| Chain sequence(s) |
A: MAEDMAADEVTAPPRKVLIISAGASHSVALLSGDIVCSWGRGEDGQLGHGDAEDRPSPTQLSALDGHQIVSVTCGADHTVAYSQSGMEVYSWGWGDFGRLGHGNSSDLFTPLPIKALHGIRIKQIACGDSHCLAVTMEGEVQSWGRNQNGQLGLGDTEDSLVPQKIQAFEGIRIKMVAAGAEHTAAVTEDGDLYGWGWGRYGNLGLGDRTDRLVPERVTSTGGEKMSMVACGWRHTISVSYSGALYTYGWSKYGQLGHGDLEDHLIPHKLEALSNSFISQISGGWRHTMALTSDGKLYGWGWNKFGQVGVGNNLDQCSPVQVRFPDDQKVVQVSCGWRHTLAVTERNNVFAWGRGTNGQLGIGESVDRNFPKIIEALSVDGASGQHIESSNIDPSSGKSWVSPAERYAVVPDETGLTDGSSKGNGGDISVPQTDVKRVRI
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] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[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 (00:04:01)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/938a2ffd213510d/tmp/folded.pdb (00:04:01)
[INFO] Main: Simulation completed successfully. (00:05:59)
|
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 | 0.4200 | |
| 2 | A | A | -0.6440 | |
| 3 | E | A | -2.1039 | |
| 4 | D | A | -2.0055 | |
| 5 | M | A | -0.4774 | |
| 6 | A | A | -0.8545 | |
| 7 | A | A | -0.9798 | |
| 8 | D | A | -1.9860 | |
| 9 | E | A | -1.8158 | |
| 10 | V | A | 0.3170 | |
| 11 | T | A | -0.1648 | |
| 12 | A | A | -0.1477 | |
| 13 | P | A | -0.3733 | |
| 14 | P | A | -1.0267 | |
| 15 | R | A | -1.5024 | |
| 16 | K | A | -1.2856 | |
| 17 | V | A | 0.0000 | |
| 18 | L | A | 0.6289 | |
| 19 | I | A | 0.7391 | |
| 20 | I | A | 0.0000 | |
| 21 | S | A | 0.0396 | |
| 22 | A | A | 0.0000 | |
| 23 | G | A | 0.0000 | |
| 24 | A | A | 0.0000 | |
| 25 | S | A | 0.0000 | |
| 26 | H | A | 0.0000 | |
| 27 | S | A | 0.0000 | |
| 28 | V | A | 0.0000 | |
| 29 | A | A | 0.0000 | |
| 30 | L | A | 0.0000 | |
| 31 | L | A | 0.0000 | |
| 32 | S | A | -0.7226 | |
| 33 | G | A | -1.3044 | |
| 34 | D | A | -1.1955 | |
| 35 | I | A | 0.0000 | |
| 36 | V | A | 0.0000 | |
| 37 | C | A | 0.0000 | |
| 38 | S | A | 0.0000 | |
| 39 | W | A | 0.0000 | |
| 40 | G | A | 0.0000 | |
| 41 | R | A | -0.8845 | |
| 42 | G | A | 0.0000 | |
| 43 | E | A | -1.0404 | |
| 44 | D | A | 0.0000 | |
| 45 | G | A | 0.0000 | |
| 46 | Q | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | G | A | 0.0000 | |
| 49 | H | A | 0.0000 | |
| 50 | G | A | -0.4252 | |
| 51 | D | A | -1.2277 | |
| 52 | A | A | -1.5651 | |
| 53 | E | A | -2.2324 | |
| 54 | D | A | -1.4150 | |
| 55 | R | A | -0.9962 | |
| 56 | P | A | -1.1329 | |
| 57 | S | A | -0.9163 | |
| 58 | P | A | 0.0000 | |
| 59 | T | A | 0.0000 | |
| 60 | Q | A | -0.9173 | |
| 61 | L | A | 0.0000 | |
| 62 | S | A | -0.8813 | |
| 63 | A | A | -0.3812 | |
| 64 | L | A | 0.0000 | |
| 65 | D | A | -1.5144 | |
| 66 | G | A | -1.5814 | |
| 67 | H | A | -1.6544 | |
| 68 | Q | A | -1.8981 | |
| 69 | I | A | 0.0000 | |
| 70 | V | A | 0.4621 | |
