| Chain sequence(s) |
A: GSKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSPKSYYELYMAISDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKDILKDLVEMCRGVQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFAEMNKLWVRMQHQGHSRDREKRERERQELRILVGTNLVRLSQLEGVNVERYKQIVLTGILEQVVNCRDALAQEYLMECIIQVFPDEFHLQTLNPFLRACAELHQNVNVKNIIIALIDRLALFAHREDGPGIPADIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMKCYPDRVDYVDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKHFHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQ
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] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:08:26)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/8cfe36694cdfa3/tmp/folded.pdb (00:08:26)
[INFO] Main: Simulation completed successfully. (00:10:43)
|
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 | -0.9757 | |
| 13 | S | A | -1.6332 | |
| 14 | K | A | -2.6934 | |
| 15 | L | A | -1.3533 | |
| 16 | L | A | -1.9610 | |
| 17 | D | A | -3.3066 | |
| 18 | E | A | -3.4027 | |
| 19 | A | A | 0.0000 | |
| 20 | I | A | -1.8524 | |
| 21 | Q | A | -2.2791 | |
| 22 | A | A | -1.4275 | |
| 23 | V | A | 0.0000 | |
| 24 | K | A | -1.2237 | |
| 25 | V | A | 0.2129 | |
| 26 | Q | A | -0.8931 | |
| 27 | S | A | 0.0000 | |
| 28 | F | A | 0.2351 | |
| 29 | Q | A | -1.2785 | |
| 30 | M | A | 0.0000 | |
| 31 | K | A | -1.8465 | |
| 32 | R | A | -3.1265 | |
| 33 | C | A | -2.9718 | |
| 34 | L | A | 0.0000 | |
| 35 | D | A | -3.8720 | |
| 36 | K | A | -3.9195 | |
| 37 | N | A | -3.4572 | |
| 38 | K | A | -3.0136 | |
| 39 | L | A | 0.0000 | |
| 40 | M | A | -0.9286 | |
| 41 | D | A | -2.2635 | |
| 42 | A | A | 0.0000 | |
| 43 | L | A | 0.0000 | |
| 44 | K | A | -2.4848 | |
| 45 | H | A | -1.6816 | |
| 46 | A | A | 0.0000 | |
| 47 | S | A | -1.7899 | |
| 48 | N | A | -1.9748 | |
| 49 | M | A | 0.0000 | |
| 50 | L | A | 0.0000 | |
| 51 | G | A | -1.4587 | |
| 52 | E | A | -1.4399 | |
| 53 | L | A | 0.0000 | |
| 54 | R | A | -1.7922 | |
| 55 | T | A | -0.6636 | |
| 56 | S | A | -0.2083 | |
| 57 | M | A | 0.8675 | |
| 58 | L | A | 0.0000 | |
| 59 | S | A | -0.6552 | |
| 60 | P | A | 0.0000 | |
| 61 | K | A | -2.3095 | |
| 62 | S | A | -1.1676 | |
| 63 | Y | A | 0.0000 | |
| 64 | Y | A | -0.7309 | |
| 65 | E | A | -1.4054 | |
| 66 | L | A | 0.0000 | |
| 67 | Y | A | 0.0000 | |
| 68 | M | A | -0.3953 | |
| 69 | A | A | -0.7416 | |
| 70 | I | A | 0.0000 | |
| 71 | S | A | -0.9050 | |
| 72 | D | A | -1.7437 | |
| 73 | E | A | 0.0000 | |
| 74 | L | A | 0.0000 | |
| 75 | H | A | -0.3468 | |
| 76 | Y | A | 0.6423 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | 0.3335 | |
| 79 | V | A | 1.3959 | |
| 80 | Y | A | 0.2075 | |
| 81 | L | A | 0.0000 | |
| 82 | T | A | -0.8001 | |
| 83 | D | A | -2.1508 | |
| 84 | E | A | 0.0000 | |
