| Chain sequence(s) |
A: MDKVMVMFCMLIAYTCACSLGRNNKTMSTADMSYFTENGLGQTPPMGWNSWNHFGCDINETLIRSTADAMVSTGLASLGYKYINLDDCWAELNRDSQGNMVPKASTFPSGIKALAYYVHGKGLKLGVYSDAGNLTCSKRMPGSLGHEVQDAKTFASWGVDYLKYDNCENNGISPRLRYPPMSEALLNSGRPIFFSMCEWGREDPATWAKSVGNSWRTTGDIKDNWKSMTSIADANDKWASYAGPGGWNDPDMLEVGNGGMTTEEYRAHFSIWALAKAPLLVGCDIQAMDNTTSELISNSEVIAVNQDTLGVQGKKVKSNSDLEVWAGPLSNNKVAVILWNRSSSNATVTASWSDLGLESGTIVDARDLWDHSTQSSVSGDISAELASHACKMYVLTPQSG
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. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:03:57)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/8989771d8309af1/tmp/folded.pdb (00:03:57)
[INFO] Main: Simulation completed successfully. (00:06:00)
|
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 | 0.0184 | |
| 2 | D | A | -1.5238 | |
| 3 | K | A | -0.9968 | |
| 4 | V | A | 1.6735 | |
| 5 | M | A | 2.5725 | |
| 6 | V | A | 3.5834 | |
| 7 | M | A | 3.6563 | |
| 8 | F | A | 3.8579 | |
| 9 | C | A | 3.2850 | |
| 10 | M | A | 3.2927 | |
| 11 | L | A | 3.6578 | |
| 12 | I | A | 3.4722 | |
| 13 | A | A | 2.1849 | |
| 14 | Y | A | 2.2178 | |
| 15 | T | A | 1.2911 | |
| 16 | C | A | 1.3235 | |
| 17 | A | A | 1.0700 | |
| 18 | C | A | 1.2315 | |
| 19 | S | A | 0.5799 | |
| 20 | L | A | 0.6882 | |
| 21 | G | A | -1.1712 | |
| 22 | R | A | -2.8993 | |
| 23 | N | A | -3.2959 | |
| 24 | N | A | -3.2807 | |
| 25 | K | A | -2.9354 | |
| 26 | T | A | -1.4588 | |
| 27 | M | A | -0.6149 | |
| 28 | S | A | -0.6216 | |
| 29 | T | A | -0.3533 | |
| 30 | A | A | -0.4084 | |
| 31 | D | A | -1.0215 | |
| 32 | M | A | -0.0023 | |
| 33 | S | A | -0.3245 | |
| 34 | Y | A | 0.1169 | |
| 35 | F | A | 0.0000 | |
| 36 | T | A | -0.9909 | |
| 37 | E | A | -1.8237 | |
| 38 | N | A | -1.2061 | |
| 39 | G | A | -1.3243 | |
| 40 | L | A | -0.8930 | |
| 41 | G | A | -0.9517 | |
| 42 | Q | A | -1.6132 | |
| 43 | T | A | -0.7034 | |
| 44 | P | A | 0.0000 | |
| 45 | P | A | 0.0000 | |
| 46 | M | A | 0.0000 | |
| 47 | G | A | 0.0000 | |
| 48 | W | A | 0.0000 | |
| 49 | N | A | 0.0000 | |
| 50 | S | A | 0.0000 | |
| 51 | W | A | -0.0567 | |
| 52 | N | A | -0.9980 | |
| 53 | H | A | -0.9838 | |
| 54 | F | A | -0.5703 | |
| 55 | G | A | -0.3876 | |
| 56 | C | A | -0.6497 | |
| 57 | D | A | -1.6176 | |
| 58 | I | A | 0.0000 | |
| 59 | N | A | -1.1473 | |
| 60 | E | A | 0.0000 | |
| 61 | T | A | -0.3604 | |
| 62 | L | A | -0.6092 | |
| 63 | I | A | 0.0000 | |
| 64 | R | A | -0.7075 | |
| 65 | S | A | -0.5650 | |
