| Chain sequence(s) |
A: MARAVGPERRLLAVYTGGTIGMRSELGVLVPGTGLAAILRTLPMFHDEEHARARGLSEDTLVLPPASRNQRILYTVLECQPLFDSSDMTIAEWVCLAQTIKRHYEQYHGFVVIHGTDTMAFAASMLSFMLENLQKTVILTGAQVPIHALWSDGRENLLGALLMAGQYVIPEVCLFFQNQLFRGNRATKVDARRFAAFCSPNLLPLATVGADITINRELVRKVDGKAGLVVHSSMEQDVGLLRLYPGIPAALVRAFLQPPLKGVVMETFGSGNGPTKPDLLQELRVATERGLVIVNCTHCLQGAVTTDYAAGMAMAGAGVISGFDMTSEAALAKLSYVLGQPGLSLDVRKELLTKDLRGEMTPPSVEERRPSLQGNTLGGGVSWLLSLSGSQEADALRNALV
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. (00:00:02)
[INFO] FoldX: Starting FoldX energy minimization (00:00:02)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:08:20)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/e9c6dee5ac1d827/tmp/folded.pdb (00:08:20)
[INFO] Main: Simulation completed successfully. (00:15:14)
|
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 | -0.2680 | |
| 2 | A | A | 0.0517 | |
| 3 | R | A | -1.0259 | |
| 4 | A | A | 0.0393 | |
| 5 | V | A | 1.1267 | |
| 6 | G | A | -0.0605 | |
| 7 | P | A | -0.8874 | |
| 8 | E | A | -0.9335 | |
| 9 | R | A | 0.0000 | |
| 10 | R | A | -1.8492 | |
| 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 | -0.4833 | |
| 20 | I | A | 0.0000 | |
| 21 | G | A | 0.0000 | |
| 22 | M | A | 0.0000 | |
| 23 | R | A | -1.6164 | |
| 24 | S | A | -0.7449 | |
| 25 | E | A | -0.9345 | |
| 26 | L | A | 0.8975 | |
| 27 | G | A | 0.4634 | |
| 28 | V | A | 1.4923 | |
| 29 | L | A | 0.7152 | |
| 30 | V | A | 0.0084 | |
| 31 | P | A | -0.6966 | |
| 32 | G | A | 0.0000 | |
| 33 | T | A | -0.5292 | |
| 34 | G | A | -0.2816 | |
| 35 | L | A | 0.0000 | |
| 36 | A | A | -0.6694 | |
| 37 | A | A | -0.4521 | |
| 38 | I | A | 0.1051 | |
| 39 | L | A | 0.0000 | |
| 40 | R | A | -0.6643 | |
| 41 | T | A | -0.1510 | |
| 42 | L | A | -0.0064 | |
| 43 | P | A | -0.2445 | |
| 44 | M | A | -0.1107 | |
| 45 | F | A | 0.0000 | |
| 46 | H | A | 0.0000 | |
| 47 | D | A | -1.4705 | |
| 48 | E | A | -2.1767 | |
| 49 | E | A | -2.9577 | |
| 50 | H | A | -2.1975 | |
| 51 | A | A | 0.0000 | |
| 52 | R | A | -3.0907 | |
| 53 | A | A | -2.0319 | |
| 54 | R | A | -2.1307 | |
| 55 | G | A | -1.7502 | |
| 56 | L | A | -1.4269 | |
| 57 | S | A | -1.6950 | |
| 58 | E | A | -2.4008 | |
| 59 | D | A | -1.8816 | |
| 60 | T | A | -1.2206 | |
| 61 | L | A | 0.0000 | |
| 62 | V | A | 0.0000 | |
| 63 | L | A | 0.0000 | |
| 64 | P | A | -0.6484 | |
| 65 | P | A | -1.1189 | |
| 66 | A | A | -0.8240 | |
| 67 | S | A | -1.6191 | |
| 68 | R | A | -2.6723 | |
| 69 | N | A | -2.5156 | |
| 70 | Q | A | -1.4915 | |
| 71 | R | A | -1.4353 | |
| 72 | I | A | 0.0000 | |
| 73 | L | A | 0.0000 | |
| 74 | Y | A | 0.0000 | |
| 75 | T | A | -0.7328 | |
| 76 | V | A | 0.0000 | |
| 77 | L | A | -0.0820 | |
| 78 | E | A | -0.5817 | |
| 79 | C | A | -0.4286 | |
