| Chain sequence(s) |
A: MTRFAVLPLSVLLLVLLFLCTESLAKSEESEEYDVAVPSCCGFSSPLLIKKDQWKPIFETKFGQISTVQIGNGCGGMGPYKIHSITLEPNTILLPLLLHSDMVFFVDSGSGILNWVDEEAKSTEIRLGDVYRLRPGSVFYLQSKPVDIFLGTKLKLYAIFSNNDECLHDPCFGAYSSITDLMFGFDETILQSAFGVPEGIIELMRNRTKPPLIVSETLCTPGVANTWQLQPRLLKLFAGSADLVDNKKKKEKKEKKEKVKKAKTFNVFESEPDFESPYGRTITINRKDLKVLKGSMVGVSMVNLTQGSMMGPHWNPWACEISIVLKGAGMVRVLRSSISSNTSSECKNVRFKVEEGDIFAVPRLHPMAQMSFNNDSLVFVGFTTSAKNNEPQFLAGEDSALRMLDRQVLAASLNVSSVTIDGLLGAQKEAVILECHSCAEGEIEKLKVEIERKKIDDERKRRHDERKKEEEEAKREEEERRKREEEEEKKRWPPQQPPQEEELRERQLPMEKEWEMEGEEES
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage |
A: MTRFAVLPLSVLLLVLLFLCTESLAKSEESEEYDVAVPSCCGFSSPLLIKKDQWKPIFETKFGQISTVQIGNGCGGMGPYKIHSITLEPNTILLPLLLHSDMVFFVDSGSGILNWVDEEAKSTEIRLGDVYRLRPGSVFYLQSKPVDIFLGTKLKLYAIFSNNDECLHDPCFGAYSSITDLMFGFDETILQSAFGVPEGIIELMRNRTKPPLIVSETLCTPGVANTWQLQPRLLKLFAGS ADLVDNKKKKEKKEKKEK VKKAKTFNVFESEPDFESPYGRTITINRKDLKVLKGSMVGVSMVNLTQGSMMGPHWNPWACEISIVLKGAGMVRVLRSSISSNTSSECKNVRFKVEEGDIFAVPRLHPMAQMSFNNDSLVFVGFTTSAKNNEPQFLAGEDSALRMLDRQVLAASLNVSSVTIDGLLGAQKEAVILECHSCAEGEIEKLKVEIERKKIDDERKRRHDERKKEEEEAKREEEERRKREEEEEKKRWPPQQPPQEEELRERQLPMEKEWEMEGEEES (Red indicates removed residues) |
| Dynamic mode | No |
| Automated mutations | No |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:02)
[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: Running AlphaCutter (00:00:03)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:29)
[INFO] FoldX: Starting FoldX energy minimization (00:00:29)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:17:30)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/709db6b150c6674/tmp/folded.pdb (00:17:30)
[INFO] Main: Simulation completed successfully. (00:22:01)
|
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 | 0.7719 | |
| 2 | T | A | 0.0579 | |
| 3 | R | A | -0.4110 | |
| 4 | F | A | 1.8390 | |
| 5 | A | A | 1.6870 | |
| 6 | V | A | 2.9140 | |
| 7 | L | A | 3.0843 | |
| 8 | P | A | 2.1204 | |
| 9 | L | A | 2.9144 | |
| 10 | S | A | 2.3170 | |
| 11 | V | A | 3.3714 | |
| 12 | L | A | 3.6886 | |
| 13 | L | A | 4.0951 | |
| 14 | L | A | 4.8959 | |
| 15 | V | A | 4.8047 | |
| 16 | L | A | 4.5637 | |
| 17 | L | A | 4.7850 | |
| 18 | F | A | 4.4786 | |
| 19 | L | A | 3.8835 | |
| 20 | C | A | 3.0738 | |
| 21 | T | A | 1.5300 | |
| 22 | E | A | 0.0684 | |
| 23 | S | A | 0.0646 | |
| 24 | L | A | 0.2951 | |
