| Chain sequence(s) |
A: FRAPPVIPNVPFLWAWNAPSEFCLGKFDVPLDMSLFSFIGSPRINATGQGVTIFYKDRLGYYPYIDLKTGVTVNGGIPQKISLQKHLDKAKKDISFYMPVDNLGLAVIDWEEWRPTWARNWKPKDVYRNKSIELVQQQNVQLSLTEATKKAKEEFEKAGKDFLVETIKLGKSLRPNHLWGYYLFPDCYNHHYKTPGYNGSCFNVEIKRNDDLSWLWNESTALYPSIYLNTQMSPSAATLFVRNRVREAIRVSKIPDAKSPLPVFAYTRLVFTDEVLKFLSQDELVYTFGETVALGASGIVIWGSWENTRSKESCQRIKEYMDTTLNPYIINVTLAAKMCSQVLCQEQGVCIRKNWNSSDYLHLNPKNFEIVLEKGGKFTVRGKPTLEDLENFSEKFRCSCYSTLSCKEKADVKDTDHVDVCIADGVCIHAL
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | No |
| 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. (00:00:03)
[INFO] runJob: FoldX not utilized. Treating input pdb file as it was already optimized. (00:00:03)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:00:03)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/42372e1c879e6aa/tmp/folded.pdb (00:00:03)
[INFO] Main: Simulation completed successfully. (00:05:22)
|
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 | F | A | 0.9798 | |
| 2 | R | A | 0.1954 | |
| 3 | A | A | 0.0000 | |
| 4 | P | A | 0.0854 | |
| 5 | P | A | -0.1200 | |
| 6 | V | A | 0.4437 | |
| 7 | I | A | 0.3142 | |
| 8 | P | A | -0.4985 | |
| 9 | N | A | -1.3158 | |
| 10 | V | A | -0.0863 | |
| 11 | P | A | -0.4678 | |
| 12 | F | A | 0.0000 | |
| 13 | L | A | 0.0000 | |
| 14 | W | A | 0.0000 | |
| 15 | A | A | 0.0000 | |
| 16 | W | A | 0.0000 | |
| 17 | N | A | 0.0000 | |
| 18 | A | A | 0.0000 | |
| 19 | P | A | 0.0000 | |
| 20 | S | A | 0.0546 | |
| 21 | E | A | -0.6497 | |
| 22 | F | A | -0.7483 | |
| 23 | C | A | 0.0000 | |
| 24 | L | A | -0.1245 | |
| 25 | G | A | -1.0597 | |
| 26 | K | A | -2.1803 | |
| 27 | F | A | -2.0509 | |
| 28 | D | A | -1.8932 | |
| 29 | V | A | 0.0000 | |
| 30 | P | A | -0.4477 | |
| 31 | L | A | -0.6691 | |
| 32 | D | A | -0.7324 | |
| 33 | M | A | -0.0205 | |
| 34 | S | A | -0.6854 | |
| 35 | L | A | 0.0000 | |
| 36 | F | A | 0.0000 | |
| 37 | S | A | 0.2603 | |
| 38 | F | A | 0.0000 | |
| 39 | I | A | 1.0034 | |
| 40 | G | A | 0.0000 | |
| 41 | S | A | 0.0000 | |
| 42 | P | A | 0.0395 | |
| 43 | R | A | -0.1362 | |
| 44 | I | A | 0.7632 | |
| 45 | N | A | -0.3582 | |
| 46 | A | A | -0.2319 | |
| 47 | T | A | 0.0830 | |
| 48 | G | A | -0.2382 | |
| 49 | Q | A | -0.1323 | |
| 50 | G | A | 0.0102 | |
| 51 | V | A | 0.0000 | |
| 52 | T | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | F | A | 0.0000 | |
| 55 | Y | A | -0.5710 | |
| 56 | K | A | -1.4416 | |
| 57 | D | A | -1.6831 | |
| 58 | R | A | -0.6062 | |
| 59 | L | A | 0.0000 | |
| 60 | G | A | 0.0000 | |
| 61 | Y | A | -0.4328 | |
| 62 | Y | A | 0.0000 | |
| 63 | P | A | 0.0000 | |
| 64 | Y | A | 0.1950 | |
| 65 | I | A | 0.0000 | |