| 80 | Q | A | -1.2327 | |
| 81 | P | A | -0.9933 | |
| 82 | L | A | -0.5611 | |
| 83 | F | A | -1.0551 | |
| 84 | D | A | -1.9945 | |
| 85 | S | A | 0.0000 | |
| 86 | S | A | -1.9372 | |
| 87 | D | A | -2.4783 | |
| 88 | M | A | 0.0000 | |
| 89 | T | A | -0.5888 | |
| 90 | I | A | 0.0011 | |
| 91 | A | A | 0.0132 | |
| 92 | E | A | -0.2969 | |
| 93 | W | A | 0.0000 | |
| 94 | V | A | 0.1655 | |
| 95 | C | A | 0.2528 | |
| 96 | L | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | Q | A | -1.6328 | |
| 99 | T | A | -1.1628 | |
| 100 | I | A | 0.0000 | |
| 101 | K | A | -2.1667 | |
| 102 | R | A | -3.0221 | |
| 103 | H | A | -2.3540 | |
| 104 | Y | A | 0.0000 | |
| 105 | E | A | -2.9280 | |
| 106 | Q | A | -2.7632 | |
| 107 | Y | A | 0.0000 | |
| 108 | H | A | -1.5330 | |
| 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 | -2.2438 | |
| 118 | T | A | -1.2593 | |
| 119 | M | A | 0.0000 | |
| 120 | A | A | 0.0000 | |
| 121 | F | A | 0.1377 | |
| 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 | -0.2909 | |
| 132 | N | A | -1.2911 | |
| 133 | L | A | 0.0000 | |
| 134 | Q | A | -1.4597 | |
| 135 | K | A | -0.5315 | |
| 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 | -0.8819 | |
| 144 | V | A | 0.3937 | |
| 145 | P | A | 0.0000 | |
| 146 | I | A | 0.0000 | |
| 147 | H | A | -0.1043 | |
| 148 | A | A | 0.7008 | |
| 149 | L | A | 2.0366 | |
| 150 | W | A | 1.8842 | |
| 151 | S | A | 0.0000 | |
| 152 | D | A | 0.0000 | |
| 153 | G | A | 0.0000 | |
| 154 | R | A | -0.9292 | |
| 155 | E | A | -2.1164 | |
| 156 | N | A | 0.0000 | |
| 157 | L | A | 0.0000 | |
| 158 | L | A | -0.2924 | |
| 159 | G | A | -0.6137 | |
| 160 | A | A | 0.0000 | |
| 161 | L | A | 0.0000 | |
| 162 | L | A | 0.3846 | |
| 163 | M | A | 0.0000 | |
| 164 | A | A | 0.0000 | |
| 165 | G | A | 0.0000 | |
| 166 | Q | A | -0.2262 | |
| 167 | Y | A | 0.0250 | |
| 168 | V | A | 0.2576 | |
| 169 | I | A | 0.0000 | |
| 170 | P | A | -0.4662 | |
| 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 | -1.6003 | |
| 178 | N | A | -1.4716 | |
| 179 | Q | A | -0.7255 | |
| 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 | 0.1538 | |
| 188 | K | A | -0.1659 | |
| 189 | V | A | 0.6280 | |
| 190 | D | A | -0.7883 | |
| 191 | A | A | -1.4939 | |
| 192 | R | A | -2.5699 | |
| 193 | R | A | -2.5739 | |
| 194 | F | A | -1.1650 | |
| 195 | A | A | -0.9439 | |
| 196 | A | A | 0.0000 | |
| 197 | F | A | 0.0000 | |
| 198 | C | A | 0.4755 | |
| 199 | S | A | 0.4153 | |
| 200 | P | A | 0.2459 | |
| 201 | N | A | -0.1225 | |
| 202 | L | A | 0.6598 | |
| 203 | L | A | 1.4889 | |
| 204 | P | A | 0.6070 | |
| 205 | L | A | 0.0000 | |
| 206 | A | A | 0.0000 | |
| 207 | T | A | -0.4013 | |
| 208 | V | A | -0.5935 | |
| 209 | G | A | -0.9719 | |
