
| 149 | K | A | -1.4414 | |
| 150 | S | A | -1.6232 | |
| 151 | I | A | 0.0000 | |
| 152 | L | A | 0.0000 | |
| 153 | E | A | -2.6703 | |
| 154 | N | A | -2.5342 | |
| 155 | A | A | -1.5914 | |
| 156 | G | A | -2.0503 | |
| 157 | K | A | -2.5587 | |
| 158 | K | A | -2.7623 | |
| 159 | V | A | -1.4555 | |
| 160 | L | A | 0.0000 | |
| 161 | V | A | 0.0450 | |
| 162 | G | A | 0.0000 | |
| 163 | G | A | 0.0000 | |
| 164 | N | A | -0.2161 | |
| 165 | G | A | 0.0000 | |
| 166 | G | A | -0.3517 | |
| 167 | G | A | -0.6323 | |
| 168 | G | A | -0.8536 | |
| 169 | F | A | -0.2968 | |
| 170 | S | A | -0.3013 | |
| 171 | G | A | 0.0000 | |
| 172 | Y | A | 0.0000 | |
| 173 | Y | A | 0.0000 | |
| 174 | D | A | -0.7026 | |
| 175 | L | A | 0.0000 | |
| 176 | I | A | 0.0000 | |
| 177 | L | A | 0.0000 | |
| 178 | E | A | -1.4018 | |
| 179 | A | A | 0.0000 | |
| 180 | S | A | -1.4700 | |
| 181 | N | A | -1.9987 | |
| 182 | D | A | -3.0060 | |
| 183 | D | A | -3.1470 | |
| 184 | Y | A | -2.3467 | |
| 185 | D | A | -2.5017 | |
| 186 | I | A | 0.0000 | |
| 187 | L | A | 0.0000 | |
| 188 | L | A | 0.0000 | |
| 189 | V | A | 0.0000 | |
| 190 | E | A | 0.0000 | |
| 191 | V | A | 0.0000 | |
| 192 | C | A | 0.0475 | |
| 193 | D | A | 0.0000 | |
| 194 | M | A | 0.4770 | |
| 195 | T | A | -0.0592 | |
| 196 | L | A | 0.0000 | |
| 197 | D | A | -0.8460 | |
| 198 | F | A | 0.0000 | |
| 199 | C | A | 0.0000 | |
| 200 | N | A | -1.0611 | |
| 201 | Y | A | 0.0611 | |
| 202 | C | A | 0.0000 | |
| 203 | F | A | 0.0000 | |
| 204 | D | A | -2.3857 | |
| 205 | F | A | 0.0000 | |
| 206 | D | A | -1.5368 | |
| 207 | M | A | 0.0000 | |
| 208 | V | A | 0.0000 | |
| 209 | G | A | 0.0000 | |
| 210 | L | A | 0.0000 | |
| 211 | T | A | 0.0000 | |
| 212 | N | A | -0.6175 | |
| 213 | I | A | -0.5858 | |
| 214 | G | A | -0.8755 | |
| 215 | N | A | -1.6077 | |
| 216 | D | A | -1.1693 | |
| 217 | H | A | -0.9604 | |
| 218 | M | A | -1.4444 | |
| 219 | D | A | -2.1382 | |
| 220 | V | A | -0.4761 | |
| 221 | H | A | 0.0000 | |
| 222 | K | A | -2.0003 | |
| 223 | T | A | -1.1310 | |
| 224 | I | A | -0.4899 | |
| 225 | A | A | -0.7008 | |
| 226 | N | A | -1.3510 | |
| 227 | Y | A | 0.0000 | |
| 228 | K | A | -1.2389 | |
| 229 | N | A | -1.7515 | |
| 230 | T | A | -1.1446 | |
| 231 | L | A | 0.0000 | |
| 232 | V | A | -1.7852 | |
| 233 | R | A | -1.8441 | |
| 234 | F | A | 0.0000 | |
| 235 | F | A | 0.0000 | |
| 236 | E | A | -2.8663 | |
| 237 | G | A | -2.0602 | |
| 238 | K | A | -1.7885 | |
| 239 | T | A | -1.3729 | |
| 240 | V | A | 0.0000 | |
| 241 | F | A | 0.0000 | |
| 242 | T | A | 0.0000 | |
| 243 | A | A | 0.0000 | |
| 244 | F | A | 0.8074 | |
| 245 | N | A | -0.9350 | |
| 246 | Q | A | -1.2561 | |
| 247 | D | A | -2.0002 | |
| 248 | F | A | -1.3454 | |
| 249 | N | A | -1.6309 | |
| 250 | A | A | -1.6039 | |
| 251 | D | A | -2.1473 | |
| 252 | F | A | 0.0000 | |
| 253 | K | A | -3.1534 | |