| 66 | D | A | -0.0900 | |
| 67 | L | A | -0.0468 | |
| 68 | K | A | -1.3018 | |
| 69 | T | A | -0.4274 | |
| 70 | G | A | 0.1124 | |
| 71 | V | A | 1.3519 | |
| 72 | T | A | 0.8031 | |
| 73 | V | A | 0.4741 | |
| 74 | N | A | -0.2208 | |
| 75 | G | A | -0.2897 | |
| 76 | G | A | 0.0000 | |
| 77 | I | A | 0.0000 | |
| 78 | P | A | 0.0000 | |
| 79 | Q | A | -1.1197 | |
| 80 | K | A | -1.1638 | |
| 81 | I | A | -0.6590 | |
| 82 | S | A | -0.9308 | |
| 83 | L | A | -1.0497 | |
| 84 | Q | A | -2.1684 | |
| 85 | K | A | -2.5333 | |
| 86 | H | A | 0.0000 | |
| 87 | L | A | -2.1006 | |
| 88 | D | A | -3.1811 | |
| 89 | K | A | -2.6560 | |
| 90 | A | A | 0.0000 | |
| 91 | K | A | -2.6882 | |
| 92 | K | A | -2.5170 | |
| 93 | D | A | -1.2175 | |
| 94 | I | A | 0.0000 | |
| 95 | S | A | -0.1754 | |
| 96 | F | A | 1.0286 | |
| 97 | Y | A | 0.0000 | |
| 98 | M | A | 0.0000 | |
| 99 | P | A | 0.6794 | |
| 100 | V | A | 1.1085 | |
| 101 | D | A | -0.5315 | |
| 102 | N | A | -1.0978 | |
| 103 | L | A | -0.0743 | |
| 104 | G | A | 0.0000 | |
| 105 | L | A | 0.0000 | |
| 106 | A | A | 0.0000 | |
| 107 | V | A | 0.0000 | |
| 108 | I | A | 0.0000 | |
| 109 | D | A | -0.6400 | |
| 110 | W | A | 0.0000 | |
| 111 | E | A | -1.0318 | |
| 112 | E | A | -0.7590 | |
| 113 | W | A | 0.0000 | |
| 114 | R | A | 0.0000 | |
| 115 | P | A | 0.0000 | |
| 116 | T | A | -0.8343 | |
| 117 | W | A | 0.0000 | |
| 118 | A | A | -0.1170 | |
| 119 | R | A | 0.0000 | |
| 120 | N | A | 0.0000 | |
| 121 | W | A | -0.3476 | |
| 122 | K | A | -1.6100 | |
| 123 | P | A | -1.0405 | |
| 124 | K | A | -0.9602 | |
| 125 | D | A | -1.0861 | |
| 126 | V | A | -0.5878 | |
| 127 | Y | A | 0.0000 | |
| 128 | R | A | -1.2878 | |
| 129 | N | A | -1.7005 | |
| 130 | K | A | -1.3803 | |
| 131 | S | A | 0.0000 | |
| 132 | I | A | -1.5901 | |
| 133 | E | A | -1.6611 | |
| 134 | L | A | -1.6656 | |
| 135 | V | A | 0.0000 | |
| 136 | Q | A | -1.4468 | |
| 137 | Q | A | -1.9529 | |
| 138 | Q | A | -1.9985 | |
| 139 | N | A | -1.2648 | |
| 140 | V | A | 0.2640 | |
| 141 | Q | A | -0.7880 | |
| 142 | L | A | -0.5358 | |
| 143 | S | A | -0.1271 | |
| 144 | L | A | 0.6035 | |
| 145 | T | A | -0.6388 | |
| 146 | E | A | -2.1845 | |
| 147 | A | A | 0.0000 | |
| 148 | T | A | -2.0545 | |
| 149 | K | A | -3.2364 | |
| 150 | K | A | -2.9077 | |
| 151 | A | A | 0.0000 | |
| 152 | K | A | -3.3225 | |
| 153 | E | A | -3.7886 | |
| 154 | E | A | -2.9114 | |
| 155 | F | A | 0.0000 | |
| 156 | E | A | -2.5955 | |
| 157 | K | A | -3.1665 | |
| 158 | A | A | -2.0067 | |
| 159 | G | A | 0.0000 | |
| 160 | K | A | -1.8511 | |
| 161 | D | A | -1.5556 | |
| 162 | F | A | 0.0000 | |