| 210 | A | A | -0.8520 | |
| 211 | D | A | -1.5756 | |
| 212 | I | A | -0.4099 | |
| 213 | T | A | -0.5278 | |
| 214 | I | A | -0.7041 | |
| 215 | N | A | -1.4150 | |
| 216 | R | A | -2.8082 | |
| 217 | E | A | -2.8547 | |
| 218 | L | A | -1.3622 | |
| 219 | V | A | 0.0000 | |
| 220 | R | A | -1.8598 | |
| 221 | K | A | -2.5714 | |
| 222 | V | A | -1.9784 | |
| 223 | D | A | -2.9843 | |
| 224 | G | A | -2.4856 | |
| 225 | K | A | -2.6368 | |
| 226 | A | A | -1.6404 | |
| 227 | G | A | -1.1131 | |
| 228 | L | A | 0.0000 | |
| 229 | V | A | 0.6449 | |
| 230 | V | A | 0.0830 | |
| 231 | H | A | -0.1161 | |
| 232 | S | A | -0.2025 | |
| 233 | S | A | -0.5121 | |
| 234 | M | A | 0.0000 | |
| 235 | E | A | -1.1349 | |
| 236 | Q | A | -1.6698 | |
| 237 | D | A | -1.5257 | |
| 238 | V | A | -0.6551 | |
| 239 | G | A | -0.0470 | |
| 240 | L | A | 0.0961 | |
| 241 | L | A | 0.0000 | |
| 242 | R | A | -1.6182 | |
| 243 | L | A | 0.0000 | |
| 244 | Y | A | 0.3762 | |
| 245 | P | A | 0.0335 | |
| 246 | G | A | -0.4213 | |
| 247 | I | A | 0.0000 | |
| 248 | P | A | -0.3527 | |
| 249 | A | A | -0.9431 | |
| 250 | A | A | -0.3229 | |
| 251 | L | A | 0.4306 | |
| 252 | V | A | 0.0000 | |
| 253 | R | A | -1.1428 | |
| 254 | A | A | -0.3095 | |
| 255 | F | A | 0.2069 | |
| 256 | L | A | 0.0000 | |
| 257 | Q | A | -1.1274 | |
| 258 | P | A | -0.9516 | |
| 259 | P | A | -0.9394 | |
| 260 | L | A | -0.8962 | |
| 261 | K | A | -1.5116 | |
| 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 | -0.1455 | |
| 269 | G | A | -0.3560 | |
| 270 | S | A | -0.5384 | |
| 271 | G | A | 0.0000 | |
| 272 | N | A | -0.1816 | |
| 273 | G | A | 0.0000 | |
| 274 | P | A | -0.4002 | |
| 275 | T | A | -0.5075 | |
| 276 | K | A | -1.2984 | |
| 277 | P | A | -1.6241 | |
| 278 | D | A | -2.4707 | |
| 279 | L | A | 0.0000 | |
| 280 | L | A | -1.4616 | |
| 281 | Q | A | -2.2671 | |
| 282 | E | A | -1.8622 | |
| 283 | L | A | 0.0000 | |
| 284 | R | A | -2.1766 | |
| 285 | V | A | -1.1287 | |
| 286 | A | A | 0.0000 | |
| 287 | T | A | -1.8391 | |
| 288 | E | A | -2.6118 | |
| 289 | R | A | -2.4229 | |
| 290 | G | A | -1.6495 | |
| 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 | -0.9050 | |
| 299 | C | A | 0.1666 | |
| 300 | L | A | 0.9049 | |
| 301 | Q | A | -0.7625 | |
| 302 | G | A | -0.6979 | |
| 303 | A | A | -0.3001 | |
| 304 | V | A | 0.0000 | |
| 305 | T | A | -0.3742 | |
| 306 | T | A | -0.3333 | |
| 307 | D | A | -1.3972 | |
| 308 | Y | A | 0.2791 | |
| 309 | A | A | 0.4113 | |
| 310 | A | A | 0.1676 | |
| 311 | G | A | 0.0000 | |
| 312 | M | A | 0.6986 | |
| 313 | A | A | 0.3765 | |
| 314 | M | A | 0.0000 | |
| 315 | A | A | -0.0092 | |
| 316 | G | A | -0.3158 | |
| 317 | A | A | 0.0000 | |
