| Chain sequence(s) |
A: MARAVGPERRLLAVYTGGTIGMRSELGVLVPGTGLAAILRTLPMFHDEEHARARGLSEDTLVLPPASRNQRILYTVLECQPLFDSSDMTIAEWVCLAQTIKRHYEQYHGFVVIHGTDTMAFAASMLSFMLENLQKTVILTGAQVPIHALWSDGRENLLGALLMAGQYVIPEVCLFFQNQLFRGNRATKVDARRFAAFCSPNLLPLATVGADITINRELVRKVDGKAGLVVHSSMEQDVGLLRLYPGIPAALVRAFLQPPLKGVVMETFGSGNGPTKPDLLQELRVATERGLVIVNCTHCLQGAVTTDYAAGMAMAGAGVISGFDMTSEAALAKLSYVLGQPGLSLDVRKELLTKDLRGEMTPPSVEERRPSLQGNTLGGGVSWLLSLSGSQEADALRNALVPSLA
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 (00:11:12)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/64fb8dcbe56390/tmp/folded.pdb (00:11:12)
[INFO] Main: Simulation completed successfully. (00:16:19)
|
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 | -0.5569 | |
| 2 | A | A | -0.1197 | |
| 3 | R | A | -1.0896 | |
| 4 | A | A | 0.0000 | |
| 5 | V | A | 1.1454 | |
| 6 | G | A | -0.0745 | |
| 7 | P | A | -0.9599 | |
| 8 | E | A | -0.9016 | |
| 9 | R | A | 0.0000 | |
| 10 | R | A | -1.2711 | |
| 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 | -0.4721 | |
| 20 | I | A | 0.0000 | |
| 21 | G | A | 0.0000 | |
| 22 | M | A | 0.0000 | |
| 23 | R | A | -1.6400 | |
| 24 | S | A | -0.4378 | |
| 25 | E | A | -0.1880 | |
| 26 | L | A | 1.2615 | |
| 27 | G | A | 0.6968 | |
| 28 | V | A | 1.7377 | |
| 29 | L | A | 0.7618 | |
| 30 | V | A | 0.2209 | |
| 31 | P | A | -0.5633 | |
| 32 | G | A | 0.0000 | |
| 33 | T | A | -0.5119 | |
| 34 | G | A | -0.2751 | |
| 35 | L | A | 0.0000 | |
| 36 | A | A | -0.5969 | |
| 37 | A | A | -0.3422 | |
| 38 | I | A | 0.2256 | |
| 39 | L | A | 0.0000 | |
| 40 | R | A | -0.5631 | |
| 41 | T | A | -0.1213 | |
| 42 | L | A | -0.0085 | |
| 43 | P | A | -0.2377 | |
| 44 | M | A | -0.0903 | |
| 45 | F | A | 0.0000 | |
| 46 | H | A | 0.0000 | |
| 47 | D | A | -1.4957 | |
| 48 | E | A | -2.2573 | |
| 49 | E | A | -3.0233 | |
| 50 | H | A | -2.2946 | |
| 51 | A | A | 0.0000 | |
| 52 | R | A | -3.1834 | |
| 53 | A | A | -2.1464 | |
| 54 | R | A | -2.3463 | |
| 55 | G | A | -1.8547 | |
| 56 | L | A | -1.5156 | |
| 57 | S | A | -1.7305 | |
| 58 | E | A | -2.4034 | |
| 59 | D | A | -1.8913 | |
| 60 | T | A | -1.1529 | |
| 61 | L | A | 0.0000 | |
| 62 | V | A | 0.0000 | |
| 63 | L | A | 0.0000 | |
| 64 | P | A | -0.6673 | |
| 65 | P | A | -1.1575 | |
| 66 | A | A | -0.8829 | |
| 67 | S | A | -1.7271 | |
| 68 | R | A | -2.7241 | |
| 69 | N | A | -2.5645 | |
| 70 | Q | A | -1.5702 | |
| 71 | R | A | -1.4469 | |
| 72 | I | A | 0.0000 | |
| 73 | L | A | 0.0000 | |
| 74 | Y | A | 0.0000 | |
| 75 | T | A | -0.6326 | |
| 76 | V | A | 0.0000 | |
| 77 | L | A | -0.0668 | |
| 78 | E | A | -0.5743 | |
| 79 | C | A | -0.4142 | |
| 80 | Q | A | -1.2272 | |
| 81 | P | A | -0.9742 | |
| 82 | L | A | -0.4746 | |
| 83 | F | A | -0.9533 | |