| 66 | T | A | 0.0000 | |
| 67 | A | A | 0.0000 | |
| 68 | D | A | -0.7970 | |
| 69 | A | A | 0.0000 | |
| 70 | M | A | 0.0000 | |
| 71 | V | A | 0.2302 | |
| 72 | S | A | -0.1523 | |
| 73 | T | A | -0.2118 | |
| 74 | G | A | 0.0591 | |
| 75 | L | A | 0.0000 | |
| 76 | A | A | -0.2898 | |
| 77 | S | A | -0.1024 | |
| 78 | L | A | 0.1165 | |
| 79 | G | A | -0.3987 | |
| 80 | Y | A | 0.0000 | |
| 81 | K | A | -1.2144 | |
| 82 | Y | A | -0.7455 | |
| 83 | I | A | 0.0000 | |
| 84 | N | A | 0.0000 | |
| 85 | L | A | 0.0000 | |
| 86 | D | A | 0.0000 | |
| 87 | D | A | 0.0000 | |
| 88 | C | A | -0.7880 | |
| 89 | W | A | 0.0000 | |
| 90 | A | A | 0.0000 | |
| 91 | E | A | -0.9313 | |
| 92 | L | A | -0.5949 | |
| 93 | N | A | -1.4295 | |
| 94 | R | A | -1.4131 | |
| 95 | D | A | -1.7280 | |
| 96 | S | A | -1.5066 | |
| 97 | Q | A | -1.8387 | |
| 98 | G | A | -1.5790 | |
| 99 | N | A | -1.4336 | |
| 100 | M | A | 0.0000 | |
| 101 | V | A | -0.2634 | |
| 102 | P | A | -0.4352 | |
| 103 | K | A | -0.7968 | |
| 104 | A | A | -0.5734 | |
| 105 | S | A | -0.6406 | |
| 106 | T | A | -0.9054 | |
| 107 | F | A | 0.0000 | |
| 108 | P | A | -0.6265 | |
| 109 | S | A | -0.7167 | |
| 110 | G | A | -0.7975 | |
| 111 | I | A | 0.0000 | |
| 112 | K | A | -1.3425 | |
| 113 | A | A | -0.4035 | |
| 114 | L | A | 0.0000 | |
| 115 | A | A | 0.0000 | |
| 116 | Y | A | 0.5578 | |
| 117 | Y | A | -0.0953 | |
| 118 | V | A | 0.0000 | |
| 119 | H | A | -0.8505 | |
| 120 | G | A | -0.8640 | |
| 121 | K | A | -1.4081 | |
| 122 | G | A | -1.2743 | |
| 123 | L | A | 0.0000 | |
| 124 | K | A | -1.2324 | |
| 125 | L | A | 0.0000 | |
| 126 | G | A | 0.0000 | |
| 127 | V | A | 0.0000 | |
| 128 | Y | A | 0.0000 | |
| 129 | S | A | 0.0000 | |
| 130 | D | A | 0.0000 | |
| 131 | A | A | 0.0000 | |
| 132 | G | A | 0.0000 | |
| 133 | N | A | -2.1427 | |
| 134 | L | A | -1.4514 | |
| 135 | T | A | 0.0000 | |
| 136 | C | A | -0.8650 | |
| 137 | S | A | -1.2349 | |
| 138 | K | A | -2.4333 | |
| 139 | R | A | -2.0987 | |
| 140 | M | A | 0.0000 | |
| 141 | P | A | 0.0000 | |
| 142 | G | A | 0.0000 | |
| 143 | S | A | 0.0000 | |
| 144 | L | A | -0.7585 | |
| 145 | G | A | -0.6553 | |
| 146 | H | A | -0.6060 | |
| 147 | E | A | -0.3224 | |
| 148 | V | A | 0.3217 | |
| 149 | Q | A | -0.8154 | |
| 150 | D | A | 0.0000 | |
| 151 | A | A | 0.0000 | |
| 152 | K | A | -1.4311 | |
| 153 | T | A | -0.7657 | |
| 154 | F | A | 0.0000 | |
| 155 | A | A | 0.0000 | |
