| Chain sequence(s) |
A: MARAVGPERRLLAVYTGGTIGMRSELGVLVPGTGLAAILRTLPMFHDEEHARARGLSEDTLVLPPASRNQRILYTVLECQPLFDSSDMTIAEWVCLAQTIKRHYEQYHGFVVIHGTDTMAFAASMLSFMLENLQKTVILTGAQVPIHALWSDGRENLLGALLMAGQYVIPEVCLFFQNQLFRGNRATKVDARRFAAFCSPNLLPLATVGADITINRELVRKVDGKAGLVVHSSMEQDVGLLRLYPGIPAALVRAFLQPPLKGVVMETFGSGNGPTKPDLLQELRVATERGLVIVNCTHCLQGAVTTDYAAGMAMAGAGVISGFDMTSEAALAKLSYVLGQPGLSLDVRKELLTKDLRGEMTPPSVEERRPSLQGNTLGGGVSWLLSLSGSQEADALRNAL
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. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:07:48)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/a2459a028ee9366/tmp/folded.pdb (00:07:48)
[INFO] Main: Simulation completed successfully. (00:14:53)
|
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 | -0.4800 | |
| 2 | A | A | -0.1378 | |
| 3 | R | A | -1.1214 | |
| 4 | A | A | 0.0000 | |
| 5 | V | A | 0.7489 | |
| 6 | G | A | -0.5302 | |
| 7 | P | A | -1.6307 | |
| 8 | E | A | -2.4098 | |
| 9 | R | A | -1.6001 | |
| 10 | R | A | -1.9328 | |
| 11 | L | A | 0.0000 | |
| 12 | L | A | 0.0000 | |
| 13 | A | A | 0.0000 | |
| 14 | V | A | 0.0000 | |
| 15 | Y | A | 0.0000 | |
| 16 | T | A | 0.0000 | |
| 17 | G | A | 0.0000 | |
| 18 | G | A | 0.0000 | |
| 19 | T | A | -0.4000 | |
| 20 | I | A | 0.0000 | |
| 21 | G | A | 0.0000 | |
| 22 | M | A | 0.0000 | |
| 23 | R | A | -1.5003 | |
| 24 | S | A | -0.6595 | |
| 25 | E | A | -0.8784 | |
| 26 | L | A | 0.9281 | |
| 27 | G | A | 0.5002 | |
| 28 | V | A | 1.5764 | |
| 29 | L | A | 0.8635 | |
| 30 | V | A | 0.2047 | |
| 31 | P | A | -0.5738 | |
| 32 | G | A | 0.0000 | |
| 33 | T | A | -0.5160 | |
| 34 | G | A | -0.3866 | |
| 35 | L | A | 0.0000 | |
| 36 | A | A | 0.0000 | |
| 37 | A | A | -0.6219 | |
| 38 | I | A | 0.0119 | |
| 39 | L | A | 0.0000 | |
| 40 | R | A | -1.1403 | |
| 41 | T | A | -0.4210 | |
| 42 | L | A | -0.2879 | |
| 43 | P | A | -0.5232 | |
| 44 | M | A | -0.1624 | |
| 45 | F | A | 0.0000 | |
| 46 | H | A | -1.1034 | |
| 47 | D | A | -2.1159 | |
| 48 | E | A | -3.4832 | |
| 49 | E | A | -3.6869 | |
| 50 | H | A | -2.9085 | |
| 51 | A | A | 0.0000 | |
| 52 | R | A | -3.8564 | |
| 53 | A | A | -2.6066 | |
| 54 | R | A | -3.0376 | |
| 55 | G | A | -2.1188 | |
| 56 | L | A | -1.8663 | |
| 57 | S | A | -2.0322 | |
| 58 | E | A | -2.9833 | |
| 59 | D | A | -2.7119 | |
| 60 | T | A | -1.5669 | |
| 61 | L | A | 0.0000 | |
| 62 | V | A | 0.0000 | |
| 63 | L | A | 0.0000 | |
| 64 | P | A | -0.7996 | |
| 65 | P | A | -1.1688 | |