| 85 | F | A | 0.0000 | |
| 86 | A | A | -2.2945 | |
| 87 | K | A | -3.0894 | |
| 88 | G | A | -2.6291 | |
| 89 | R | A | -3.1377 | |
| 90 | K | A | -2.4400 | |
| 91 | V | A | -0.8234 | |
| 92 | A | A | -1.1479 | |
| 93 | D | A | -2.1209 | |
| 94 | L | A | 0.0000 | |
| 95 | Y | A | -0.8914 | |
| 96 | E | A | -1.8213 | |
| 97 | L | A | -0.4760 | |
| 98 | V | A | 0.0000 | |
| 99 | Q | A | -0.3020 | |
| 100 | Y | A | 0.6978 | |
| 101 | A | A | -0.1947 | |
| 102 | G | A | -0.6582 | |
| 103 | N | A | -1.2738 | |
| 104 | I | A | -0.3669 | |
| 105 | I | A | 0.0000 | |
| 106 | P | A | 0.0000 | |
| 107 | R | A | -0.3018 | |
| 108 | L | A | 0.0000 | |
| 109 | Y | A | 0.0000 | |
| 110 | L | A | 0.0000 | |
| 111 | L | A | 0.0000 | |
| 112 | I | A | 0.0000 | |
| 113 | T | A | 0.0000 | |
| 114 | V | A | 0.0000 | |
| 115 | G | A | 0.0000 | |
| 116 | V | A | 0.0000 | |
| 117 | V | A | 0.0000 | |
| 118 | Y | A | -0.3468 | |
| 119 | V | A | 0.0000 | |
| 120 | K | A | -1.4136 | |
| 121 | S | A | -0.9547 | |
| 122 | F | A | -0.5305 | |
| 123 | P | A | -1.6942 | |
| 124 | Q | A | -2.4325 | |
| 125 | S | A | -1.5085 | |
| 126 | R | A | 0.0000 | |
| 127 | K | A | -2.4817 | |
| 128 | D | A | -2.9024 | |
| 129 | I | A | 0.0000 | |
| 130 | L | A | 0.0000 | |
| 131 | K | A | -2.6513 | |
| 132 | D | A | -1.9469 | |
| 133 | L | A | 0.0000 | |
| 134 | V | A | 0.0000 | |
| 135 | E | A | -1.3093 | |
| 136 | M | A | -0.9833 | |
| 137 | C | A | 0.0000 | |
| 138 | R | A | -2.3291 | |
| 139 | G | A | -1.4814 | |
| 140 | V | A | 0.0000 | |
| 141 | Q | A | -1.9277 | |
| 142 | H | A | -1.3209 | |
| 143 | P | A | 0.0000 | |
| 144 | L | A | 0.0000 | |
| 145 | R | A | -0.8236 | |
| 146 | G | A | 0.0000 | |
| 147 | L | A | 0.0000 | |
| 148 | F | A | 0.0000 | |
| 149 | L | A | 0.0000 | |
| 150 | R | A | 0.0000 | |
| 151 | N | A | 0.0000 | |
| 152 | Y | A | 0.0000 | |
| 153 | L | A | 0.0000 | |
| 154 | L | A | 0.0000 | |
| 155 | Q | A | -1.1082 | |
| 156 | C | A | -0.8594 | |
| 157 | T | A | 0.0000 | |
| 158 | R | A | -2.3417 | |
| 159 | N | A | -2.1419 | |
| 160 | I | A | -1.1591 | |
| 161 | L | A | 0.0000 | |
| 162 | P | A | 0.0000 | |
| 163 | D | A | -2.8543 | |
| 164 | E | A | -3.2757 | |
| 165 | G | A | -2.2366 | |
| 166 | E | A | -2.1959 | |
| 167 | P | A | -1.7477 | |
| 168 | T | A | -2.0610 | |
| 169 | D | A | -3.5744 | |
| 170 | E | A | -3.7685 | |
| 171 | E | A | -3.5645 | |
| 172 | T | A | -2.7187 | |
| 173 | T | A | -2.2319 | |
| 174 | G | A | -1.9977 | |
| 175 | D | A | -2.5800 | |
| 176 | I | A | 0.0000 | |
| 177 | S | A | -1.4668 | |
| 178 | D | A | -2.2410 | |
| 179 | S | A | 0.0000 | |
| 180 | M | A | 0.0000 | |
| 181 | D | A | -1.8716 | |
| 182 | F | A | 0.0000 | |
| 183 | V | A | 0.0000 | |
| 184 | L | A | -0.2584 | |
| 185 | L | A | -0.2477 | |
| 186 | N | A | 0.0000 | |