| 71 | S | A | 0.2542 | |
| 72 | V | A | 0.0000 | |
| 73 | T | A | 0.0108 | |
| 74 | C | A | 0.0000 | |
| 75 | G | A | 0.0000 | |
| 76 | A | A | 0.0000 | |
| 77 | D | A | 0.0000 | |
| 78 | H | A | 0.0000 | |
| 79 | T | A | 0.0000 | |
| 80 | V | A | 0.0000 | |
| 81 | A | A | 0.0000 | |
| 82 | Y | A | 0.0000 | |
| 83 | S | A | 0.0000 | |
| 84 | Q | A | -1.4158 | |
| 85 | S | A | -1.1590 | |
| 86 | G | A | -1.3293 | |
| 87 | M | A | -1.4144 | |
| 88 | E | A | -1.6949 | |
| 89 | V | A | 0.0000 | |
| 90 | Y | A | 0.0000 | |
| 91 | S | A | 0.0000 | |
| 92 | W | A | 0.0000 | |
| 93 | G | A | 0.0000 | |
| 94 | W | A | 0.0000 | |
| 95 | G | A | 0.0000 | |
| 96 | D | A | -0.4783 | |
| 97 | F | A | -0.3872 | |
| 98 | G | A | 0.0000 | |
| 99 | R | A | 0.0000 | |
| 100 | L | A | 0.0000 | |
| 101 | G | A | 0.0000 | |
| 102 | H | A | 0.0000 | |
| 103 | G | A | -0.4773 | |
| 104 | N | A | -0.9023 | |
| 105 | S | A | -0.6912 | |
| 106 | S | A | -0.6943 | |
| 107 | D | A | -0.5559 | |
| 108 | L | A | 0.2658 | |
| 109 | F | A | 0.3923 | |
| 110 | T | A | 0.2643 | |
| 111 | P | A | 0.4594 | |
| 112 | L | A | 0.5845 | |
| 113 | P | A | -0.5289 | |
| 114 | I | A | 0.0000 | |
| 115 | K | A | -2.0388 | |
| 116 | A | A | -1.1675 | |
| 117 | L | A | 0.0000 | |
| 118 | H | A | -2.0775 | |
| 119 | G | A | -1.5820 | |
| 120 | I | A | -1.1396 | |
| 121 | R | A | -2.4172 | |
| 122 | I | A | 0.0000 | |
| 123 | K | A | -1.3866 | |
| 124 | Q | A | -0.7174 | |
| 125 | I | A | 0.0000 | |
| 126 | A | A | 0.0000 | |
| 127 | C | A | 0.0272 | |
| 128 | G | A | 0.0000 | |
| 129 | D | A | -0.2273 | |
| 130 | S | A | 0.0000 | |
| 131 | H | A | 0.0000 | |
| 132 | C | A | 0.0000 | |
| 133 | L | A | 0.0000 | |
| 134 | A | A | 0.0000 | |
| 135 | V | A | 0.0000 | |
| 136 | T | A | 0.0000 | |
| 137 | M | A | -1.5954 | |
| 138 | E | A | -2.6167 | |
| 139 | G | A | 0.0000 | |
| 140 | E | A | -2.6194 | |
| 141 | V | A | 0.0000 | |
| 142 | Q | A | -1.3868 | |
| 143 | S | A | 0.0000 | |
| 144 | W | A | 0.0000 | |
| 145 | G | A | 0.0000 | |
| 146 | R | A | -0.9790 | |
| 147 | N | A | 0.0000 | |
| 148 | Q | A | -1.6742 | |
| 149 | N | A | -1.1238 | |
| 150 | G | A | 0.0000 | |
| 151 | Q | A | 0.0000 | |
| 152 | L | A | 0.0000 | |
| 153 | G | A | 0.0000 | |
| 154 | L | A | -0.7269 | |
| 155 | G | A | -0.5589 | |
| 156 | D | A | -1.6161 | |
| 157 | T | A | -1.8755 | |
| 158 | E | A | -2.5477 | |
| 159 | D | A | -1.4279 | |
| 160 | S | A | 0.0000 | |
| 161 | L | A | 0.0597 | |
| 162 | V | A | 0.2073 | |
| 163 | P | A | -0.6362 | |
| 164 | Q | A | -1.5928 | |
| 165 | K | A | -2.8348 | |
| 166 | I | A | 0.0000 | |
| 167 | Q | A | -2.3686 | |
| 168 | A | A | -1.1545 | |
| 169 | F | A | 0.0000 | |