| 66 | A | A | -0.8592 | |
| 67 | S | A | -1.7049 | |
| 68 | R | A | -2.7095 | |
| 69 | N | A | -2.5550 | |
| 70 | Q | A | -1.9679 | |
| 71 | R | A | -1.9106 | |
| 72 | I | A | 0.0000 | |
| 73 | L | A | -0.7667 | |
| 74 | Y | A | 0.0000 | |
| 75 | T | A | -0.9326 | |
| 76 | V | A | 0.0000 | |
| 77 | L | A | -0.2309 | |
| 78 | E | A | -0.6870 | |
| 79 | C | A | -0.5197 | |
| 80 | Q | A | -1.2403 | |
| 81 | P | A | -1.0056 | |
| 82 | L | A | -0.5295 | |
| 83 | F | A | -1.0407 | |
| 84 | D | A | -2.0827 | |
| 85 | S | A | 0.0000 | |
| 86 | S | A | -1.9729 | |
| 87 | D | A | -2.5106 | |
| 88 | M | A | 0.0000 | |
| 89 | T | A | -0.5681 | |
| 90 | I | A | 0.0328 | |
| 91 | A | A | 0.0335 | |
| 92 | E | A | -0.2872 | |
| 93 | W | A | 0.0000 | |
| 94 | V | A | 0.1508 | |
| 95 | C | A | 0.2094 | |
| 96 | L | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | Q | A | -1.7273 | |
| 99 | T | A | -1.2310 | |
| 100 | I | A | 0.0000 | |
| 101 | K | A | -2.3036 | |
| 102 | R | A | -3.0970 | |
| 103 | H | A | -2.3966 | |
| 104 | Y | A | 0.0000 | |
| 105 | E | A | -2.9352 | |
| 106 | Q | A | -2.7069 | |
| 107 | Y | A | 0.0000 | |
| 108 | H | A | -1.6707 | |
| 109 | G | A | 0.0000 | |
| 110 | F | A | 0.0000 | |
| 111 | V | A | 0.0000 | |
| 112 | V | A | 0.0000 | |
| 113 | I | A | 0.0000 | |
| 114 | H | A | 0.0000 | |
| 115 | G | A | 0.0000 | |
| 116 | T | A | 0.0000 | |
| 117 | D | A | -2.2553 | |
| 118 | T | A | -1.2627 | |
| 119 | M | A | 0.0000 | |
| 120 | A | A | 0.0000 | |
| 121 | F | A | 0.1815 | |
| 122 | A | A | 0.0000 | |
| 123 | A | A | 0.0000 | |
| 124 | S | A | 0.0000 | |
| 125 | M | A | 0.0000 | |
| 126 | L | A | 0.0000 | |
| 127 | S | A | 0.0000 | |
| 128 | F | A | 0.0000 | |
| 129 | M | A | 0.0000 | |
| 130 | L | A | 0.0000 | |
| 131 | E | A | -0.3127 | |
| 132 | N | A | -1.3820 | |
| 133 | L | A | 0.0000 | |
| 134 | Q | A | -2.0360 | |
| 135 | K | A | -0.7173 | |
| 136 | T | A | 0.0000 | |
| 137 | V | A | 0.0000 | |
| 138 | I | A | 0.0000 | |
| 139 | L | A | 0.0000 | |
| 140 | T | A | 0.0000 | |
| 141 | G | A | 0.0000 | |
| 142 | A | A | 0.0000 | |
| 143 | Q | A | -0.6620 | |
| 144 | V | A | 0.3543 | |
| 145 | P | A | 0.0000 | |
| 146 | I | A | 0.0000 | |
| 147 | H | A | -0.1150 | |
| 148 | A | A | 0.7546 | |
| 149 | L | A | 2.0481 | |
| 150 | W | A | 1.8862 | |
| 151 | S | A | 0.7326 | |
| 152 | D | A | 0.0000 | |
| 153 | G | A | 0.0000 | |
| 154 | R | A | -1.0429 | |
| 155 | E | A | -2.1627 | |