| 187 | F | A | 0.0000 | |
| 188 | A | A | -0.3990 | |
| 189 | E | A | 0.0000 | |
| 190 | M | A | 0.0000 | |
| 191 | N | A | 0.0000 | |
| 192 | K | A | -1.3131 | |
| 193 | L | A | 0.0000 | |
| 194 | W | A | 0.0000 | |
| 195 | V | A | -0.7904 | |
| 196 | R | A | -1.4649 | |
| 197 | M | A | -1.4029 | |
| 198 | Q | A | -1.9117 | |
| 199 | H | A | -2.2671 | |
| 200 | Q | A | -2.3916 | |
| 201 | G | A | -2.2677 | |
| 202 | H | A | -2.6326 | |
| 203 | S | A | -2.6918 | |
| 204 | R | A | -3.3521 | |
| 205 | D | A | -3.7384 | |
| 206 | R | A | -4.6036 | |
| 207 | E | A | -3.7379 | |
| 208 | K | A | -4.2903 | |
| 209 | R | A | -4.3267 | |
| 210 | E | A | -3.8426 | |
| 211 | R | A | -4.5352 | |
| 212 | E | A | -4.0607 | |
| 213 | R | A | 0.0000 | |
| 214 | Q | A | -3.0913 | |
| 215 | E | A | -3.2836 | |
| 216 | L | A | 0.0000 | |
| 217 | R | A | -0.8672 | |
| 218 | I | A | 1.0963 | |
| 219 | L | A | 0.0000 | |
| 220 | V | A | 0.0000 | |
| 221 | G | A | 0.0000 | |
| 222 | T | A | 0.6064 | |
| 223 | N | A | 0.0000 | |
| 224 | L | A | 0.0000 | |
| 225 | V | A | 0.4860 | |
| 226 | R | A | 0.0000 | |
| 227 | L | A | 0.0000 | |
| 228 | S | A | -0.7904 | |
| 229 | Q | A | -1.7316 | |
| 230 | L | A | 0.0000 | |
| 231 | E | A | -3.0492 | |
| 232 | G | A | 0.0000 | |
| 233 | V | A | 0.0000 | |
| 234 | N | A | -1.9016 | |
| 235 | V | A | -1.6543 | |
| 236 | E | A | -2.6840 | |
| 237 | R | A | -1.8999 | |
| 238 | Y | A | 0.0000 | |
| 239 | K | A | -2.2907 | |
| 240 | Q | A | -1.8754 | |
| 241 | I | A | -0.6920 | |
| 242 | V | A | 0.0000 | |
| 243 | L | A | 0.0000 | |
| 244 | T | A | -0.9239 | |
| 245 | G | A | -0.9352 | |
| 246 | I | A | 0.0000 | |
| 247 | L | A | -0.9521 | |
| 248 | E | A | -2.1370 | |
| 249 | Q | A | -1.7495 | |
| 250 | V | A | 0.0000 | |
| 251 | V | A | -1.8038 | |
| 252 | N | A | -2.4005 | |
| 253 | C | A | -1.8603 | |
| 254 | R | A | -2.3871 | |
| 255 | D | A | -1.4901 | |
| 256 | A | A | -1.1450 | |
| 257 | L | A | -0.7827 | |
| 258 | A | A | 0.0000 | |
| 259 | Q | A | 0.0000 | |
| 260 | E | A | -1.2079 | |
| 261 | Y | A | -0.5174 | |
| 262 | L | A | 0.0000 | |
| 263 | M | A | 0.0000 | |
| 264 | E | A | -1.5867 | |
| 265 | C | A | -0.5435 | |
| 266 | I | A | 0.0000 | |
| 267 | I | A | 0.0000 | |
| 268 | Q | A | -1.2803 | |
| 269 | V | A | -0.3946 | |
| 270 | F | A | 0.0000 | |
| 271 | P | A | -0.5661 | |
| 272 | D | A | 0.0000 | |
| 273 | E | A | -1.4728 | |
| 274 | F | A | -1.1790 | |
| 275 | H | A | 0.0000 | |
| 276 | L | A | 0.0000 | |
| 277 | Q | A | -1.6671 | |
| 278 | T | A | 0.0000 | |
| 279 | L | A | 0.0000 | |
| 280 | N | A | -1.5821 | |
| 281 | P | A | -1.3351 | |
| 282 | F | A | 0.0000 | |
| 283 | L | A | 0.0000 | |
| 284 | R | A | -2.5234 | |
| 285 | A | A | 0.0000 | |
| 286 | C | A | 0.0000 | |
| 287 | A | A | -1.8074 | |
| 288 | E | A | -2.7379 | |
