| Chain sequence(s) |
A: MHKLLFSLLSVVSLSFLLFFHGAEARQREAPFPNACHFSQINSLAPAQATKFEAGQMEVWDHMSPELRCAGVTVARITLQPNSIFLPAFFSPPALAYVVQGEGVMGTIASGCPETFAEVEGSSGRGGGGDPGRRFEDMHQKLENFRRGDVFASLAGVSQWWYNRGDSDAVIVIVLDVTNRENQLDQVPRMFQLAGSRTQEEEQPLTWPSGNNAFSGFDPNIIAEAFKINIETAKQLQNQKDNRGNIIRANGPLHFVIPPPREWQQDGIANGIEETYCTAKIHENIDDPERSDHFSTRAGRISTLNSLNLPVLRLVRLNALRGYLYSGGMVLPQWTANAHTVLYVTGGQAKIQVVDDNGQSVFNEQVGQGQIIVIPQGFAVSKTAGETGFEWISFKTNDNAYINTLSGQTSYLRAVPVDVIKASYGVNEEEAKRIKFSQQETMLSMTPSSSS
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage |
A: MHKLLFSLLSVVSLSFLLFFHGAEARQREAPFPNACHFSQINSLAPAQATKFEAGQMEVWDHMSPELRCAGVTVARITLQPNSIFLPAFFSPPALAYVVQGEGVMGTIASGCPETFAEVEGSSGRGGGGDPGRRFEDMHQKLENFRRGDVFASLAGVSQWWYNRGDSDAVIVIVLDVTNRENQLDQVPRMFQLAGSRTQEEEQPLTWPSGNNAFSGFDPNIIAEAFKINIETAKQLQNQKDNRGNIIRANGPLHFVI PPPREWQQDGIANG IEETYCTAKIHENIDDPERSDHFSTRAGRISTLNSLNLPVLRLVRLNALRGYLYSGGMVLPQWTANAHTVLYVTGGQAKIQVVDDNGQSVFNEQVGQGQIIVIPQGFAVSKTAGETGFEWISFKTNDNAYINTLSGQTSYLRAVPVDVIKASYGVNEEEAKRIKFSQQETMLSMTPSSSS(Red indicates removed residues) |
| 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: Running AlphaCutter (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:19)
[INFO] FoldX: Starting FoldX energy minimization (00:00:19)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:11:41)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/69a6c0a28a906c1/tmp/folded.pdb (00:11:41)
[INFO] Main: Simulation completed successfully. (00:17:53)
|
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 | 0.7710 | |
| 2 | H | A | -0.3104 | |
| 3 | K | A | -0.4415 | |
| 4 | L | A | 1.5801 | |
| 5 | L | A | 2.2160 | |
| 6 | F | A | 2.9155 | |
| 7 | S | A | 2.2535 | |
| 8 | L | A | 3.3206 | |
| 9 | L | A | 3.6905 | |
| 10 | S | A | 2.8805 | |
| 11 | V | A | 3.7659 | |
| 12 | V | A | 3.3133 | |
| 13 | S | A | 3.1104 | |
| 14 | L | A | 4.1168 | |
| 15 | S | A | 3.8768 | |
| 16 | F | A | 4.5421 | |
| 17 | L | A | 4.3292 | |
| 18 | L | A | 4.0987 | |
| 19 | F | A | 4.2439 | |
| 20 | F | A | 3.5438 | |
| 21 | H | A | 1.2232 | |
| 22 | G | A | 0.8352 | |
| 23 | A | A | -0.8659 | |
| 24 | E | A | -2.6733 | |
| 25 | A | A | -2.3196 | |
| 26 | R | A | -4.1991 | |
| 27 | Q | A | -4.1032 | |
| 28 | R | A | -4.3655 | |
| 29 | E | A | -3.3878 | |
| 30 | A | A | -1.2668 | |
| 31 | P | A | -0.4862 | |
| 32 | F | A | 0.9041 | |
| 33 | P | A | -0.0925 | |
| 34 | N | A | -1.1610 | |
| 35 | A | A | -0.5584 | |
| 36 | C | A | -0.8314 | |
| 37 | H | A | -1.7279 | |
| 38 | F | A | -1.1760 | |
| 39 | S | A | -0.9878 | |
| 40 | Q | A | -1.6559 | |
| 41 | I | A | 0.0000 | |
| 42 | N | A | -1.6676 | |
| 43 | S | A | -1.0096 | |
| 44 | L | A | -0.3278 | |
| 45 | A | A | -0.2626 | |
| 46 | P | A | -0.3046 | |
| 47 | A | A | -0.0199 | |
| 48 | Q | A | -0.0199 | |
| 49 | A | A | -0.5932 | |
| 50 | T | A | -1.2036 | |