| 254 | E | A | -3.2452 | |
| 255 | V | A | -2.4113 | |
| 256 | A | A | -2.4185 | |
| 257 | S | A | -1.9703 | |
| 258 | K | A | -1.9760 | |
| 259 | A | A | -1.3160 | |
| 260 | I | A | -0.1909 | |
| 261 | P | A | 0.5930 | |
| 262 | F | A | 0.0000 | |
| 263 | F | A | 1.6153 | |
| 264 | E | A | -0.3187 | |
| 265 | Y | A | -1.3727 | |
| 266 | D | A | -2.7467 | |
| 267 | E | A | -3.4813 | |
| 268 | K | A | -3.4335 | |
| 269 | L | A | -2.4723 | |
| 270 | Q | A | -2.2011 | |
| 271 | V | A | -1.2929 | |
| 272 | W | A | -0.5263 | |
| 273 | G | A | -1.1300 | |
| 274 | R | A | -1.8883 | |
| 275 | F | A | -0.5770 | |
| 276 | N | A | 0.0000 | |
| 277 | A | A | -0.9356 | |
| 278 | L | A | 0.0830 | |
| 279 | N | A | 0.0000 | |
| 280 | A | A | 0.0000 | |
| 281 | G | A | 0.0000 | |
| 282 | L | A | 0.0000 | |
| 283 | V | A | 0.0000 | |
| 284 | A | A | 0.0059 | |
| 285 | A | A | 0.0654 | |
| 286 | I | A | 0.0000 | |
| 287 | A | A | 0.0000 | |
| 288 | T | A | -1.1414 | |
| 289 | E | A | -0.8113 | |
| 290 | L | A | -0.7135 | |
| 291 | K | A | -1.9941 | |
| 292 | I | A | 0.0000 | |
| 293 | P | A | -1.8306 | |
| 294 | K | A | -2.9574 | |
| 295 | D | A | -2.8592 | |
| 296 | I | A | -1.9844 | |
| 297 | I | A | 0.0000 | |
| 298 | M | A | -2.3906 | |
| 299 | E | A | -3.2722 | |
| 300 | S | A | 0.0000 | |
| 301 | L | A | 0.0000 | |
| 302 | A | A | -2.6632 | |
| 303 | D | A | -3.0894 | |
| 304 | F | A | 0.0000 | |
| 305 | K | A | -2.6107 | |
| 306 | A | A | -1.6134 | |
| 307 | V | A | -1.1888 | |
| 308 | E | A | -2.6046 | |
| 309 | G | A | 0.0000 | |
| 310 | R | A | -1.2557 | |
| 311 | M | A | 0.0000 | |
| 312 | N | A | -0.8730 | |
| 313 | V | A | -0.1128 | |
| 314 | Y | A | -0.8289 | |
| 315 | K | A | -2.4019 | |
| 316 | I | A | 0.0000 | |
| 317 | N | A | -2.5169 | |
| 318 | N | A | -3.1432 | |
| 319 | A | A | 0.0000 | |
| 320 | S | A | -1.6420 | |
| 321 | I | A | 0.0000 | |
| 322 | F | A | 0.0000 | |
| 323 | V | A | 0.0000 | |
| 324 | G | A | 0.0000 | |
| 325 | K | A | -1.1011 | |
| 326 | T | A | 0.0000 | |
| 327 | D | A | -0.7416 | |
| 328 | N | A | 0.0000 | |
| 329 | S | A | -1.0580 | |
| 330 | D | A | -1.4536 | |
| 331 | A | A | -0.7068 | |
| 332 | L | A | 0.0000 | |
| 333 | T | A | -1.0397 | |
| 334 | S | A | -1.2086 | |
| 335 | V | A | 0.0000 | |
| 336 | L | A | 0.0000 | |
| 337 | N | A | -2.2597 | |
| 338 | E | A | -2.2740 | |
| 339 | N | A | -2.3097 | |
| 340 | D | A | -2.6920 | |
| 341 | F | A | 0.0000 | |
| 342 | Y | A | -1.4160 | |
| 343 | A | A | 0.0000 | |
| 344 | L | A | 0.0000 | |
| 345 | F | A | 0.0000 | |
| 346 | I | A | 0.0000 | |
| 347 | G | A | 0.0000 | |
| 348 | T | A | 0.0000 | |
| 349 | P | A | 0.0000 | |
| 350 | R | A | -2.9110 | |
| 351 | A | A | -2.3269 | |
| 352 | N | A | -2.7040 | |
| 353 | E | A | -3.0635 | |
| 354 | E | A | -3.0625 | |
| 355 | H | A | -2.3545 | |
| 356 | R | A | -1.7643 | |
| 357 | L | A | 0.0000 | |
| 358 | S | A | -0.9767 | |
| 359 | I | A | 0.0000 | |