| 170 | E | A | -2.9027 | |
| 171 | G | A | -1.7818 | |
| 172 | I | A | -2.2070 | |
| 173 | R | A | -3.4291 | |
| 174 | I | A | 0.0000 | |
| 175 | K | A | -2.2200 | |
| 176 | M | A | -0.7391 | |
| 177 | V | A | 0.0000 | |
| 178 | A | A | 0.0000 | |
| 179 | A | A | -0.0369 | |
| 180 | G | A | 0.0000 | |
| 181 | A | A | 0.0000 | |
| 182 | E | A | -0.5079 | |
| 183 | H | A | 0.0000 | |
| 184 | T | A | 0.0000 | |
| 185 | A | A | 0.0000 | |
| 186 | A | A | 0.0000 | |
| 187 | V | A | 0.0000 | |
| 188 | T | A | 0.0000 | |
| 189 | E | A | -3.6249 | |
| 190 | D | A | -3.5652 | |
| 191 | G | A | -2.5041 | |
| 192 | D | A | -2.4374 | |
| 193 | L | A | 0.0000 | |
| 194 | Y | A | 0.0000 | |
| 195 | G | A | 0.0000 | |
| 196 | W | A | 0.0000 | |
| 197 | G | A | 0.0000 | |
| 198 | W | A | -0.7649 | |
| 199 | G | A | 0.0000 | |
| 200 | R | A | -1.9758 | |
| 201 | Y | A | 0.0000 | |
| 202 | G | A | 0.0000 | |
| 203 | N | A | 0.0000 | |
| 204 | L | A | 0.0000 | |
| 205 | G | A | 0.0000 | |
| 206 | L | A | -0.3809 | |
| 207 | G | A | -0.3252 | |
| 208 | D | A | -1.2476 | |
| 209 | R | A | -1.8762 | |
| 210 | T | A | -1.2457 | |
| 211 | D | A | -0.7790 | |
| 212 | R | A | -0.2233 | |
| 213 | L | A | 0.2612 | |
| 214 | V | A | 0.5377 | |
| 215 | P | A | -0.2451 | |
| 216 | E | A | -1.0912 | |
| 217 | R | A | -1.6809 | |
| 218 | V | A | 0.0000 | |
| 219 | T | A | -0.7412 | |
| 220 | S | A | -0.3822 | |
| 221 | T | A | -1.0307 | |
| 222 | G | A | -1.2330 | |
| 223 | G | A | -1.2529 | |
| 224 | E | A | -1.4152 | |
| 225 | K | A | -2.4490 | |
| 226 | M | A | 0.0000 | |
| 227 | S | A | -0.7471 | |
| 228 | M | A | -0.1706 | |
| 229 | V | A | 0.0000 | |
| 230 | A | A | 0.0384 | |
| 231 | C | A | 0.0604 | |
| 232 | G | A | 0.0000 | |
| 233 | W | A | 0.0000 | |
| 234 | R | A | 0.0000 | |
| 235 | H | A | 0.0000 | |
| 236 | T | A | 0.0000 | |
| 237 | I | A | 0.0000 | |
| 238 | S | A | 0.0000 | |
| 239 | V | A | 0.0000 | |
| 240 | S | A | 0.0000 | |
| 241 | Y | A | 0.8692 | |
| 242 | S | A | 0.4892 | |
| 243 | G | A | 0.0000 | |
| 244 | A | A | -0.0638 | |
| 245 | L | A | 0.0000 | |
| 246 | Y | A | 0.0000 | |
| 247 | T | A | 0.0000 | |
| 248 | Y | A | 0.0000 | |
| 249 | G | A | 0.0000 | |
| 250 | W | A | 0.0000 | |
| 251 | S | A | 0.0000 | |
| 252 | K | A | -1.0001 | |
| 253 | Y | A | 0.0000 | |
| 254 | G | A | 0.0000 | |
| 255 | Q | A | 0.0000 | |
| 256 | L | A | 0.0000 | |
| 257 | G | A | 0.0000 | |
| 258 | H | A | -1.3434 | |
| 259 | G | A | -1.0402 | |
| 260 | D | A | -1.4444 | |
| 261 | L | A | -0.4264 | |
| 262 | E | A | -1.8771 | |
| 263 | D | A | -1.1074 | |
| 264 | H | A | -0.3669 | |
| 265 | L | A | -0.1790 | |
| 266 | I | A | 0.5518 | |
| 267 | P | A | 0.0000 | |