| 25 | A | A | -1.2570 | |
| 26 | K | A | -2.6802 | |
| 27 | S | A | -2.7637 | |
| 28 | E | A | -3.8734 | |
| 29 | E | A | -4.1024 | |
| 30 | S | A | -3.6755 | |
| 31 | E | A | -4.2315 | |
| 32 | E | A | -4.0631 | |
| 33 | Y | A | -2.4426 | |
| 34 | D | A | -2.5934 | |
| 35 | V | A | -0.8345 | |
| 36 | A | A | -0.2544 | |
| 37 | V | A | 0.0000 | |
| 38 | P | A | -0.7393 | |
| 39 | S | A | -0.7487 | |
| 40 | C | A | 0.0000 | |
| 41 | C | A | -0.4290 | |
| 42 | G | A | -0.6803 | |
| 43 | F | A | 0.0000 | |
| 44 | S | A | -0.9410 | |
| 45 | S | A | 0.0000 | |
| 46 | P | A | -0.2327 | |
| 47 | L | A | 0.0000 | |
| 48 | L | A | 0.0000 | |
| 49 | I | A | 0.0000 | |
| 50 | K | A | -2.6637 | |
| 51 | K | A | -3.6916 | |
| 52 | D | A | -3.5485 | |
| 53 | Q | A | -3.1406 | |
| 54 | W | A | 0.0000 | |
| 55 | K | A | -2.2818 | |
| 56 | P | A | -1.0034 | |
| 57 | I | A | 0.6253 | |
| 58 | F | A | -0.2256 | |
| 59 | E | A | -1.8707 | |
| 60 | T | A | -1.7547 | |
| 61 | K | A | -2.1407 | |
| 62 | F | A | -1.3141 | |
| 63 | G | A | -1.4888 | |
| 64 | Q | A | -1.2981 | |
| 65 | I | A | 0.0000 | |
| 66 | S | A | 0.0000 | |
| 67 | T | A | 0.0000 | |
| 68 | V | A | 0.0000 | |
| 69 | Q | A | -1.5814 | |
| 70 | I | A | 0.0000 | |
| 71 | G | A | -1.2693 | |
| 72 | N | A | -1.8128 | |
| 73 | G | A | -1.2168 | |
| 74 | C | A | 0.0000 | |
| 75 | G | A | -0.7398 | |
| 76 | G | A | -1.0109 | |
| 77 | M | A | -0.8040 | |
| 78 | G | A | -1.5345 | |
| 79 | P | A | -1.3605 | |
| 80 | Y | A | 0.0000 | |
| 81 | K | A | -1.0457 | |
| 82 | I | A | 0.0000 | |
| 83 | H | A | 0.0000 | |
| 84 | S | A | -0.4118 | |
| 85 | I | A | 0.0000 | |
| 86 | T | A | -1.0141 | |
| 87 | L | A | 0.0000 | |
| 88 | E | A | -1.6279 | |
| 89 | P | A | -1.0055 | |
| 90 | N | A | -0.6470 | |
| 91 | T | A | 0.0000 | |
| 92 | I | A | 0.0000 | |
| 93 | L | A | 0.0000 | |
| 94 | L | A | 0.3184 | |
| 95 | P | A | 0.4122 | |
| 96 | L | A | 0.0000 | |
| 97 | L | A | 0.4013 | |
| 98 | L | A | 0.0000 | |
| 99 | H | A | -0.1495 | |
| 100 | S | A | 0.0000 | |
| 101 | D | A | -1.2728 | |
| 102 | M | A | 0.0000 | |
| 103 | V | A | 0.0000 | |
| 104 | F | A | 0.0000 | |
| 105 | F | A | 0.0000 | |
| 106 | V | A | 0.0000 | |
| 107 | D | A | -0.2819 | |
| 108 | S | A | -0.3960 | |
| 109 | G | A | -0.6886 | |
| 110 | S | A | -1.0498 | |
| 111 | G | A | 0.0000 | |
| 112 | I | A | 0.0000 | |
| 113 | L | A | 0.0000 | |