| 51 | K | A | -2.3325 | |
| 52 | F | A | -2.0763 | |
| 53 | E | A | -2.2859 | |
| 54 | A | A | 0.0000 | |
| 55 | G | A | 0.0000 | |
| 56 | Q | A | -1.1824 | |
| 57 | M | A | 0.0000 | |
| 58 | E | A | -0.6057 | |
| 59 | V | A | 0.0000 | |
| 60 | W | A | 0.0000 | |
| 61 | D | A | -0.3582 | |
| 62 | H | A | -0.2433 | |
| 63 | M | A | 0.0901 | |
| 64 | S | A | -0.5385 | |
| 65 | P | A | -0.8339 | |
| 66 | E | A | 0.0000 | |
| 67 | L | A | 0.0000 | |
| 68 | R | A | -1.1134 | |
| 69 | C | A | 0.0000 | |
| 70 | A | A | 0.0000 | |
| 71 | G | A | 0.0000 | |
| 72 | V | A | 0.0000 | |
| 73 | T | A | 0.0000 | |
| 74 | V | A | 0.0000 | |
| 75 | A | A | 0.0000 | |
| 76 | R | A | -0.3049 | |
| 77 | I | A | 0.0000 | |
| 78 | T | A | -0.6595 | |
| 79 | L | A | 0.0000 | |
| 80 | Q | A | -1.7834 | |
| 81 | P | A | -2.1234 | |
| 82 | N | A | -1.8169 | |
| 83 | S | A | 0.0000 | |
| 84 | I | A | -0.3299 | |
| 85 | F | A | 0.0000 | |
| 86 | L | A | 0.3733 | |
| 87 | P | A | 0.5722 | |
| 88 | A | A | 0.0000 | |
| 89 | F | A | 0.7222 | |
| 90 | F | A | 0.0000 | |
| 91 | S | A | 0.0000 | |
| 92 | P | A | 0.0000 | |
| 93 | P | A | 0.0000 | |
| 94 | A | A | 0.0000 | |
| 95 | L | A | 0.0000 | |
| 96 | A | A | 0.0000 | |
| 97 | Y | A | 0.0000 | |
| 98 | V | A | 0.0000 | |
| 99 | V | A | -0.9681 | |
| 100 | Q | A | -1.9443 | |
| 101 | G | A | -2.8770 | |
| 102 | E | A | -3.8836 | |
| 103 | G | A | 0.0000 | |
| 104 | V | A | 0.0000 | |
| 105 | M | A | 0.0000 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.3790 | |
| 108 | I | A | 0.5684 | |
| 109 | A | A | 0.1934 | |
| 110 | S | A | -0.1731 | |
| 111 | G | A | -0.5531 | |
| 112 | C | A | 0.0000 | |
| 113 | P | A | -1.0973 | |
| 114 | E | A | -2.0361 | |
| 115 | T | A | -1.1477 | |
| 116 | F | A | -0.2698 | |
| 117 | A | A | -0.8446 | |
| 118 | E | A | -1.7668 | |
| 119 | V | A | -2.3006 | |
| 120 | E | A | -3.5359 | |
| 121 | G | A | -2.4049 | |
| 122 | S | A | -1.4944 | |
| 123 | S | A | -1.2761 | |
| 124 | G | A | -2.0084 | |
| 125 | R | A | -2.5317 | |
| 126 | G | A | -1.8328 | |
| 127 | G | A | -1.6623 | |
| 128 | G | A | -1.4237 | |
| 129 | G | A | -1.7656 | |
| 130 | D | A | -2.8583 | |
| 131 | P | A | -2.0321 | |
| 132 | G | A | -2.3693 | |
| 133 | R | A | -3.6155 | |
| 134 | R | A | -3.6558 | |
| 135 | F | A | -2.4879 | |
| 136 | E | A | -3.4778 | |
| 137 | D | A | -2.8027 | |
| 138 | M | A | -1.2055 | |
| 139 | H | A | -0.8649 | |
| 140 | Q | A | -1.0178 | |
| 141 | K | A | -0.8928 | |
| 142 | L | A | -0.3605 | |
| 143 | E | A | -1.3914 | |
| 144 | N | A | -2.3513 | |
| 145 | F | A | 0.0000 | |
| 146 | R | A | -3.6240 | |
| 147 | R | A | -2.9027 | |
| 148 | G | A | 0.0000 | |
| 149 | D | A | 0.0000 | |
| 150 | V | A | 0.0000 | |
| 151 | F | A | 0.0000 | |
| 152 | A | A | 0.0000 | |
| 153 | S | A | 0.0000 | |