| 163 | L | A | 0.0000 | |
| 164 | V | A | 0.0000 | |
| 165 | E | A | -1.1572 | |
| 166 | T | A | 0.0000 | |
| 167 | I | A | 0.0000 | |
| 168 | K | A | -1.0554 | |
| 169 | L | A | -0.8675 | |
| 170 | G | A | 0.0000 | |
| 171 | K | A | -0.9709 | |
| 172 | S | A | -0.7708 | |
| 173 | L | A | -0.4408 | |
| 174 | R | A | -0.7453 | |
| 175 | P | A | -1.1989 | |
| 176 | N | A | -1.3466 | |
| 177 | H | A | 0.0000 | |
| 178 | L | A | -0.0173 | |
| 179 | W | A | 0.0000 | |
| 180 | G | A | 0.0000 | |
| 181 | Y | A | 0.0000 | |
| 182 | Y | A | 0.0000 | |
| 183 | L | A | 0.0075 | |
| 184 | F | A | 0.0000 | |
| 185 | P | A | 0.0000 | |
| 186 | D | A | 0.0000 | |
| 187 | C | A | 0.0000 | |
| 188 | Y | A | 0.1683 | |
| 189 | N | A | 0.0000 | |
| 190 | H | A | -1.1803 | |
| 191 | H | A | -1.2708 | |
| 192 | Y | A | -1.4769 | |
| 193 | K | A | -2.1488 | |
| 194 | T | A | -1.3444 | |
| 195 | P | A | -1.0296 | |
| 196 | G | A | -1.0621 | |
| 197 | Y | A | -1.2286 | |
| 198 | N | A | -1.3602 | |
| 199 | G | A | 0.0000 | |
| 200 | S | A | -0.3597 | |
| 201 | C | A | 0.0000 | |
| 202 | F | A | 1.2953 | |
| 203 | N | A | -0.1166 | |
| 204 | V | A | 0.7867 | |
| 205 | E | A | 0.0000 | |
| 206 | I | A | -0.4686 | |
| 207 | K | A | -1.9497 | |
| 208 | R | A | -1.5151 | |
| 209 | N | A | 0.0000 | |
| 210 | D | A | -2.0314 | |
| 211 | D | A | -2.6528 | |
| 212 | L | A | 0.0000 | |
| 213 | S | A | -1.0860 | |
| 214 | W | A | -0.8977 | |
| 215 | L | A | 0.0000 | |
| 216 | W | A | 0.0000 | |
| 217 | N | A | -1.4961 | |
| 218 | E | A | -1.1797 | |
| 219 | S | A | 0.0000 | |
| 220 | T | A | -0.3991 | |
| 221 | A | A | 0.0000 | |
| 222 | L | A | 0.0000 | |
| 223 | Y | A | 0.0000 | |
| 224 | P | A | 0.0000 | |
| 225 | S | A | 0.0000 | |
| 226 | I | A | 0.0000 | |
| 227 | Y | A | 0.1603 | |
| 228 | L | A | 0.0000 | |
| 229 | N | A | -0.9692 | |
| 230 | T | A | -1.3350 | |
| 231 | Q | A | -1.6969 | |
| 232 | M | A | -1.0973 | |
| 233 | S | A | -0.7987 | |
| 234 | P | A | -0.8085 | |
| 235 | S | A | -0.4238 | |
| 236 | A | A | 0.0000 | |
| 237 | A | A | 0.0000 | |
| 238 | T | A | 0.0000 | |
| 239 | L | A | -0.3250 | |
| 240 | F | A | 0.0000 | |
| 241 | V | A | 0.0000 | |
| 242 | R | A | 0.0000 | |
| 243 | N | A | 0.0000 | |
| 244 | R | A | 0.0000 | |
| 245 | V | A | 0.0000 | |
| 246 | R | A | -1.1936 | |
| 247 | E | A | 0.0000 | |
| 248 | A | A | 0.0000 | |
| 249 | I | A | 0.0000 | |
| 250 | R | A | -0.9601 | |
| 251 | V | A | 0.0000 | |
| 252 | S | A | 0.0000 | |
| 253 | K | A | -1.1465 | |
| 254 | I | A | -0.7044 | |
| 255 | P | A | -1.2031 | |
| 256 | D | A | -1.9068 | |
| 257 | A | A | -1.2543 | |
| 258 | K | A | -1.7978 | |
| 259 | S | A | -1.1502 | |