| 268 | H | A | -0.9386 | |
| 269 | K | A | -1.5185 | |
| 270 | L | A | 0.0000 | |
| 271 | E | A | -2.3888 | |
| 272 | A | A | -1.2735 | |
| 273 | L | A | 0.0000 | |
| 274 | S | A | -1.3127 | |
| 275 | N | A | -1.2744 | |
| 276 | S | A | -0.5202 | |
| 277 | F | A | 1.1275 | |
| 278 | I | A | 0.0000 | |
| 279 | S | A | 0.0788 | |
| 280 | Q | A | -0.0860 | |
| 281 | I | A | 0.0000 | |
| 282 | S | A | -0.1299 | |
| 283 | G | A | -0.0250 | |
| 284 | G | A | 0.0000 | |
| 285 | W | A | 0.0000 | |
| 286 | R | A | 0.0000 | |
| 287 | H | A | 0.0000 | |
| 288 | T | A | 0.0000 | |
| 289 | M | A | 0.0000 | |
| 290 | A | A | 0.0000 | |
| 291 | L | A | 0.0000 | |
| 292 | T | A | 0.0000 | |
| 293 | S | A | -0.8916 | |
| 294 | D | A | -2.1301 | |
| 295 | G | A | -2.3025 | |
| 296 | K | A | -2.8539 | |
| 297 | L | A | 0.0000 | |
| 298 | Y | A | -0.7743 | |
| 299 | G | A | 0.0000 | |
| 300 | W | A | 0.0000 | |
| 301 | G | A | 0.0000 | |
| 302 | W | A | 0.0000 | |
| 303 | N | A | 0.0000 | |
| 304 | K | A | -1.5956 | |
| 305 | F | A | 0.0000 | |
| 306 | G | A | 0.0000 | |
| 307 | Q | A | 0.0000 | |
| 308 | V | A | 0.0000 | |
| 309 | G | A | 0.0000 | |
| 310 | V | A | -0.0216 | |
| 311 | G | A | -0.3328 | |
| 312 | N | A | -0.8194 | |
| 313 | N | A | -1.3117 | |
| 314 | L | A | -0.1010 | |
| 315 | D | A | -1.1954 | |
| 316 | Q | A | -0.5953 | |
| 317 | C | A | -0.3449 | |
| 318 | S | A | -0.6774 | |
| 319 | P | A | -0.1463 | |
| 320 | V | A | -0.2478 | |
| 321 | Q | A | -1.6290 | |
| 322 | V | A | 0.0000 | |
| 323 | R | A | -2.8330 | |
| 324 | F | A | 0.0000 | |
| 325 | P | A | -2.2532 | |
| 326 | D | A | -3.1821 | |
| 327 | D | A | -3.6847 | |
| 328 | Q | A | 0.0000 | |
| 329 | K | A | -3.2524 | |
| 330 | V | A | 0.0000 | |
| 331 | V | A | -0.2372 | |
| 332 | Q | A | 0.1582 | |
| 333 | V | A | 0.0000 | |
| 334 | S | A | -0.0719 | |
| 335 | C | A | 0.0000 | |
| 336 | G | A | 0.0000 | |
| 337 | W | A | 0.0141 | |
| 338 | R | A | -0.3966 | |
| 339 | H | A | 0.0000 | |
| 340 | T | A | 0.0000 | |
| 341 | L | A | 0.0000 | |
| 342 | A | A | 0.0000 | |
| 343 | V | A | 0.0000 | |
| 344 | T | A | 0.0000 | |
| 345 | E | A | -2.0492 | |
| 346 | R | A | -2.0820 | |
| 347 | N | A | 0.0000 | |
| 348 | N | A | 0.0000 | |
| 349 | V | A | 0.0000 | |
| 350 | F | A | 0.0000 | |
| 351 | A | A | 0.0000 | |
| 352 | W | A | 0.0000 | |
| 353 | G | A | 0.0000 | |
| 354 | R | A | -0.7206 | |
| 355 | G | A | 0.0000 | |
| 356 | T | A | -0.6832 | |
| 357 | N | A | -1.0734 | |
| 358 | G | A | 0.0000 | |
| 359 | Q | A | 0.0000 | |
| 360 | L | A | 0.0000 | |
| 361 | G | A | 0.0000 | |
| 362 | I | A | -0.7336 | |
| 363 | G | A | -1.3675 | |
| 364 | E | A | -1.9745 | |