| 114 | N | A | 0.0000 | |
| 115 | W | A | 0.0000 | |
| 116 | V | A | 0.0000 | |
| 117 | D | A | -3.1405 | |
| 118 | E | A | -3.0581 | |
| 119 | E | A | -2.5218 | |
| 120 | A | A | 0.0000 | |
| 121 | K | A | -1.4349 | |
| 122 | S | A | -1.0385 | |
| 123 | T | A | 0.0000 | |
| 124 | E | A | -2.2694 | |
| 125 | I | A | 0.0000 | |
| 126 | R | A | -0.8329 | |
| 127 | L | A | 0.6624 | |
| 128 | G | A | 0.0000 | |
| 129 | D | A | 0.0000 | |
| 130 | V | A | 0.0000 | |
| 131 | Y | A | 0.0000 | |
| 132 | R | A | -1.1927 | |
| 133 | L | A | 0.0000 | |
| 134 | R | A | -2.4841 | |
| 135 | P | A | -1.4487 | |
| 136 | G | A | -1.2285 | |
| 137 | S | A | 0.0000 | |
| 138 | V | A | -0.2211 | |
| 139 | F | A | 0.0000 | |
| 140 | Y | A | 0.0000 | |
| 141 | L | A | 0.0000 | |
| 142 | Q | A | 0.0000 | |
| 143 | S | A | 0.0000 | |
| 144 | K | A | -1.3575 | |
| 145 | P | A | -0.4688 | |
| 146 | V | A | 1.0485 | |
| 147 | D | A | 0.6680 | |
| 148 | I | A | 2.8235 | |
| 149 | F | A | 3.2291 | |
| 150 | L | A | 2.4335 | |
| 151 | G | A | 0.8065 | |
| 152 | T | A | -0.1207 | |
| 153 | K | A | -1.3904 | |
| 154 | L | A | 0.0000 | |
| 155 | K | A | -0.9680 | |
| 156 | L | A | 0.0000 | |
| 157 | Y | A | 0.0000 | |
| 158 | A | A | 0.0000 | |
| 159 | I | A | 0.0000 | |
| 160 | F | A | 0.0000 | |
| 161 | S | A | -0.9189 | |
| 162 | N | A | -1.6873 | |
| 163 | N | A | -2.5838 | |
| 164 | D | A | -3.0006 | |
| 165 | E | A | -2.7534 | |
| 166 | C | A | -0.8207 | |
| 167 | L | A | 0.0285 | |
| 168 | H | A | -1.2833 | |
| 169 | D | A | -1.6820 | |
| 170 | P | A | -0.3933 | |
| 171 | C | A | 0.7733 | |
| 172 | F | A | 1.7405 | |
| 173 | G | A | 0.5601 | |
| 174 | A | A | 0.0000 | |
| 175 | Y | A | 0.3956 | |
| 176 | S | A | 0.1801 | |
| 177 | S | A | -0.1471 | |
| 178 | I | A | 0.1692 | |
| 179 | T | A | -0.5960 | |
| 180 | D | A | -1.3210 | |
| 181 | L | A | 0.2346 | |
| 182 | M | A | 0.4073 | |
| 183 | F | A | 0.1444 | |
| 184 | G | A | 0.0207 | |
| 185 | F | A | 1.1455 | |
| 186 | D | A | -0.4572 | |
| 187 | E | A | -1.9206 | |
| 188 | T | A | -0.5257 | |
| 189 | I | A | 1.3244 | |
| 190 | L | A | 0.0000 | |
| 191 | Q | A | -0.4542 | |
| 192 | S | A | 0.1892 | |
| 193 | A | A | 1.1653 | |
| 194 | F | A | 1.9739 | |
| 195 | G | A | 0.3473 | |
| 196 | V | A | 0.1577 | |
| 197 | P | A | -0.9948 | |
| 198 | E | A | -2.4169 | |
| 199 | G | A | -1.1170 | |