| 289 | L | A | 0.0000 | |
| 290 | H | A | -2.1820 | |
| 291 | Q | A | -2.8517 | |
| 292 | N | A | -2.3674 | |
| 293 | V | A | 0.0000 | |
| 294 | N | A | -1.4584 | |
| 295 | V | A | 0.0000 | |
| 296 | K | A | -0.6080 | |
| 297 | N | A | -1.1442 | |
| 298 | I | A | 0.0000 | |
| 299 | I | A | 0.0000 | |
| 300 | I | A | -0.3694 | |
| 301 | A | A | -1.0894 | |
| 302 | L | A | 0.0000 | |
| 303 | I | A | 0.0000 | |
| 304 | D | A | -1.6733 | |
| 305 | R | A | -0.9873 | |
| 306 | L | A | 0.0000 | |
| 307 | A | A | 0.0000 | |
| 308 | L | A | -0.4460 | |
| 309 | F | A | 0.0000 | |
| 310 | A | A | -1.2322 | |
| 311 | H | A | -2.4294 | |
| 312 | R | A | -3.5329 | |
| 313 | E | A | -4.0550 | |
| 314 | D | A | -3.4820 | |
| 315 | G | A | -2.6275 | |
| 316 | P | A | -1.5692 | |
| 317 | G | A | -1.4755 | |
| 318 | I | A | -0.4919 | |
| 319 | P | A | -0.7273 | |
| 320 | A | A | -1.0955 | |
| 321 | D | A | -2.1200 | |
| 322 | I | A | -1.6837 | |
| 323 | K | A | -2.3846 | |
| 324 | L | A | 0.0000 | |
| 325 | F | A | 0.0000 | |
| 326 | D | A | -2.0473 | |
| 327 | I | A | -1.3708 | |
| 328 | F | A | 0.0000 | |
| 329 | S | A | -1.1370 | |
| 330 | Q | A | -1.6435 | |
| 331 | Q | A | -1.4275 | |
| 332 | V | A | 0.0000 | |
| 333 | A | A | -0.6030 | |
| 334 | T | A | -1.0155 | |
| 335 | V | A | 0.0000 | |
| 336 | I | A | -0.7310 | |
| 337 | Q | A | -1.5328 | |
| 338 | S | A | -1.5609 | |
| 339 | R | A | -2.2041 | |
| 340 | Q | A | -2.6503 | |
| 341 | D | A | -2.7681 | |
| 342 | M | A | -1.6879 | |
| 343 | P | A | -0.9276 | |
| 344 | S | A | -0.5588 | |
| 345 | E | A | -1.0126 | |
| 346 | D | A | -0.7206 | |
| 347 | V | A | -0.1212 | |
| 348 | V | A | 0.0000 | |
| 349 | S | A | -0.7099 | |
| 350 | L | A | 0.0000 | |
| 351 | Q | A | 0.0000 | |
| 352 | V | A | 0.0000 | |
| 353 | S | A | 0.0000 | |
| 354 | L | A | 0.0000 | |
| 355 | I | A | 0.0000 | |
| 356 | N | A | -0.4768 | |
| 357 | L | A | 0.0000 | |
| 358 | A | A | 0.0000 | |
| 359 | M | A | 0.0000 | |
| 360 | K | A | -1.2289 | |
| 361 | C | A | -0.6315 | |
| 362 | Y | A | -0.8021 | |
| 363 | P | A | -1.2908 | |
| 364 | D | A | -2.3652 | |
| 365 | R | A | -1.9464 | |
| 366 | V | A | -1.0302 | |
| 367 | D | A | -2.1564 | |
| 368 | Y | A | -1.5033 | |
| 369 | V | A | 0.0000 | |
| 370 | D | A | -2.0137 | |
| 371 | K | A | -2.0575 | |
| 372 | V | A | 0.0000 | |
| 373 | L | A | 0.0000 | |
| 374 | E | A | -2.4988 | |
| 375 | T | A | -1.6440 | |
| 376 | T | A | 0.0000 | |
| 377 | V | A | -1.9542 | |
| 378 | E | A | -2.8416 | |
| 379 | I | A | -1.7949 | |
| 380 | F | A | 0.0000 | |
| 381 | N | A | -2.6910 | |
| 382 | K | A | -2.8490 | |
| 383 | L | A | -1.7600 | |
| 384 | N | A | -2.0604 | |
| 385 | L | A | -1.5147 | |
| 386 | E | A | -2.2244 | |
| 387 | H | A | -1.9157 | |
| 388 | I | A | 0.0000 | |
| 389 | A | A | -0.8575 | |