| 156 | N | A | 0.0000 | |
| 157 | L | A | 0.0000 | |
| 158 | L | A | -0.3373 | |
| 159 | G | A | -0.6087 | |
| 160 | A | A | 0.0000 | |
| 161 | L | A | 0.0000 | |
| 162 | L | A | 0.3640 | |
| 163 | M | A | 0.0000 | |
| 164 | A | A | 0.0000 | |
| 165 | G | A | 0.0000 | |
| 166 | Q | A | -0.2907 | |
| 167 | Y | A | -0.0440 | |
| 168 | V | A | 0.0382 | |
| 169 | I | A | 0.0000 | |
| 170 | P | A | 0.0000 | |
| 171 | E | A | 0.0000 | |
| 172 | V | A | 0.0000 | |
| 173 | C | A | 0.0000 | |
| 174 | L | A | 0.0000 | |
| 175 | F | A | 0.0000 | |
| 176 | F | A | 0.0000 | |
| 177 | Q | A | -1.2868 | |
| 178 | N | A | -1.3422 | |
| 179 | Q | A | -0.5579 | |
| 180 | L | A | 0.0000 | |
| 181 | F | A | 0.0000 | |
| 182 | R | A | 0.0000 | |
| 183 | G | A | 0.0000 | |
| 184 | N | A | 0.0000 | |
| 185 | R | A | 0.0000 | |
| 186 | A | A | 0.0000 | |
| 187 | T | A | 0.1325 | |
| 188 | K | A | -0.2235 | |
| 189 | V | A | 0.5385 | |
| 190 | D | A | -0.7811 | |
| 191 | A | A | -1.4543 | |
| 192 | R | A | -2.4261 | |
| 193 | R | A | -2.2214 | |
| 194 | F | A | -0.4701 | |
| 195 | A | A | -0.5950 | |
| 196 | A | A | 0.0000 | |
| 197 | F | A | 0.0000 | |
| 198 | C | A | 0.4756 | |
| 199 | S | A | 0.4168 | |
| 200 | P | A | 0.2338 | |
| 201 | N | A | -0.1220 | |
| 202 | L | A | 0.6596 | |
| 203 | L | A | 1.4987 | |
| 204 | P | A | 0.6580 | |
| 205 | L | A | 0.0000 | |
| 206 | A | A | 0.0000 | |
| 207 | T | A | -0.3107 | |
| 208 | V | A | -0.5124 | |
| 209 | G | A | -0.9430 | |
| 210 | A | A | -0.8477 | |
| 211 | D | A | -1.5578 | |
| 212 | I | A | -0.3571 | |
| 213 | T | A | -0.4825 | |
| 214 | I | A | -0.6491 | |
| 215 | N | A | -1.3317 | |
| 216 | R | A | -2.7991 | |
| 217 | E | A | -2.8211 | |
| 218 | L | A | -1.2639 | |
| 219 | V | A | -1.3831 | |
| 220 | R | A | -1.9374 | |
| 221 | K | A | -2.6499 | |
| 222 | V | A | -2.1810 | |
| 223 | D | A | -3.0709 | |
| 224 | G | A | -2.5983 | |
| 225 | K | A | -2.6829 | |
| 226 | A | A | -1.7165 | |
| 227 | G | A | -1.1878 | |
| 228 | L | A | 0.0000 | |
| 229 | V | A | 0.6543 | |
| 230 | V | A | 0.0715 | |
| 231 | H | A | -0.1395 | |
| 232 | S | A | -0.2262 | |
| 233 | S | A | -0.5460 | |
| 234 | M | A | 0.0000 | |
| 235 | E | A | -1.1534 | |
| 236 | Q | A | -1.6567 | |
| 237 | D | A | -1.4706 | |
| 238 | V | A | -0.6222 | |
| 239 | G | A | -0.0134 | |
| 240 | L | A | 0.1250 | |
| 241 | L | A | 0.0000 | |
| 242 | R | A | -1.5638 | |
| 243 | L | A | 0.0000 | |
| 244 | Y | A | 0.3787 | |