| 154 | L | A | 0.4437 | |
| 155 | A | A | -0.1514 | |
| 156 | G | A | -0.0262 | |
| 157 | V | A | 0.5471 | |
| 158 | S | A | 0.7244 | |
| 159 | Q | A | 0.0000 | |
| 160 | W | A | 0.4440 | |
| 161 | W | A | 0.0000 | |
| 162 | Y | A | 0.0000 | |
| 163 | N | A | 0.0000 | |
| 164 | R | A | -2.8406 | |
| 165 | G | A | -2.8225 | |
| 166 | D | A | -2.8311 | |
| 167 | S | A | -2.2277 | |
| 168 | D | A | -2.0809 | |
| 169 | A | A | 0.0000 | |
| 170 | V | A | -0.9201 | |
| 171 | I | A | 0.0000 | |
| 172 | V | A | 0.0000 | |
| 173 | I | A | 0.0000 | |
| 174 | V | A | 0.0000 | |
| 175 | L | A | 0.0000 | |
| 176 | D | A | 0.0000 | |
| 177 | V | A | 0.0000 | |
| 178 | T | A | -1.3028 | |
| 179 | N | A | 0.0000 | |
| 180 | R | A | -1.9449 | |
| 181 | E | A | -1.1686 | |
| 182 | N | A | -1.2571 | |
| 183 | Q | A | -2.0851 | |
| 184 | L | A | -0.2802 | |
| 185 | D | A | -1.7322 | |
| 186 | Q | A | -1.1499 | |
| 187 | V | A | 0.2287 | |
| 188 | P | A | 0.0000 | |
| 189 | R | A | -0.2025 | |
| 190 | M | A | 0.0000 | |
| 191 | F | A | 0.4788 | |
| 192 | Q | A | 0.0000 | |
| 193 | L | A | 0.6434 | |
| 194 | A | A | 0.1017 | |
| 195 | G | A | 0.0000 | |
| 196 | S | A | 0.0000 | |
| 197 | R | A | -2.8367 | |
| 198 | T | A | -3.0693 | |
| 199 | Q | A | -3.0583 | |
| 200 | E | A | -3.6187 | |
| 201 | E | A | -3.0770 | |
| 202 | E | A | -2.9905 | |
| 203 | Q | A | -1.9767 | |
| 204 | P | A | -0.4606 | |
| 205 | L | A | 0.8551 | |
| 206 | T | A | 0.0000 | |
| 207 | W | A | 0.0000 | |
| 208 | P | A | -0.4390 | |
| 209 | S | A | 0.0000 | |
| 210 | G | A | -1.1132 | |
| 211 | N | A | -1.8443 | |
| 212 | N | A | 0.0000 | |
| 213 | A | A | 0.3632 | |
| 214 | F | A | 0.0322 | |
| 215 | S | A | -0.6767 | |
| 216 | G | A | -0.1279 | |
| 217 | F | A | 0.9709 | |
| 218 | D | A | -0.7352 | |
| 219 | P | A | -1.1523 | |
| 220 | N | A | -1.1092 | |
| 221 | I | A | 0.8315 | |
| 222 | I | A | 0.0000 | |
| 223 | A | A | -1.1533 | |
| 224 | E | A | -1.4396 | |
| 225 | A | A | 0.0472 | |
| 226 | F | A | 0.7412 | |
| 227 | K | A | -1.0777 | |
| 228 | I | A | -0.8384 | |
| 229 | N | A | -1.8595 | |
| 230 | I | A | -1.5633 | |
| 231 | E | A | -2.4510 | |
| 232 | T | A | -1.3005 | |
| 233 | A | A | 0.0000 | |
| 234 | K | A | -2.4969 | |
| 235 | Q | A | -2.2465 | |
| 236 | L | A | -0.6240 | |
| 237 | Q | A | 0.0000 | |
| 238 | N | A | -2.2997 | |
| 239 | Q | A | -2.9932 | |
| 240 | K | A | -3.2319 | |
| 241 | D | A | -2.9107 | |
| 242 | N | A | -3.2409 | |
| 243 | R | A | -2.6813 | |
| 244 | G | A | 0.0000 | |
| 245 | N | A | 0.0000 | |
| 246 | I | A | 0.0000 | |
| 247 | I | A | -1.2188 | |
| 248 | R | A | -1.8907 | |
| 249 | A | A | 0.0000 | |
| 250 | N | A | -1.6616 | |
| 251 | G | A | -1.2062 | |
| 252 | P | A | -1.1571 | |
| 253 | L | A | -0.6702 | |
| 254 | H | A | -0.3915 | |
| 255 | F | A | 0.3682 | |