| 390 | T | A | -0.8791 | |
| 391 | S | A | -0.5689 | |
| 392 | S | A | -0.7277 | |
| 393 | A | A | -0.8902 | |
| 394 | V | A | -0.9273 | |
| 395 | S | A | 0.0000 | |
| 396 | K | A | -2.2552 | |
| 397 | E | A | -1.7444 | |
| 398 | L | A | 0.0000 | |
| 399 | T | A | -1.4035 | |
| 400 | R | A | -1.9424 | |
| 401 | L | A | 0.0000 | |
| 402 | L | A | 0.0000 | |
| 403 | K | A | -1.2340 | |
| 404 | I | A | -0.8217 | |
| 405 | P | A | 0.0000 | |
| 406 | V | A | 0.0000 | |
| 407 | D | A | -2.0557 | |
| 408 | T | A | -1.2816 | |
| 409 | Y | A | -1.1188 | |
| 410 | N | A | -1.8169 | |
| 411 | N | A | -1.4496 | |
| 412 | I | A | 0.0000 | |
| 413 | L | A | 0.0000 | |
| 414 | T | A | -0.7626 | |
| 415 | V | A | 0.0000 | |
| 416 | L | A | 0.0000 | |
| 417 | K | A | -2.5486 | |
| 418 | L | A | 0.0000 | |
| 419 | K | A | -2.9102 | |
| 420 | H | A | -1.8002 | |
| 421 | F | A | 0.0000 | |
| 422 | H | A | -1.0207 | |
| 423 | P | A | -1.1785 | |
| 424 | L | A | 0.0000 | |
| 425 | F | A | 0.0000 | |
| 426 | E | A | -1.8016 | |
| 427 | Y | A | -1.1392 | |
| 428 | F | A | 0.0000 | |
| 429 | D | A | -0.9853 | |
| 430 | Y | A | -0.5540 | |
| 431 | E | A | -1.7573 | |
| 432 | S | A | 0.0000 | |
| 433 | R | A | -1.1946 | |
| 434 | K | A | -1.2709 | |
| 435 | S | A | -0.9451 | |
| 436 | M | A | 0.0000 | |
| 437 | S | A | 0.0000 | |
| 438 | C | A | 0.5534 | |
| 439 | Y | A | 0.2616 | |
| 440 | V | A | 0.0000 | |
| 441 | L | A | 0.6683 | |
| 442 | S | A | 0.3655 | |
| 443 | N | A | -0.2149 | |
| 444 | V | A | 0.0000 | |
| 445 | L | A | 0.6843 | |
| 446 | D | A | -0.8005 | |
| 447 | Y | A | 0.0488 | |
| 448 | N | A | -1.0288 | |
| 449 | T | A | -0.4656 | |
| 450 | E | A | -0.4807 | |
| 451 | I | A | 1.3926 | |
| 452 | V | A | 0.3651 | |
| 453 | S | A | -0.9282 | |
| 454 | Q | A | -1.9127 | |
| 455 | D | A | -2.6118 | |
| 456 | Q | A | -1.5551 | |
| 457 | V | A | -0.5022 | |
| 458 | D | A | -1.9592 | |
| 459 | S | A | -1.2589 | |
| 460 | I | A | 0.3710 | |
| 461 | M | A | 0.7385 | |
| 462 | N | A | -0.1622 | |
| 463 | L | A | 0.0000 | |
| 464 | V | A | 1.3015 | |
| 465 | S | A | 0.5552 | |
| 466 | T | A | 0.0679 | |
| 467 | L | A | 0.6223 | |
| 468 | I | A | 1.4621 | |
| 469 | Q | A | -0.1395 |
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 | -0.8845 | 2.4397 | View | CSV | PDB |
| 4.5 | -0.9685 | 2.3201 | View | CSV | PDB |
| 5.0 | -1.0722 | 2.1699 | View | CSV | PDB |
| 5.5 | -1.1778 | 2.1451 | View | CSV | PDB |
| 6.0 | -1.2663 | 2.1799 | View | CSV | PDB |
| 6.5 | -1.3254 | 2.2353 | View | CSV | PDB |
| 7.0 | -1.3549 | 2.304 | View | CSV | PDB |
| 7.5 | -1.3639 | 2.3783 | View | CSV | PDB |
| 8.0 | -1.3607 | 2.4547 | View | CSV | PDB |
| 8.5 | -1.3469 | 2.5313 | View | CSV | PDB |
| 9.0 | -1.3199 | 2.6071 | 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