| 156 | S | A | -0.9174 | |
| 157 | W | A | -0.7071 | |
| 158 | G | A | 0.0000 | |
| 159 | V | A | 0.0000 | |
| 160 | D | A | -0.6050 | |
| 161 | Y | A | 0.0000 | |
| 162 | L | A | 0.0000 | |
| 163 | K | A | 0.0000 | |
| 164 | Y | A | 0.0000 | |
| 165 | D | A | -0.2564 | |
| 166 | N | A | 0.0000 | |
| 167 | C | A | -1.2657 | |
| 168 | E | A | -2.5007 | |
| 169 | N | A | -1.7936 | |
| 170 | N | A | -2.0285 | |
| 171 | G | A | -1.0818 | |
| 172 | I | A | -0.0682 | |
| 173 | S | A | -0.3788 | |
| 174 | P | A | 0.0000 | |
| 175 | R | A | -0.8215 | |
| 176 | L | A | 1.0091 | |
| 177 | R | A | 0.0000 | |
| 178 | Y | A | 0.0000 | |
| 179 | P | A | -0.5177 | |
| 180 | P | A | -0.3842 | |
| 181 | M | A | 0.0000 | |
| 182 | S | A | 0.0000 | |
| 183 | E | A | -1.6391 | |
| 184 | A | A | 0.0000 | |
| 185 | L | A | 0.0000 | |
| 186 | L | A | -0.8108 | |
| 187 | N | A | -1.7521 | |
| 188 | S | A | 0.0000 | |
| 189 | G | A | -1.3771 | |
| 190 | R | A | -1.3768 | |
| 191 | P | A | -0.8839 | |
| 192 | I | A | 0.0000 | |
| 193 | F | A | 0.0000 | |
| 194 | F | A | 0.0000 | |
| 195 | S | A | 0.0000 | |
| 196 | M | A | 0.0000 | |
| 197 | C | A | 0.0000 | |
| 198 | E | A | 0.0000 | |
| 199 | W | A | -1.0861 | |
| 200 | G | A | -1.5157 | |
| 201 | R | A | -2.7655 | |
| 202 | E | A | -2.6996 | |
| 203 | D | A | -2.1432 | |
| 204 | P | A | 0.0000 | |
| 205 | A | A | 0.0000 | |
| 206 | T | A | -0.4925 | |
| 207 | W | A | -0.5027 | |
| 208 | A | A | 0.0000 | |
| 209 | K | A | -0.6469 | |
| 210 | S | A | -0.3829 | |
| 211 | V | A | 0.0000 | |
| 212 | G | A | 0.0000 | |
| 213 | N | A | 0.0000 | |
| 214 | S | A | 0.0000 | |
| 215 | W | A | 0.0000 | |
| 216 | R | A | 0.0000 | |
| 217 | T | A | 0.0000 | |
| 218 | T | A | 0.0000 | |
| 219 | G | A | -1.4056 | |
| 220 | D | A | -2.3037 | |
| 221 | I | A | 0.0000 | |
| 222 | K | A | -2.8855 | |
| 223 | D | A | -2.1132 | |
| 224 | N | A | -1.9979 | |
| 225 | W | A | -1.4828 | |
| 226 | K | A | -2.1744 | |
| 227 | S | A | -2.0269 | |
| 228 | M | A | 0.0000 | |
| 229 | T | A | 0.0000 | |
| 230 | S | A | -0.9701 | |
| 231 | I | A | 0.0000 | |
| 232 | A | A | 0.0000 | |
| 233 | D | A | -1.6151 | |
| 234 | A | A | -1.0436 | |
| 235 | N | A | 0.0000 | |
| 236 | D | A | -1.8640 | |
| 237 | K | A | -2.1751 | |
| 238 | W | A | -1.1220 | |
| 239 | A | A | -0.7352 | |
| 240 | S | A | -0.2961 | |
| 241 | Y | A | 0.1966 | |
| 242 | A | A | 0.1711 | |
| 243 | G | A | -0.0873 | |
| 244 | P | A | -0.8793 | |