| 200 | I | A | 0.1875 | |
| 201 | I | A | 0.0000 | |
| 202 | E | A | -2.4634 | |
| 203 | L | A | -0.3131 | |
| 204 | M | A | -1.1203 | |
| 205 | R | A | -2.1952 | |
| 206 | N | A | -2.5493 | |
| 207 | R | A | -2.9774 | |
| 208 | T | A | -2.2093 | |
| 209 | K | A | -2.7330 | |
| 210 | P | A | -1.1535 | |
| 211 | P | A | -0.5702 | |
| 212 | L | A | -0.1955 | |
| 213 | I | A | 0.0000 | |
| 214 | V | A | 0.0000 | |
| 215 | S | A | 0.1686 | |
| 216 | E | A | 0.0000 | |
| 217 | T | A | 0.8126 | |
| 218 | L | A | 1.6642 | |
| 219 | C | A | 1.2859 | |
| 220 | T | A | 0.7373 | |
| 221 | P | A | 0.3536 | |
| 222 | G | A | 0.0585 | |
| 223 | V | A | 0.8700 | |
| 224 | A | A | -0.0095 | |
| 225 | N | A | -0.8851 | |
| 226 | T | A | -0.2801 | |
| 227 | W | A | -0.1377 | |
| 228 | Q | A | -1.3587 | |
| 229 | L | A | -0.8789 | |
| 230 | Q | A | -1.0993 | |
| 231 | P | A | -1.2649 | |
| 232 | R | A | -2.0090 | |
| 233 | L | A | -0.5670 | |
| 234 | L | A | 0.0000 | |
| 235 | K | A | -1.1834 | |
| 236 | L | A | 0.6250 | |
| 237 | F | A | 0.0119 | |
| 238 | A | A | -1.0367 | |
| 239 | G | A | -0.5410 | |
| 240 | S | A | -0.4455 | |
| 259 | V | A | 0.2673 | |
| 260 | K | A | -2.0682 | |
| 261 | K | A | -2.7554 | |
| 262 | A | A | -2.0543 | |
| 263 | K | A | -2.4917 | |
| 264 | T | A | -1.3552 | |
| 265 | F | A | -0.4010 | |
| 266 | N | A | 0.0000 | |
| 267 | V | A | 0.0000 | |
| 268 | F | A | 0.5117 | |
| 269 | E | A | -1.4925 | |
| 270 | S | A | -1.5535 | |
| 271 | E | A | -2.7360 | |
| 272 | P | A | -2.4279 | |
| 273 | D | A | -2.6685 | |
| 274 | F | A | -1.9820 | |
| 275 | E | A | -2.6741 | |
| 276 | S | A | -1.3188 | |
| 277 | P | A | -0.9391 | |
| 278 | Y | A | -1.0776 | |
| 279 | G | A | 0.0000 | |
| 280 | R | A | -2.0702 | |
| 281 | T | A | -1.5375 | |
| 282 | I | A | 0.0000 | |
| 283 | T | A | -1.1659 | |
| 284 | I | A | 0.0000 | |
| 285 | N | A | -2.7226 | |
| 286 | R | A | -4.1626 | |
| 287 | K | A | -4.2638 | |
| 288 | D | A | -3.6408 | |
| 289 | L | A | 0.0000 | |
| 290 | K | A | -3.6048 | |
| 291 | V | A | -2.2545 | |
| 292 | L | A | 0.0000 | |
| 293 | K | A | -3.5273 | |
| 294 | G | A | -2.1915 | |
| 295 | S | A | 0.0000 | |
| 296 | M | A | -0.6984 | |
| 297 | V | A | 0.0000 | |
| 298 | G | A | 0.0000 | |
| 299 | V | A | 0.0000 | |
| 300 | S | A | -0.0862 | |
| 301 | M | A | 0.0000 | |
| 302 | V | A | 0.0000 | |