| 256 | V | A | 0.4161 | |
| 257 | I | A | 1.8911 | |
| 272 | I | A | 1.0520 | |
| 273 | E | A | -1.3469 | |
| 274 | E | A | -1.6263 | |
| 275 | T | A | -0.1811 | |
| 276 | Y | A | 1.0015 | |
| 277 | C | A | -0.2675 | |
| 278 | T | A | -0.7335 | |
| 279 | A | A | -0.6574 | |
| 280 | K | A | -1.3641 | |
| 281 | I | A | -0.6131 | |
| 282 | H | A | -0.9661 | |
| 283 | E | A | -0.8490 | |
| 284 | N | A | -1.4054 | |
| 285 | I | A | 0.0000 | |
| 286 | D | A | -1.5859 | |
| 287 | D | A | -2.1135 | |
| 288 | P | A | -1.8647 | |
| 289 | E | A | -2.9175 | |
| 290 | R | A | -3.0838 | |
| 291 | S | A | -1.9987 | |
| 292 | D | A | -2.1544 | |
| 293 | H | A | -0.4637 | |
| 294 | F | A | 0.6909 | |
| 295 | S | A | 0.1926 | |
| 296 | T | A | -0.4155 | |
| 297 | R | A | -1.4992 | |
| 298 | A | A | 0.0000 | |
| 299 | G | A | 0.0000 | |
| 300 | R | A | 0.0000 | |
| 301 | I | A | 0.0000 | |
| 302 | S | A | 0.0000 | |
| 303 | T | A | -0.6914 | |
| 304 | L | A | 0.0000 | |
| 305 | N | A | -0.2943 | |
| 306 | S | A | -0.1913 | |
| 307 | L | A | 0.8101 | |
| 308 | N | A | -0.3214 | |
| 309 | L | A | 0.0000 | |
| 310 | P | A | -0.4253 | |
| 311 | V | A | 0.0000 | |
| 312 | L | A | 0.0000 | |
| 313 | R | A | -0.9270 | |
| 314 | L | A | 0.3281 | |
| 315 | V | A | 0.0000 | |
| 316 | R | A | -0.9915 | |
| 317 | L | A | 0.0000 | |
| 318 | N | A | 0.0000 | |
| 319 | A | A | 0.0000 | |
| 320 | L | A | 0.1186 | |
| 321 | R | A | 0.0000 | |
| 322 | G | A | 0.0000 | |
| 323 | Y | A | 0.2769 | |
| 324 | L | A | 0.0000 | |
| 325 | Y | A | -0.1205 | |
| 326 | S | A | -0.8772 | |
| 327 | G | A | -0.7035 | |
| 328 | G | A | 0.0000 | |
| 329 | M | A | 0.0551 | |
| 330 | V | A | 0.0000 | |
| 331 | L | A | 0.0000 | |
| 332 | P | A | -0.0231 | |
| 333 | Q | A | 0.0000 | |
| 334 | W | A | 0.3373 | |
| 335 | T | A | 0.0000 | |
| 336 | A | A | 0.1115 | |
| 337 | N | A | -0.1814 | |
| 338 | A | A | 0.0000 | |
| 339 | H | A | -0.5643 | |
| 340 | T | A | 0.0000 | |
| 341 | V | A | 0.0000 | |
| 342 | L | A | 0.0000 | |
| 343 | Y | A | 0.0000 | |
| 344 | V | A | 0.0000 | |
| 345 | T | A | 0.0000 | |
| 346 | G | A | -0.9075 | |
| 347 | G | A | -1.2013 | |
| 348 | Q | A | -2.1048 | |
| 349 | A | A | 0.0000 | |
| 350 | K | A | -3.3217 | |
| 351 | I | A | 0.0000 | |
| 352 | Q | A | -2.0744 | |
| 353 | V | A | 0.0000 | |
| 354 | V | A | -1.2968 | |
| 355 | D | A | -2.1927 | |
| 356 | D | A | -2.9666 | |
| 357 | N | A | -2.7601 | |
| 358 | G | A | -2.1989 | |
| 359 | Q | A | -2.3037 | |
| 360 | S | A | -1.6859 | |
| 361 | V | A | 0.0000 | |
| 362 | F | A | 0.0000 | |
| 363 | N | A | -3.2320 | |
| 364 | E | A | -3.8310 | |
| 365 | Q | A | -3.3329 | |
| 366 | V | A | 0.0000 | |
| 367 | G | A | -1.6061 | |
| 368 | Q | A | -1.6240 | |
| 369 | G | A | -0.8434 | |
| 370 | Q | A | -0.7021 | |
| 371 | I | A | 0.0000 | |