| 365 | S | A | -1.1606 | |
| 366 | V | A | -0.5241 | |
| 367 | D | A | -0.8730 | |
| 368 | R | A | -0.8951 | |
| 369 | N | A | -0.5150 | |
| 370 | F | A | 0.7106 | |
| 371 | P | A | 0.0000 | |
| 372 | K | A | -0.3627 | |
| 373 | I | A | -0.1774 | |
| 374 | I | A | 0.0000 | |
| 375 | E | A | -1.3402 | |
| 376 | A | A | -1.0894 | |
| 377 | L | A | 0.0000 | |
| 378 | S | A | 0.0000 | |
| 379 | V | A | -0.3663 | |
| 380 | D | A | -1.3730 | |
| 381 | G | A | -0.9323 | |
| 382 | A | A | -0.6069 | |
| 383 | S | A | -0.9902 | |
| 384 | G | A | -1.0954 | |
| 385 | Q | A | -1.4716 | |
| 386 | H | A | -1.7769 | |
| 387 | I | A | -1.3972 | |
| 388 | E | A | -2.2202 | |
| 389 | S | A | -1.2717 | |
| 390 | S | A | -0.9964 | |
| 391 | N | A | -1.1734 | |
| 392 | I | A | 0.2285 | |
| 393 | D | A | -1.4809 | |
| 394 | P | A | -1.0299 | |
| 395 | S | A | -1.0930 | |
| 396 | S | A | -1.5910 | |
| 397 | G | A | -1.5961 | |
| 398 | K | A | -2.1417 | |
| 399 | S | A | -0.8308 | |
| 400 | W | A | 0.5735 | |
| 401 | V | A | 0.0000 | |
| 402 | S | A | -0.3749 | |
| 403 | P | A | -0.5398 | |
| 404 | A | A | -0.6243 | |
| 405 | E | A | -1.5731 | |
| 406 | R | A | -0.6391 | |
| 407 | Y | A | 0.4331 | |
| 408 | A | A | 0.9087 | |
| 409 | V | A | 1.6108 | |
| 410 | V | A | 0.7368 | |
| 411 | P | A | -0.4086 | |
| 412 | D | A | -2.1464 | |
| 413 | E | A | -2.5445 | |
| 414 | T | A | -1.3621 | |
| 415 | G | A | -0.7908 | |
| 416 | L | A | 0.5572 | |
| 417 | T | A | -0.4152 | |
| 418 | D | A | -1.8568 | |
| 419 | G | A | -1.3861 | |
| 420 | S | A | -1.3575 | |
| 421 | S | A | -1.7261 | |
| 422 | K | A | -2.4014 | |
| 423 | G | A | -2.1646 | |
| 424 | N | A | -2.3645 | |
| 425 | G | A | -1.7230 | |
| 426 | G | A | -1.1908 | |
| 427 | D | A | -0.8202 | |
| 428 | I | A | 0.9359 | |
| 429 | S | A | 0.5701 | |
| 430 | V | A | 0.1136 | |
| 431 | P | A | -0.4252 | |
| 432 | Q | A | -1.0672 | |
| 433 | T | A | -0.7833 | |
| 434 | D | A | -0.9875 | |
| 435 | V | A | 0.2259 | |
| 436 | K | A | -1.4034 | |
| 437 | R | A | -1.1896 | |
| 438 | V | A | 0.5060 | |
| 439 | R | A | -0.6036 | |
| 440 | I | A | 1.3474 |
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 | -0.34 | 3.1416 | View | CSV | PDB |
| 4.5 | -0.4032 | 3.0007 | View | CSV | PDB |
| 5.0 | -0.4804 | 2.839 | View | CSV | PDB |
| 5.5 | -0.5612 | 2.6689 | View | CSV | PDB |
| 6.0 | -0.6337 | 2.5288 | View | CSV | PDB |
| 6.5 | -0.6889 | 2.5413 | View | CSV | PDB |
| 7.0 | -0.7242 | 2.5633 | View | CSV | PDB |
| 7.5 | -0.7437 | 2.5924 | View | CSV | PDB |
| 8.0 | -0.7521 | 2.625 | View | CSV | PDB |
| 8.5 | -0.7507 | 2.6588 | View | CSV | PDB |
| 9.0 | -0.7388 | 2.693 | 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