| 260 | P | A | 0.0000 | |
| 261 | L | A | -0.5419 | |
| 262 | P | A | -0.0257 | |
| 263 | V | A | 0.0000 | |
| 264 | F | A | 0.0000 | |
| 265 | A | A | 0.0000 | |
| 266 | Y | A | 0.0000 | |
| 267 | T | A | 0.0000 | |
| 268 | R | A | 0.0000 | |
| 269 | L | A | 0.0000 | |
| 270 | V | A | 0.0000 | |
| 271 | F | A | 0.0000 | |
| 272 | T | A | -0.7722 | |
| 273 | D | A | -1.7834 | |
| 274 | E | A | -1.3545 | |
| 275 | V | A | -0.0728 | |
| 276 | L | A | 0.1020 | |
| 277 | K | A | -0.8683 | |
| 278 | F | A | -0.4123 | |
| 279 | L | A | 0.0000 | |
| 280 | S | A | -1.4456 | |
| 281 | Q | A | -2.1279 | |
| 282 | D | A | -2.4840 | |
| 283 | E | A | -1.4815 | |
| 284 | L | A | 0.0000 | |
| 285 | V | A | -0.8094 | |
| 286 | Y | A | -0.5071 | |
| 287 | T | A | 0.0000 | |
| 288 | F | A | 0.0000 | |
| 289 | G | A | 0.0000 | |
| 290 | E | A | 0.0000 | |
| 291 | T | A | 0.0000 | |
| 292 | V | A | 0.0000 | |
| 293 | A | A | 0.0000 | |
| 294 | L | A | 0.0000 | |
| 295 | G | A | 0.0000 | |
| 296 | A | A | 0.0000 | |
| 297 | S | A | 0.0416 | |
| 298 | G | A | 0.0000 | |
| 299 | I | A | 0.0000 | |
| 300 | V | A | 0.0000 | |
| 301 | I | A | 0.0000 | |
| 302 | W | A | 0.1779 | |
| 303 | G | A | 0.3050 | |
| 304 | S | A | 0.2457 | |
| 305 | W | A | 0.4541 | |
| 306 | E | A | -0.0557 | |
| 307 | N | A | 0.0000 | |
| 308 | T | A | 0.0000 | |
| 309 | R | A | -1.8829 | |
| 310 | S | A | -2.2192 | |
| 311 | K | A | -3.0186 | |
| 312 | E | A | -3.3029 | |
| 313 | S | A | -2.4321 | |
| 314 | C | A | 0.0000 | |
| 315 | Q | A | -3.3599 | |
| 316 | R | A | -3.0391 | |
| 317 | I | A | 0.0000 | |
| 318 | K | A | -2.5050 | |
| 319 | E | A | -2.8654 | |
| 320 | Y | A | 0.0000 | |
| 321 | M | A | 0.0000 | |
| 322 | D | A | -1.3503 | |
| 323 | T | A | -0.7950 | |
| 324 | T | A | -0.7810 | |
| 325 | L | A | 0.0000 | |
| 326 | N | A | 0.0000 | |
| 327 | P | A | -0.2347 | |
| 328 | Y | A | 0.0000 | |
| 329 | I | A | 0.0000 | |
| 330 | I | A | 0.0000 | |
| 331 | N | A | -0.5151 | |
| 332 | V | A | 0.0000 | |
| 333 | T | A | 0.0000 | |
| 334 | L | A | 0.0000 | |
| 335 | A | A | 0.0000 | |
| 336 | A | A | -0.1287 | |
| 337 | K | A | -0.8710 | |
| 338 | M | A | 0.0000 | |
| 339 | C | A | 0.0000 | |
| 340 | S | A | 0.0000 | |
| 341 | Q | A | -1.8194 | |
| 342 | V | A | 0.0000 | |
| 343 | L | A | 0.0000 | |
| 344 | C | A | 0.0000 | |
| 345 | Q | A | -2.7749 | |
| 346 | E | A | -2.8299 | |
| 347 | Q | A | -1.8531 | |
| 348 | G | A | 0.0000 | |
| 349 | V | A | -0.4409 | |
| 350 | C | A | 0.0000 | |
| 351 | I | A | -0.7132 | |
| 352 | R | A | 0.0000 | |
| 353 | K | A | -2.8182 | |
| 354 | N | A | -2.2953 | |
| 355 | W | A | -1.1680 | |
| 356 | N | A | -1.3829 | |