| 360 | L | A | 0.0000 | |
| 361 | D | A | -0.8869 | |
| 362 | E | A | -1.1508 | |
| 363 | A | A | 0.0000 | |
| 364 | V | A | -1.4710 | |
| 365 | K | A | -1.8370 | |
| 366 | Y | A | -1.5490 | |
| 367 | N | A | -2.4259 | |
| 368 | P | A | 0.0000 | |
| 369 | E | A | -2.3848 | |
| 370 | V | A | 0.0000 | |
| 371 | I | A | 0.0000 | |
| 372 | V | A | 0.0000 | |
| 373 | L | A | 0.0000 | |
| 374 | F | A | 0.0000 | |
| 375 | P | A | -1.1030 | |
| 376 | G | A | -1.0463 | |
| 377 | L | A | -0.9258 | |
| 378 | D | A | -1.9483 | |
| 379 | D | A | -2.6149 | |
| 380 | T | A | 0.0000 | |
| 381 | V | A | -0.9261 | |
| 382 | D | A | -1.1594 | |
| 383 | M | A | -0.5899 | |
| 384 | G | A | 0.0000 | |
| 385 | L | A | 0.0982 | |
| 386 | Y | A | 0.2064 | |
| 387 | R | A | -0.7083 | |
| 388 | L | A | 0.0000 | |
| 389 | N | A | -1.8371 | |
| 390 | R | A | -2.0168 | |
| 391 | L | A | -1.1601 | |
| 392 | G | A | -1.6941 | |
| 393 | Y | A | 0.0000 | |
| 394 | E | A | -2.6092 | |
| 395 | G | A | -2.1568 | |
| 396 | R | A | -1.4597 | |
| 397 | I | A | -0.3995 | |
| 398 | E | A | 0.1291 | |
| 399 | V | A | 0.1983 | |
| 400 | A | A | 0.0000 | |
| 401 | N | A | -1.8638 | |
| 402 | S | A | -1.4712 | |
| 403 | L | A | -1.6851 | |
| 404 | D | A | -2.4432 | |
| 405 | E | A | -2.0640 | |
| 406 | I | A | 0.0000 | |
| 407 | I | A | -0.8723 | |
| 408 | A | A | -0.9741 | |
| 409 | L | A | -0.7302 | |
| 410 | I | A | 0.0000 | |
| 411 | A | A | -0.9146 | |
| 412 | E | A | -1.4556 | |
| 413 | F | A | 0.0000 | |
| 414 | S | A | 0.0000 | |
| 415 | H | A | -2.5824 | |
| 416 | E | A | -2.3277 | |
| 417 | D | A | -3.1074 | |
| 418 | A | A | 0.0000 | |
| 419 | L | A | 0.0000 | |
| 420 | F | A | 0.0000 | |
| 421 | I | A | 0.0000 | |
| 422 | G | A | 0.0000 | |
| 423 | G | A | 0.0000 | |
| 424 | N | A | 0.0000 | |
| 425 | G | A | 0.0000 | |
| 426 | Q | A | -1.7387 | |
| 427 | E | A | -2.4835 | |
| 428 | A | A | -1.3816 | |
| 429 | I | A | 0.0000 | |
| 430 | I | A | -2.0842 | |
| 431 | E | A | -2.8751 | |
| 432 | I | A | 0.0000 | |
| 433 | Q | A | 0.0000 | |
| 434 | E | A | -2.0620 | |
| 435 | R | A | -1.5463 | |
| 436 | I | A | 0.0000 | |
| 437 | R | A | -1.6929 | |
| 438 | L | A | -0.3949 | |
| 439 | L | A | -0.4480 | |
| 440 | S | A | -1.4057 | |
| 441 | E | A | -1.9261 | |
| 442 | N | A | -1.1299 | |
| 443 | L | A | 0.1628 |
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 | -0.6011 | 5.2657 | View | CSV | PDB |
| 4.5 | -0.6948 | 5.148 | View | CSV | PDB |
| 5.0 | -0.8095 | 5.0075 | View | CSV | PDB |
| 5.5 | -0.9269 | 4.8613 | View | CSV | PDB |
| 6.0 | -1.0277 | 4.7239 | View | CSV | PDB |
| 6.5 | -1.0989 | 4.6087 | View | CSV | PDB |
| 7.0 | -1.1403 | 4.5194 | View | CSV | PDB |
| 7.5 | -1.1614 | 4.53 | View | CSV | PDB |
| 8.0 | -1.1694 | 4.5468 | View | CSV | PDB |
| 8.5 | -1.1652 | 4.5634 | View | CSV | PDB |
| 9.0 | -1.146 | 4.578 | 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