| 303 | N | A | -0.9991 | |
| 304 | L | A | 0.0000 | |
| 305 | T | A | -1.2709 | |
| 306 | Q | A | -2.2521 | |
| 307 | G | A | 0.0000 | |
| 308 | S | A | 0.0000 | |
| 309 | M | A | -0.5233 | |
| 310 | M | A | 0.0000 | |
| 311 | G | A | 0.0000 | |
| 312 | P | A | 0.0764 | |
| 313 | H | A | 0.0000 | |
| 314 | W | A | -0.0078 | |
| 315 | N | A | 0.0000 | |
| 316 | P | A | -0.3393 | |
| 317 | W | A | 0.0242 | |
| 318 | A | A | 0.0000 | |
| 319 | C | A | 0.0000 | |
| 320 | E | A | -0.2608 | |
| 321 | I | A | 0.0000 | |
| 322 | S | A | 0.0000 | |
| 323 | I | A | 0.0000 | |
| 324 | V | A | 0.0000 | |
| 325 | L | A | -1.2583 | |
| 326 | K | A | -2.2009 | |
| 327 | G | A | -1.9339 | |
| 328 | A | A | 0.0000 | |
| 329 | G | A | 0.0000 | |
| 330 | M | A | 0.0000 | |
| 331 | V | A | 0.0000 | |
| 332 | R | A | -1.1039 | |
| 333 | V | A | 0.0000 | |
| 334 | L | A | -0.7811 | |
| 335 | R | A | -0.7294 | |
| 336 | S | A | -0.0573 | |
| 337 | S | A | 0.4198 | |
| 338 | I | A | 1.6052 | |
| 339 | S | A | 0.2263 | |
| 340 | S | A | -0.7483 | |
| 341 | N | A | -1.2793 | |
| 342 | T | A | -0.9289 | |
| 343 | S | A | -1.4325 | |
| 344 | S | A | -1.8088 | |
| 345 | E | A | -2.4090 | |
| 346 | C | A | 0.0000 | |
| 347 | K | A | -2.9262 | |
| 348 | N | A | -2.2616 | |
| 349 | V | A | 0.0000 | |
| 350 | R | A | -1.3030 | |
| 351 | F | A | 0.0000 | |
| 352 | K | A | -0.8964 | |
| 353 | V | A | 0.0000 | |
| 354 | E | A | -2.5108 | |
| 355 | E | A | -2.7223 | |
| 356 | G | A | -2.1209 | |
| 357 | D | A | 0.0000 | |
| 358 | I | A | 0.0000 | |
| 359 | F | A | 0.0000 | |
| 360 | A | A | 0.0000 | |
| 361 | V | A | 0.0000 | |
| 362 | P | A | 0.0000 | |
| 363 | R | A | -0.4444 | |
| 364 | L | A | 0.2758 | |
| 365 | H | A | 0.0000 | |
| 366 | P | A | -0.1288 | |
| 367 | M | A | 0.0000 | |
| 368 | A | A | 0.0000 | |
| 369 | Q | A | 0.0000 | |
| 370 | M | A | 0.0000 | |
| 371 | S | A | 0.0000 | |
| 372 | F | A | -1.2255 | |
| 373 | N | A | -1.7906 | |
| 374 | N | A | -2.0650 | |
| 375 | D | A | -1.9601 | |
| 376 | S | A | -1.4826 | |
| 377 | L | A | 0.0000 | |
| 378 | V | A | 0.0000 | |
| 379 | F | A | 0.0000 | |
| 380 | V | A | 0.0000 | |
| 381 | G | A | 0.0000 | |
| 382 | F | A | 0.0000 | |
| 383 | T | A | 0.0000 | |
| 384 | T | A | 0.0000 | |
| 385 | S | A | 0.0000 | |
| 386 | A | A | 0.0000 | |
| 387 | K | A | -2.2050 | |
| 388 | N | A | -2.1038 | |
| 389 | N | A | -1.5592 | |