| 245 | P | A | 0.0356 | |
| 246 | G | A | -0.5513 | |
| 247 | I | A | 0.0000 | |
| 248 | P | A | -0.5569 | |
| 249 | A | A | -1.1449 | |
| 250 | A | A | -0.3859 | |
| 251 | L | A | 0.3354 | |
| 252 | V | A | 0.0000 | |
| 253 | R | A | -1.6191 | |
| 254 | A | A | -0.4390 | |
| 255 | F | A | 0.1040 | |
| 256 | L | A | 0.0000 | |
| 257 | Q | A | -1.2324 | |
| 258 | P | A | -0.9642 | |
| 259 | P | A | -0.9276 | |
| 260 | L | A | -0.8827 | |
| 261 | K | A | -1.4765 | |
| 262 | G | A | 0.0000 | |
| 263 | V | A | 0.0000 | |
| 264 | V | A | 0.0000 | |
| 265 | M | A | 0.0000 | |
| 266 | E | A | 0.0000 | |
| 267 | T | A | 0.0000 | |
| 268 | F | A | -0.0435 | |
| 269 | G | A | -0.2811 | |
| 270 | S | A | -0.4601 | |
| 271 | G | A | 0.0000 | |
| 272 | N | A | -0.0828 | |
| 273 | G | A | 0.0000 | |
| 274 | P | A | -0.7594 | |
| 275 | T | A | -1.0928 | |
| 276 | K | A | -2.5489 | |
| 277 | P | A | -2.1755 | |
| 278 | D | A | -2.8995 | |
| 279 | L | A | 0.0000 | |
| 280 | L | A | -1.7790 | |
| 281 | Q | A | -2.5396 | |
| 282 | E | A | -1.9155 | |
| 283 | L | A | 0.0000 | |
| 284 | R | A | -2.3332 | |
| 285 | V | A | -1.5839 | |
| 286 | A | A | 0.0000 | |
| 287 | T | A | -1.9450 | |
| 288 | E | A | -2.7317 | |
| 289 | R | A | -2.5368 | |
| 290 | G | A | -1.6845 | |
| 291 | L | A | 0.0000 | |
| 292 | V | A | 0.0000 | |
| 293 | I | A | 0.0000 | |
| 294 | V | A | 0.0000 | |
| 295 | N | A | 0.0000 | |
| 296 | C | A | 0.0000 | |
| 297 | T | A | 0.0000 | |
| 298 | H | A | -0.6687 | |
| 299 | C | A | 0.2679 | |
| 300 | L | A | 0.9071 | |
| 301 | Q | A | -0.7496 | |
| 302 | G | A | -0.6742 | |
| 303 | A | A | -0.2906 | |
| 304 | V | A | 0.0000 | |
| 305 | T | A | -0.3421 | |
| 306 | T | A | -0.2834 | |
| 307 | D | A | -1.2861 | |
| 308 | Y | A | 0.3678 | |
| 309 | A | A | 0.4533 | |
| 310 | A | A | 0.1247 | |
| 311 | G | A | 0.0000 | |
| 312 | M | A | 0.7141 | |
| 313 | A | A | 0.2478 | |
| 314 | M | A | 0.0000 | |
| 315 | A | A | -0.0369 | |
| 316 | G | A | -0.3447 | |
| 317 | A | A | 0.0000 | |
| 318 | G | A | -0.8626 | |
| 319 | V | A | 0.0000 | |
| 320 | I | A | 0.0000 | |
| 321 | S | A | 0.0334 | |
| 322 | G | A | 0.0000 | |
| 323 | F | A | 0.1542 | |
| 324 | D | A | 0.0000 | |
| 325 | M | A | 0.0000 | |
| 326 | T | A | -0.0207 | |
| 327 | S | A | 0.1209 | |
| 328 | E | A | 0.0542 | |
| 329 | A | A | 0.0000 | |
| 330 | A | A | 0.0000 | |
| 331 | L | A | 0.3178 | |
| 332 | A | A | 0.0000 | |
| 333 | K | A | 0.0000 | |