| 372 | I | A | 0.0000 | |
| 373 | V | A | 0.0000 | |
| 374 | I | A | 0.0000 | |
| 375 | P | A | 0.0000 | |
| 376 | Q | A | -0.8751 | |
| 377 | G | A | -0.8601 | |
| 378 | F | A | 0.0000 | |
| 379 | A | A | -0.3469 | |
| 380 | V | A | 0.0000 | |
| 381 | S | A | -0.5672 | |
| 382 | K | A | 0.0000 | |
| 383 | T | A | -0.9970 | |
| 384 | A | A | 0.0000 | |
| 385 | G | A | -1.6846 | |
| 386 | E | A | -2.0041 | |
| 387 | T | A | -1.1733 | |
| 388 | G | A | -0.7413 | |
| 389 | F | A | 0.0000 | |
| 390 | E | A | -0.6740 | |
| 391 | W | A | 0.0000 | |
| 392 | I | A | 0.0000 | |
| 393 | S | A | 0.0000 | |
| 394 | F | A | 0.0000 | |
| 395 | K | A | 0.0000 | |
| 396 | T | A | -0.5580 | |
| 397 | N | A | -0.8184 | |
| 398 | D | A | 0.0000 | |
| 399 | N | A | -0.3090 | |
| 400 | A | A | 0.1863 | |
| 401 | Y | A | 1.3260 | |
| 402 | I | A | 0.9720 | |
| 403 | N | A | 0.4499 | |
| 404 | T | A | 0.0000 | |
| 405 | L | A | 0.5330 | |
| 406 | S | A | -0.0704 | |
| 407 | G | A | 0.0000 | |
| 408 | Q | A | -1.1109 | |
| 409 | T | A | -0.5951 | |
| 410 | S | A | 0.0000 | |
| 411 | Y | A | 0.6629 | |
| 412 | L | A | 0.5665 | |
| 413 | R | A | -0.3832 | |
| 414 | A | A | -0.0473 | |
| 415 | V | A | 0.1717 | |
| 416 | P | A | -0.4805 | |
| 417 | V | A | -1.3767 | |
| 418 | D | A | -1.8449 | |
| 419 | V | A | 0.1981 | |
| 420 | I | A | 0.0000 | |
| 421 | K | A | -1.6893 | |
| 422 | A | A | -0.4737 | |
| 423 | S | A | 0.1572 | |
| 424 | Y | A | 0.5647 | |
| 425 | G | A | -0.4321 | |
| 426 | V | A | -1.5019 | |
| 427 | N | A | -3.2988 | |
| 428 | E | A | -4.0260 | |
| 429 | E | A | -4.0627 | |
| 430 | E | A | -3.3876 | |
| 431 | A | A | 0.0000 | |
| 432 | K | A | -3.0396 | |
| 433 | R | A | -2.8701 | |
| 434 | I | A | -0.9578 | |
| 435 | K | A | -0.8662 | |
| 436 | F | A | -0.6092 | |
| 437 | S | A | -1.0347 | |
| 438 | Q | A | -1.2278 | |
| 439 | Q | A | -1.6954 | |
| 440 | E | A | -1.4936 | |
| 441 | T | A | -0.7883 | |
| 442 | M | A | 0.0000 | |
| 443 | L | A | 0.0000 | |
| 444 | S | A | 0.0000 | |
| 445 | M | A | -0.4241 | |
| 446 | T | A | -0.2231 | |
| 447 | P | A | -0.4654 | |
| 448 | S | A | -0.4699 | |
| 449 | S | A | -0.6255 | |
| 450 | S | A | -0.6962 | |
| 451 | S | A | -0.4371 |
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 | -0.228 | 8.0473 | View | CSV | PDB |
| 4.5 | -0.2898 | 8.0508 | View | CSV | PDB |
| 5.0 | -0.3705 | 8.0613 | View | CSV | PDB |
| 5.5 | -0.4569 | 8.0895 | View | CSV | PDB |
| 6.0 | -0.5336 | 8.1491 | View | CSV | PDB |
| 6.5 | -0.5883 | 8.2353 | View | CSV | PDB |
| 7.0 | -0.6169 | 8.3142 | View | CSV | PDB |
| 7.5 | -0.6255 | 8.3608 | View | CSV | PDB |
| 8.0 | -0.6228 | 8.3805 | View | CSV | PDB |
| 8.5 | -0.6126 | 8.3875 | View | CSV | PDB |
| 9.0 | -0.5954 | 8.3898 | 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