| 245 | G | A | 0.0000 | |
| 246 | G | A | 0.0000 | |
| 247 | W | A | 0.0000 | |
| 248 | N | A | 0.0000 | |
| 249 | D | A | 0.0000 | |
| 250 | P | A | 0.0000 | |
| 251 | D | A | 0.0000 | |
| 252 | M | A | 0.0000 | |
| 253 | L | A | 0.0000 | |
| 254 | E | A | 0.0000 | |
| 255 | V | A | 0.0000 | |
| 256 | G | A | -1.1865 | |
| 257 | N | A | -1.3321 | |
| 258 | G | A | -1.0705 | |
| 259 | G | A | -1.3666 | |
| 260 | M | A | 0.0000 | |
| 261 | T | A | -0.5903 | |
| 262 | T | A | -0.5775 | |
| 263 | E | A | -0.7765 | |
| 264 | E | A | 0.0000 | |
| 265 | Y | A | 0.0000 | |
| 266 | R | A | -0.8037 | |
| 267 | A | A | 0.0000 | |
| 268 | H | A | 0.0000 | |
| 269 | F | A | 0.0000 | |
| 270 | S | A | 0.0000 | |
| 271 | I | A | 0.0000 | |
| 272 | W | A | 0.0000 | |
| 273 | A | A | 0.0000 | |
| 274 | L | A | 0.0000 | |
| 275 | A | A | 0.0000 | |
| 276 | K | A | 0.0000 | |
| 277 | A | A | 0.0000 | |
| 278 | P | A | 0.0000 | |
| 279 | L | A | 0.0000 | |
| 280 | L | A | 0.0000 | |
| 281 | V | A | 0.0000 | |
| 282 | G | A | 0.0000 | |
| 283 | C | A | 0.0000 | |
| 284 | D | A | -1.0575 | |
| 285 | I | A | 0.0000 | |
| 286 | Q | A | -1.5453 | |
| 287 | A | A | -1.1709 | |
| 288 | M | A | -1.7087 | |
| 289 | D | A | -2.7989 | |
| 290 | N | A | -2.6451 | |
| 291 | T | A | -1.8828 | |
| 292 | T | A | 0.0000 | |
| 293 | S | A | -1.8957 | |
| 294 | E | A | -2.4929 | |
| 295 | L | A | 0.0000 | |
| 296 | I | A | 0.0000 | |
| 297 | S | A | -0.7840 | |
| 298 | N | A | 0.0000 | |
| 299 | S | A | -0.6175 | |
| 300 | E | A | -0.9143 | |
| 301 | V | A | 0.0000 | |
| 302 | I | A | 0.0000 | |
| 303 | A | A | -0.3391 | |
| 304 | V | A | 0.0000 | |
| 305 | N | A | 0.0000 | |
| 306 | Q | A | -0.4602 | |
| 307 | D | A | -0.1956 | |
| 308 | T | A | -0.1808 | |
| 309 | L | A | 0.2720 | |
| 310 | G | A | 0.0000 | |
| 311 | V | A | 0.6198 | |
| 312 | Q | A | 0.0000 | |
| 313 | G | A | 0.0000 | |
| 314 | K | A | -1.7777 | |
| 315 | K | A | -1.4698 | |
| 316 | V | A | -0.5635 | |
| 317 | K | A | -1.0870 | |
| 318 | S | A | -1.2424 | |
| 319 | N | A | -1.7572 | |
| 320 | S | A | -1.3496 | |
| 321 | D | A | -1.4463 | |
| 322 | L | A | -0.9498 | |
| 323 | E | A | 0.0000 | |
| 324 | V | A | 0.0000 | |
| 325 | W | A | 0.0000 | |
| 326 | A | A | 0.0000 | |
| 327 | G | A | -0.3519 | |
| 328 | P | A | -0.6573 | |
| 329 | L | A | 0.0000 | |
| 330 | S | A | -1.0117 | |
| 331 | N | A | -2.0369 | |
| 332 | N | A | -2.1462 | |
| 333 | K | A | -1.6576 | |