| 334 | L | A | 0.0000 | |
| 335 | S | A | 0.0000 | |
| 336 | Y | A | 0.0000 | |
| 337 | V | A | 0.0000 | |
| 338 | L | A | 0.0000 | |
| 339 | G | A | -0.6813 | |
| 340 | Q | A | -0.4572 | |
| 341 | P | A | -0.4729 | |
| 342 | G | A | -0.2810 | |
| 343 | L | A | 0.0608 | |
| 344 | S | A | -0.3714 | |
| 345 | L | A | -0.3923 | |
| 346 | D | A | -1.7085 | |
| 347 | V | A | -0.5961 | |
| 348 | R | A | -0.7725 | |
| 349 | K | A | -1.6570 | |
| 350 | E | A | -2.3951 | |
| 351 | L | A | -1.2996 | |
| 352 | L | A | 0.0000 | |
| 353 | T | A | -1.5402 | |
| 354 | K | A | -2.3329 | |
| 355 | D | A | -1.3537 | |
| 356 | L | A | -0.6424 | |
| 357 | R | A | -0.6518 | |
| 358 | G | A | -0.4690 | |
| 359 | E | A | 0.0000 | |
| 360 | M | A | 0.0000 | |
| 361 | T | A | -0.5340 | |
| 362 | P | A | -0.7138 | |
| 363 | P | A | -0.9851 | |
| 364 | S | A | -1.0745 | |
| 365 | V | A | -0.5055 | |
| 366 | E | A | -2.8485 | |
| 367 | E | A | -3.8090 | |
| 368 | R | A | -3.8683 | |
| 369 | R | A | -3.7167 | |
| 370 | P | A | -2.2984 | |
| 371 | S | A | -1.2528 | |
| 372 | L | A | 0.3323 | |
| 373 | Q | A | -0.9773 | |
| 374 | G | A | -1.0768 | |
| 375 | N | A | -0.6359 | |
| 376 | T | A | 0.1990 | |
| 377 | L | A | 1.4427 | |
| 378 | G | A | 0.7668 | |
| 379 | G | A | 0.5644 | |
| 380 | G | A | 1.2493 | |
| 381 | V | A | 2.2016 | |
| 382 | S | A | 1.6643 | |
| 383 | W | A | 2.2099 | |
| 384 | L | A | 2.4859 | |
| 385 | L | A | 2.5575 | |
| 386 | S | A | 1.4251 | |
| 387 | L | A | 0.6537 | |
| 388 | S | A | -0.1461 | |
| 389 | G | A | -1.3484 | |
| 390 | S | A | -1.7925 | |
| 391 | Q | A | -2.6929 | |
| 392 | E | A | -2.9366 | |
| 393 | A | A | -2.4111 | |
| 394 | D | A | -3.6290 | |
| 395 | A | A | -2.3574 | |
| 396 | L | A | -1.6644 | |
| 397 | R | A | -2.6477 | |
| 398 | N | A | -1.9892 | |
| 399 | A | A | -0.4773 | |
| 400 | L | A | 0.7366 |
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 | -0.3329 | 4.1013 | View | CSV | PDB |
| 4.5 | -0.3906 | 4.1062 | View | CSV | PDB |
| 5.0 | -0.4629 | 4.1176 | View | CSV | PDB |
| 5.5 | -0.5391 | 4.1361 | View | CSV | PDB |
| 6.0 | -0.6097 | 4.1553 | View | CSV | PDB |
| 6.5 | -0.6666 | 4.1681 | View | CSV | PDB |
| 7.0 | -0.7066 | 4.174 | View | CSV | PDB |
| 7.5 | -0.7327 | 4.1761 | View | CSV | PDB |
| 8.0 | -0.7499 | 4.1768 | View | CSV | PDB |
| 8.5 | -0.7601 | 4.1771 | View | CSV | PDB |
| 9.0 | -0.762 | 4.1771 | 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