| 84 | D | A | -1.8346 | |
| 85 | S | A | 0.0000 | |
| 86 | S | A | -1.9197 | |
| 87 | D | A | -2.4529 | |
| 88 | M | A | 0.0000 | |
| 89 | T | A | -0.5544 | |
| 90 | I | A | 0.0424 | |
| 91 | A | A | 0.0349 | |
| 92 | E | A | -0.2244 | |
| 93 | W | A | 0.0000 | |
| 94 | V | A | 0.2447 | |
| 95 | C | A | 0.3846 | |
| 96 | L | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | Q | A | -1.2756 | |
| 99 | T | A | 0.0000 | |
| 100 | I | A | 0.0000 | |
| 101 | K | A | -2.2274 | |
| 102 | R | A | -3.0420 | |
| 103 | H | A | -2.4365 | |
| 104 | Y | A | 0.0000 | |
| 105 | E | A | -2.9689 | |
| 106 | Q | A | -2.6957 | |
| 107 | Y | A | 0.0000 | |
| 108 | H | A | -1.2439 | |
| 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 | -2.2330 | |
| 118 | T | A | -1.2152 | |
| 119 | M | A | 0.0000 | |
| 120 | A | A | 0.0000 | |
| 121 | F | A | 0.2653 | |
| 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 | -0.4357 | |
| 132 | N | A | -1.1741 | |
| 133 | L | A | 0.0000 | |
| 134 | Q | A | -1.2590 | |
| 135 | K | A | -0.3583 | |
| 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 | -0.8847 | |
| 144 | V | A | 0.2673 | |
| 145 | P | A | 0.0000 | |
| 146 | I | A | 0.0000 | |
| 147 | H | A | -0.5051 | |
| 148 | A | A | 0.5208 | |
| 149 | L | A | 1.9358 | |
| 150 | W | A | 1.8210 | |
| 151 | S | A | 0.0000 | |
| 152 | D | A | 0.0000 | |
| 153 | G | A | 0.0000 | |
| 154 | R | A | -1.0210 | |
| 155 | E | A | -2.1513 | |
| 156 | N | A | 0.0000 | |
| 157 | L | A | 0.0000 | |
| 158 | L | A | -0.2961 | |
| 159 | G | A | -0.6274 | |
| 160 | A | A | 0.0000 | |
| 161 | L | A | 0.0000 | |
| 162 | L | A | 0.3936 | |
| 163 | M | A | 0.0000 | |
| 164 | A | A | 0.0000 | |
| 165 | G | A | 0.0000 | |
| 166 | Q | A | -0.2323 | |
| 167 | Y | A | 0.0472 | |
| 168 | V | A | 0.3905 | |
| 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 | -1.7123 | |
| 178 | N | A | -1.4920 | |
| 179 | Q | A | -0.7037 | |
| 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 | 0.1809 | |
| 188 | K | A | -0.1843 | |
| 189 | V | A | 0.5968 | |
| 190 | D | A | -0.8018 | |
| 191 | A | A | -1.5031 | |
| 192 | R | A | -2.5779 | |
| 193 | R | A | -2.5975 | |
| 194 | F | A | -1.2130 | |
| 195 | A | A | -0.9774 | |
| 196 | A | A | 0.0000 | |
| 197 | F | A | 0.0000 | |
| 198 | C | A | 0.5513 | |
| 199 | S | A | 0.4170 | |
| 200 | P | A | 0.2362 | |
| 201 | N | A | -0.1184 | |
| 202 | L | A | 0.6655 | |
| 203 | L | A | 1.4899 | |
| 204 | P | A | 0.6283 | |
| 205 | L | A | 0.0000 | |
| 206 | A | A | 0.0000 | |
| 207 | T | A | -0.4127 | |
| 208 | V | A | -0.6183 | |
| 209 | G | A | -0.9728 | |
| 210 | A | A | -0.8546 | |
| 211 | D | A | -1.5690 | |
| 212 | I | A | -0.3779 | |
| 213 | T | A | -0.5373 | |
| 214 | I | A | -0.7279 | |