| 318 | G | A | -0.7241 | |
| 319 | V | A | 0.0000 | |
| 320 | I | A | 0.0000 | |
| 321 | S | A | 0.0293 | |
| 322 | G | A | 0.0000 | |
| 323 | F | A | 0.1588 | |
| 324 | D | A | 0.0000 | |
| 325 | M | A | 0.0000 | |
| 326 | T | A | -0.0514 | |
| 327 | S | A | 0.0774 | |
| 328 | E | A | 0.0633 | |
| 329 | A | A | 0.0000 | |
| 330 | A | A | 0.0000 | |
| 331 | L | A | 0.2974 | |
| 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 | -0.6598 | |
| 340 | Q | A | -0.4428 | |
| 341 | P | A | -0.4680 | |
| 342 | G | A | -0.2732 | |
| 343 | L | A | 0.1224 | |
| 344 | S | A | -0.1844 | |
| 345 | L | A | -0.3861 | |
| 346 | D | A | -1.7284 | |
| 347 | V | A | -0.5937 | |
| 348 | R | A | -0.7853 | |
| 349 | K | A | -1.8110 | |
| 350 | E | A | -2.3991 | |
| 351 | L | A | -1.2486 | |
| 352 | L | A | 0.0000 | |
| 353 | T | A | -1.5068 | |
| 354 | K | A | -2.2589 | |
| 355 | D | A | -1.2201 | |
| 356 | L | A | -0.5314 | |
| 357 | R | A | -0.6139 | |
| 358 | G | A | -0.4737 | |
| 359 | E | A | 0.0000 | |
| 360 | M | A | 0.0000 | |
| 361 | T | A | -0.4682 | |
| 362 | P | A | -0.4136 | |
| 363 | P | A | -0.8431 | |
| 364 | S | A | -0.9804 | |
| 365 | V | A | -0.5455 | |
| 366 | E | A | -2.9014 | |
| 367 | E | A | -3.7232 | |
| 368 | R | A | -3.8313 | |
| 369 | R | A | -3.6182 | |
| 370 | P | A | -2.1622 | |
| 371 | S | A | -0.8602 | |
| 372 | L | A | 0.5361 | |
| 373 | Q | A | -0.8129 | |
| 374 | G | A | -0.8811 | |
| 375 | N | A | -0.4765 | |
| 376 | T | A | 0.1564 | |
| 377 | L | A | 1.3610 | |
| 378 | G | A | 0.6710 | |
| 379 | G | A | 0.4473 | |
| 380 | G | A | 1.2580 | |
| 381 | V | A | 1.7507 | |
| 382 | S | A | 1.4295 | |
| 383 | W | A | 2.0159 | |
| 384 | L | A | 2.1417 | |
| 385 | L | A | 2.3330 | |
| 386 | S | A | 1.3056 | |
| 387 | L | A | 0.6320 | |
| 388 | S | A | -0.2158 | |
| 389 | G | A | -1.3422 | |
| 390 | S | A | -1.7506 | |
| 391 | Q | A | -2.7779 | |
| 392 | E | A | -2.7351 | |
| 393 | A | A | -2.1879 | |
| 394 | D | A | -3.5669 | |
| 395 | A | A | -2.2831 | |
| 396 | L | A | -1.2934 | |
| 397 | R | A | -2.3111 | |
| 398 | N | A | -1.4414 | |
| 399 | A | A | 0.0228 | |
| 400 | L | A | 1.5236 | |
| 401 | V | A | 1.7594 |
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 | -0.2724 | 4.1666 | View | CSV | PDB |
| 4.5 | -0.3234 | 4.1719 | View | CSV | PDB |
| 5.0 | -0.3877 | 4.1839 | View | CSV | PDB |
| 5.5 | -0.4567 | 4.2026 | View | CSV | PDB |
| 6.0 | -0.5213 | 4.2213 | View | CSV | PDB |
| 6.5 | -0.5742 | 4.2331 | View | CSV | PDB |
| 7.0 | -0.6121 | 4.2384 | View | CSV | PDB |
| 7.5 | -0.6377 | 4.2403 | View | CSV | PDB |
| 8.0 | -0.6553 | 4.2409 | View | CSV | PDB |
| 8.5 | -0.6662 | 4.2411 | View | CSV | PDB |
| 9.0 | -0.6694 | 4.2412 | 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