| 390 | E | A | -2.2050 | |
| 391 | P | A | -0.9553 | |
| 392 | Q | A | -0.7088 | |
| 393 | F | A | 0.0000 | |
| 394 | L | A | 0.2569 | |
| 395 | A | A | -0.3830 | |
| 396 | G | A | 0.0000 | |
| 397 | E | A | -2.8207 | |
| 398 | D | A | -1.6505 | |
| 399 | S | A | 0.0000 | |
| 400 | A | A | 0.1855 | |
| 401 | L | A | 0.2352 | |
| 402 | R | A | -0.4946 | |
| 403 | M | A | 0.7997 | |
| 404 | L | A | 0.4301 | |
| 405 | D | A | -1.3758 | |
| 406 | R | A | -1.4967 | |
| 407 | Q | A | -1.0486 | |
| 408 | V | A | 0.2077 | |
| 409 | L | A | 0.0000 | |
| 410 | A | A | 0.0000 | |
| 411 | A | A | -0.1311 | |
| 412 | S | A | 0.2284 | |
| 413 | L | A | 0.7800 | |
| 414 | N | A | -0.3202 | |
| 415 | V | A | 0.4691 | |
| 416 | S | A | 0.0772 | |
| 417 | S | A | -0.1413 | |
| 418 | V | A | 0.9788 | |
| 419 | T | A | 0.5705 | |
| 420 | I | A | 0.0000 | |
| 421 | D | A | -1.2436 | |
| 422 | G | A | -0.3148 | |
| 423 | L | A | 0.7678 | |
| 424 | L | A | 0.0000 | |
| 425 | G | A | -1.2716 | |
| 426 | A | A | -0.8950 | |
| 427 | Q | A | -1.7110 | |
| 428 | K | A | -2.7526 | |
| 429 | E | A | -2.1819 | |
| 430 | A | A | -1.6181 | |
| 431 | V | A | -0.5779 | |
| 432 | I | A | 0.0000 | |
| 433 | L | A | 0.0000 | |
| 434 | E | A | -2.1728 | |
| 435 | C | A | -1.3407 | |
| 436 | H | A | -1.7209 | |
| 437 | S | A | -1.1681 | |
| 438 | C | A | -0.7145 | |
| 439 | A | A | 0.0000 | |
| 440 | E | A | -1.2785 | |
| 441 | G | A | -1.2640 | |
| 442 | E | A | 0.0000 | |
| 443 | I | A | -1.5102 | |
| 444 | E | A | -2.6662 | |
| 445 | K | A | -2.5315 | |
| 446 | L | A | 0.0000 | |
| 447 | K | A | -2.8482 | |
| 448 | V | A | -2.3225 | |
| 449 | E | A | -2.9124 | |
| 450 | I | A | -2.9521 | |
| 451 | E | A | -3.5211 | |
| 452 | R | A | -3.7050 | |
| 453 | K | A | -3.3028 |
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 | -0.199 | 7.5538 | View | CSV | PDB |
| 4.5 | -0.2797 | 7.5049 | View | CSV | PDB |
| 5.0 | -0.3802 | 7.4393 | View | CSV | PDB |
| 5.5 | -0.4828 | 7.3682 | View | CSV | PDB |
| 6.0 | -0.5683 | 7.3024 | View | CSV | PDB |
| 6.5 | -0.6213 | 7.2531 | View | CSV | PDB |
| 7.0 | -0.6374 | 7.2254 | View | CSV | PDB |
| 7.5 | -0.626 | 7.2138 | View | CSV | PDB |
| 8.0 | -0.5983 | 7.2097 | View | CSV | PDB |
| 8.5 | -0.5593 | 7.2083 | View | CSV | PDB |
| 9.0 | -0.5102 | 7.2079 | 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