| 215 | N | A | -1.3465 | |
| 216 | R | A | -2.8691 | |
| 217 | E | A | -2.8729 | |
| 218 | L | A | -1.3102 | |
| 219 | V | A | -1.3906 | |
| 220 | R | A | -1.9516 | |
| 221 | K | A | -2.4548 | |
| 222 | V | A | -1.5664 | |
| 223 | D | A | -2.6163 | |
| 224 | G | A | -2.2964 | |
| 225 | K | A | -2.3846 | |
| 226 | A | A | -1.4497 | |
| 227 | G | A | -0.9298 | |
| 228 | L | A | 0.0000 | |
| 229 | V | A | 0.5610 | |
| 230 | V | A | 0.1017 | |
| 231 | H | A | -0.0619 | |
| 232 | S | A | -0.1048 | |
| 233 | S | A | -0.5287 | |
| 234 | M | A | 0.0000 | |
| 235 | E | A | -1.1948 | |
| 236 | Q | A | -1.7562 | |
| 237 | D | A | -1.6818 | |
| 238 | V | A | -0.6940 | |
| 239 | G | A | -0.0042 | |
| 240 | L | A | 0.2294 | |
| 241 | L | A | 0.0000 | |
| 242 | R | A | -1.6077 | |
| 243 | L | A | 0.0000 | |
| 244 | Y | A | 0.2441 | |
| 245 | P | A | -0.0284 | |
| 246 | G | A | -0.4739 | |
| 247 | I | A | 0.0000 | |
| 248 | P | A | -0.5166 | |
| 249 | A | A | -1.0367 | |
| 250 | A | A | -0.4301 | |
| 251 | L | A | 0.3550 | |
| 252 | V | A | 0.0000 | |
| 253 | R | A | -1.7252 | |
| 254 | A | A | -0.4439 | |
| 255 | F | A | 0.1632 | |
| 256 | L | A | 0.0000 | |
| 257 | Q | A | -1.1925 | |
| 258 | P | A | -0.9418 | |
| 259 | P | A | -0.9503 | |
| 260 | L | A | -0.8922 | |
| 261 | K | A | -1.4442 | |
| 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 | -0.0264 | |
| 269 | G | A | -0.2167 | |
| 270 | S | A | -0.4494 | |
| 271 | G | A | 0.0000 | |
| 272 | N | A | -0.0779 | |
| 273 | G | A | 0.0000 | |
| 274 | P | A | -0.3951 | |
| 275 | T | A | -0.4990 | |
| 276 | K | A | -1.3446 | |
| 277 | P | A | -1.6189 | |
| 278 | D | A | -2.7928 | |
| 279 | L | A | 0.0000 | |
| 280 | L | A | -1.5255 | |
| 281 | Q | A | -2.4228 | |
| 282 | E | A | -1.9983 | |
| 283 | L | A | 0.0000 | |
| 284 | R | A | -2.6392 | |
| 285 | V | A | -1.6106 | |
| 286 | A | A | 0.0000 | |
| 287 | T | A | -1.9854 | |
| 288 | E | A | -2.7810 | |
| 289 | R | A | -2.5753 | |
| 290 | G | A | -1.7365 | |
| 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 | -0.9418 | |
| 299 | C | A | 0.0757 | |
| 300 | L | A | 0.8188 | |
| 301 | Q | A | -0.7989 | |
| 302 | G | A | -0.7217 | |
| 303 | A | A | -0.3480 | |
| 304 | V | A | 0.0000 | |
| 305 | T | A | -0.3622 | |
| 306 | T | A | -0.2931 | |
| 307 | D | A | -1.1427 | |
| 308 | Y | A | 0.4160 | |
| 309 | A | A | 0.4840 | |
| 310 | A | A | 0.2933 | |
| 311 | G | A | 0.0000 | |
| 312 | M | A | 0.7545 | |
| 313 | A | A | 0.4048 | |
| 314 | M | A | 0.0000 | |
| 315 | A | A | -0.0333 | |
| 316 | G | A | -0.3626 | |
| 317 | A | A | 0.0000 | |
| 318 | G | A | -0.9205 | |
| 319 | V | A | 0.0000 | |
| 320 | I | A | 0.0000 | |
| 321 | S | A | -0.0038 | |
| 322 | G | A | 0.0000 | |