| 357 | S | A | -1.1660 | |
| 358 | S | A | -0.6311 | |
| 359 | D | A | -0.9555 | |
| 360 | Y | A | -0.0965 | |
| 361 | L | A | 0.0000 | |
| 362 | H | A | -0.4240 | |
| 363 | L | A | 0.0000 | |
| 364 | N | A | -1.9136 | |
| 365 | P | A | -1.8543 | |
| 366 | K | A | -2.6114 | |
| 367 | N | A | -2.5407 | |
| 368 | F | A | 0.0000 | |
| 369 | E | A | -2.7341 | |
| 370 | I | A | -0.6961 | |
| 371 | V | A | -0.5892 | |
| 372 | L | A | -0.6210 | |
| 373 | E | A | -1.7495 | |
| 374 | K | A | -2.4836 | |
| 375 | G | A | -2.0258 | |
| 376 | G | A | -1.9882 | |
| 377 | K | A | -2.6671 | |
| 378 | F | A | 0.0000 | |
| 379 | T | A | -0.9671 | |
| 380 | V | A | -1.2280 | |
| 381 | R | A | -2.6581 | |
| 382 | G | A | -2.8513 | |
| 383 | K | A | -2.5785 | |
| 384 | P | A | -1.3866 | |
| 385 | T | A | -1.0118 | |
| 386 | L | A | -0.8308 | |
| 387 | E | A | -1.9119 | |
| 388 | D | A | 0.0000 | |
| 389 | L | A | 0.0000 | |
| 390 | E | A | -2.2033 | |
| 391 | N | A | -1.9612 | |
| 392 | F | A | 0.0000 | |
| 393 | S | A | -2.4788 | |
| 394 | E | A | -2.9305 | |
| 395 | K | A | -2.6963 | |
| 396 | F | A | 0.0000 | |
| 397 | R | A | -2.5557 | |
| 398 | C | A | -1.6134 | |
| 399 | S | A | 0.0000 | |
| 400 | C | A | -0.2955 | |
| 401 | Y | A | 0.0000 | |
| 402 | S | A | -0.1051 | |
| 403 | T | A | 0.1237 | |
| 404 | L | A | 0.6347 | |
| 405 | S | A | -0.0437 | |
| 406 | C | A | -1.3014 | |
| 407 | K | A | -2.4816 | |
| 408 | E | A | -2.7690 | |
| 409 | K | A | -2.4044 | |
| 410 | A | A | -1.5848 | |
| 411 | D | A | -2.3423 | |
| 412 | V | A | 0.0000 | |
| 413 | K | A | -3.2745 | |
| 414 | D | A | -3.4379 | |
| 415 | T | A | -2.4754 | |
| 416 | D | A | -2.6456 | |
| 417 | H | A | -1.9738 | |
| 418 | V | A | 0.0000 | |
| 419 | D | A | -1.6745 | |
| 420 | V | A | 0.0000 | |
| 421 | C | A | -0.4394 | |
| 422 | I | A | -0.1506 | |
| 423 | A | A | -0.4898 | |
| 424 | D | A | -1.6409 | |
| 425 | G | A | -1.1033 | |
| 426 | V | A | 0.0000 | |
| 427 | C | A | -0.6608 | |
| 428 | I | A | 0.0000 | |
| 429 | H | A | -1.8078 | |
| 430 | A | A | 0.0000 | |
| 431 | L | A | 0.0454 |
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 | -0.5937 | 3.3928 | View | CSV | PDB |
| 4.5 | -0.6487 | 3.3667 | View | CSV | PDB |
| 5.0 | -0.7139 | 3.3387 | View | CSV | PDB |
| 5.5 | -0.7738 | 3.3101 | View | CSV | PDB |
| 6.0 | -0.8113 | 3.2812 | View | CSV | PDB |
| 6.5 | -0.8161 | 3.2746 | View | CSV | PDB |
| 7.0 | -0.7909 | 3.4292 | View | CSV | PDB |
| 7.5 | -0.7471 | 3.6011 | View | CSV | PDB |
| 8.0 | -0.6938 | 3.7801 | View | CSV | PDB |
| 8.5 | -0.6334 | 3.963 | View | CSV | PDB |
| 9.0 | -0.5656 | 4.1489 | 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