| 334 | V | A | 0.0000 | |
| 335 | A | A | 0.0000 | |
| 336 | V | A | 0.0000 | |
| 337 | I | A | 0.0000 | |
| 338 | L | A | 0.0000 | |
| 339 | W | A | 0.0000 | |
| 340 | N | A | 0.0000 | |
| 341 | R | A | -0.8498 | |
| 342 | S | A | -0.9200 | |
| 343 | S | A | -0.8286 | |
| 344 | S | A | -1.1175 | |
| 345 | N | A | -1.8793 | |
| 346 | A | A | -1.3983 | |
| 347 | T | A | -1.1031 | |
| 348 | V | A | 0.0000 | |
| 349 | T | A | -0.6461 | |
| 350 | A | A | 0.0000 | |
| 351 | S | A | -0.8999 | |
| 352 | W | A | 0.0000 | |
| 353 | S | A | -1.0999 | |
| 354 | D | A | -0.8459 | |
| 355 | L | A | -0.7019 | |
| 356 | G | A | -0.9658 | |
| 357 | L | A | -1.2296 | |
| 358 | E | A | -2.0654 | |
| 359 | S | A | -1.4651 | |
| 360 | G | A | -0.9878 | |
| 361 | T | A | -0.8643 | |
| 362 | I | A | -0.2215 | |
| 363 | V | A | 0.0000 | |
| 364 | D | A | -1.2393 | |
| 365 | A | A | 0.0000 | |
| 366 | R | A | -1.6931 | |
| 367 | D | A | 0.0000 | |
| 368 | L | A | 0.0000 | |
| 369 | W | A | -1.6013 | |
| 370 | D | A | -2.4105 | |
| 371 | H | A | -2.1336 | |
| 372 | S | A | -1.6799 | |
| 373 | T | A | -1.6540 | |
| 374 | Q | A | -1.7286 | |
| 375 | S | A | -1.2329 | |
| 376 | S | A | -0.6452 | |
| 377 | V | A | 0.0000 | |
| 378 | S | A | -0.6929 | |
| 379 | G | A | -1.0232 | |
| 380 | D | A | -1.1110 | |
| 381 | I | A | 0.0000 | |
| 382 | S | A | -0.8377 | |
| 383 | A | A | -1.0673 | |
| 384 | E | A | -2.2041 | |
| 385 | L | A | 0.0000 | |
| 386 | A | A | -1.1791 | |
| 387 | S | A | -1.0494 | |
| 388 | H | A | -0.8010 | |
| 389 | A | A | 0.0000 | |
| 390 | C | A | 0.0000 | |
| 391 | K | A | -0.9835 | |
| 392 | M | A | 0.0000 | |
| 393 | Y | A | -0.6826 | |
| 394 | V | A | -0.3201 | |
| 395 | L | A | 0.0000 | |
| 396 | T | A | -1.0315 | |
| 397 | P | A | -0.8967 | |
| 398 | Q | A | -0.7814 | |
| 399 | S | A | -0.6198 | |
| 400 | G | A | -0.6206 |
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 | -0.4044 | 6.8664 | View | CSV | PDB |
| 4.5 | -0.4444 | 6.8664 | View | CSV | PDB |
| 5.0 | -0.492 | 6.8664 | View | CSV | PDB |
| 5.5 | -0.5393 | 6.8664 | View | CSV | PDB |
| 6.0 | -0.5772 | 6.8664 | View | CSV | PDB |
| 6.5 | -0.5989 | 6.8664 | View | CSV | PDB |
| 7.0 | -0.6038 | 6.8664 | View | CSV | PDB |
| 7.5 | -0.597 | 6.8664 | View | CSV | PDB |
| 8.0 | -0.5827 | 6.8664 | View | CSV | PDB |
| 8.5 | -0.5625 | 6.8664 | View | CSV | PDB |
| 9.0 | -0.5359 | 6.8664 | 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