| 323 | F | A | 0.0746 | |
| 324 | D | A | 0.0000 | |
| 325 | M | A | 0.0000 | |
| 326 | T | A | 0.0390 | |
| 327 | S | A | 0.2034 | |
| 328 | E | A | 0.0000 | |
| 329 | A | A | 0.0000 | |
| 330 | A | A | 0.0000 | |
| 331 | L | A | 0.4003 | |
| 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 | -0.6830 | |
| 340 | Q | A | -0.4265 | |
| 341 | P | A | -0.4581 | |
| 342 | G | A | -0.2565 | |
| 343 | L | A | 0.0981 | |
| 344 | S | A | -0.3620 | |
| 345 | L | A | -0.4629 | |
| 346 | D | A | -1.7432 | |
| 347 | V | A | -0.5296 | |
| 348 | R | A | -0.8198 | |
| 349 | K | A | -1.7431 | |
| 350 | E | A | -2.3090 | |
| 351 | L | A | -1.2246 | |
| 352 | L | A | 0.0000 | |
| 353 | T | A | -1.3740 | |
| 354 | K | A | -1.9459 | |
| 355 | D | A | -1.6064 | |
| 356 | L | A | -0.6273 | |
| 357 | R | A | -0.7496 | |
| 358 | G | A | -0.5787 | |
| 359 | E | A | 0.0000 | |
| 360 | M | A | 0.0000 | |
| 361 | T | A | -0.5775 | |
| 362 | P | A | -0.4726 | |
| 363 | P | A | -0.9126 | |
| 364 | S | A | -1.1747 | |
| 365 | V | A | -0.6490 | |
| 366 | E | A | -3.0775 | |
| 367 | E | A | -3.7825 | |
| 368 | R | A | -3.8504 | |
| 369 | R | A | -3.5480 | |
| 370 | P | A | -2.3883 | |
| 371 | S | A | -1.1804 | |
| 372 | L | A | 0.2528 | |
| 373 | Q | A | -1.0022 | |
| 374 | G | A | -1.0926 | |
| 375 | N | A | -0.8917 | |
| 376 | T | A | -0.0184 | |
| 377 | L | A | 1.2809 | |
| 378 | G | A | 0.0000 | |
| 379 | G | A | 0.3766 | |
| 380 | G | A | 1.0867 | |
| 381 | V | A | 1.7492 | |
| 382 | S | A | 1.5051 | |
| 383 | W | A | 2.1123 | |
| 384 | L | A | 2.1440 | |
| 385 | L | A | 2.3054 | |
| 386 | S | A | 1.2961 | |
| 387 | L | A | 0.7098 | |
| 388 | S | A | -0.1641 | |
| 389 | G | A | -1.0240 | |
| 390 | S | A | -1.3249 | |
| 391 | Q | A | -2.1809 | |
| 392 | E | A | -1.9437 | |
| 393 | A | A | -1.5746 | |
| 394 | D | A | -2.1807 | |
| 395 | A | A | -1.4778 | |
| 396 | L | A | -0.6390 | |
| 397 | R | A | -1.6308 | |
| 398 | N | A | -0.9080 | |
| 399 | A | A | 0.2745 | |
| 400 | L | A | 1.4805 | |
| 401 | V | A | 1.8291 | |
| 402 | P | A | 0.7994 | |
| 403 | S | A | 0.7225 | |
| 404 | L | A | 1.6623 | |
| 405 | A | A | 0.7145 |
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 | -0.2415 | 3.9827 | View | CSV | PDB |
| 4.5 | -0.2894 | 3.9904 | View | CSV | PDB |
| 5.0 | -0.3495 | 4.0087 | View | CSV | PDB |
| 5.5 | -0.4136 | 4.0402 | View | CSV | PDB |
| 6.0 | -0.474 | 4.0753 | View | CSV | PDB |
| 6.5 | -0.5244 | 4.1 | View | CSV | PDB |
| 7.0 | -0.5614 | 4.1118 | View | CSV | PDB |
| 7.5 | -0.5872 | 4.1162 | View | CSV | PDB |
| 8.0 | -0.6053 | 4.1177 | View | CSV | PDB |
| 8.5 | -0.6167 | 4.1182 | View | CSV | PDB |
| 9.0 | -0.6203 | 4.1183 | 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