| Chain sequence(s) |
A: MGSSHHHHHHHENLYFQGKAAVIGLGVEGKKAVNSLLSHGWEVYATDLNSNVDLSDLELPMISMNLVSGGETVSIVSDNLTVDLGFSNSSAIEECDAIAISPSMYGGAFADKLLEKGKLLSNVVTKHKDIFTIGITGTNGKTTSVHMLKSILENAGKKVLVGGNGGGGFSGYYDLILEASNDDYDILLVEVCDMTLDFCNYCFDFDMVGLTNIGNDHMDVHKTIANYKNTLVRFFEGKTVFTAFNQDFNADFKEVASKAIPFFEYDEKLQVWGRFNALNAGLVAAIATELKIPKDIIMESLADFKAVEGRMNVYKINNASIFVGKTDNSDALTSVLNENDFYALFIGTPRANEEHRLSILDEAVKYNPEVIVLFPGLDDTVDMGLYRLNRLGYEGRIEVANSLDEIIALIAEFSHEDALFIGGNGQEAIIEIQERIRLLSENL
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] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:13:30)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/e73c5068d42feb8/tmp/folded.pdb (00:13:30)
[INFO] Main: Simulation completed successfully. (00:22:15)
|
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 | 0.7450 | |
| 2 | G | A | -0.2506 | |
| 3 | S | A | -0.6882 | |
| 4 | S | A | -1.2240 | |
| 5 | H | A | -2.1374 | |
| 6 | H | A | -2.4956 | |
| 7 | H | A | -2.7374 | |
| 8 | H | A | -2.8545 | |
| 9 | H | A | -2.9942 | |
| 10 | H | A | -3.2081 | |
| 11 | H | A | -2.9654 | |
| 12 | E | A | -2.6966 | |
| 13 | N | A | -1.3040 | |
| 14 | L | A | 1.2116 | |
| 15 | Y | A | 1.7216 | |
| 16 | F | A | 2.1869 | |
| 17 | Q | A | -0.2164 | |
| 18 | G | A | 0.0000 | |
| 19 | K | A | -1.9010 | |
| 20 | A | A | 0.0000 | |
| 21 | A | A | 0.0000 | |
| 22 | V | A | 0.0000 | |
| 23 | I | A | 0.0000 | |
| 24 | G | A | 0.1191 | |
| 25 | L | A | 0.0000 | |
| 26 | G | A | -0.3135 | |
| 27 | V | A | 0.6318 | |
| 28 | E | A | 0.1111 | |
| 29 | G | A | 0.0000 | |
| 30 | K | A | 0.0000 | |
| 31 | K | A | -0.8303 | |
| 32 | A | A | 0.0000 | |
| 33 | V | A | 0.0000 | |
| 34 | N | A | -1.0230 | |
| 35 | S | A | 0.0000 | |
| 36 | L | A | 0.0000 | |
| 37 | L | A | -0.7093 | |
| 38 | S | A | -0.6638 | |
| 39 | H | A | -0.5657 | |
| 40 | G | A | -0.5699 | |
| 41 | W | A | 0.0000 | |
| 42 | E | A | -2.1208 | |
| 43 | V | A | 0.0000 | |
| 44 | Y | A | 0.0000 | |
| 45 | A | A | 0.0000 | |
| 46 | T | A | 0.0000 | |
| 47 | D | A | 0.0000 | |
| 48 | L | A | 0.9264 | |
| 49 | N | A | -1.2859 | |
| 50 | S | A | -1.3117 | |
| 51 | N | A | -2.0006 | |
| 52 | V | A | -1.4407 | |
| 53 | D | A | -2.2409 | |
| 54 | L | A | -1.4218 | |
| 55 | S | A | -1.6859 | |
| 56 | D | A | -2.3849 | |
| 57 | L | A | 0.0000 | |
| 58 | E | A | -1.9545 | |
| 59 | L | A | -0.1108 | |
| 60 | P | A | 0.2802 | |
| 61 | M | A | 1.2981 | |
| 62 | I | A | 0.9610 | |
| 63 | S | A | 0.1640 | |
| 64 | M | A | 0.5696 | |
| 65 | N | A | 0.2368 | |
| 66 | L | A | 1.7394 | |
| 67 | V | A | 2.0269 | |
| 68 | S | A | 0.2535 | |
| 69 | G | A | -0.6811 | |
| 70 | G | A | -1.5859 | |
| 71 | E | A | -2.4253 | |
| 72 | T | A | -0.8800 | |
| 73 | V | A | 0.3734 | |
| 74 | S | A | 1.0618 | |
| 75 | I | A | 0.0000 | |
| 76 | V | A | 0.7371 | |
| 77 | S | A | -0.4297 | |
| 78 | D | A | -1.8978 | |
| 79 | N | A | -1.6763 | |
| 80 | L | A | 0.0000 | |
| 81 | T | A | -0.3467 | |
| 82 | V | A | 0.0000 | |
| 83 | D | A | 0.0000 | |
| 84 | L | A | 0.0000 | |
| 85 | G | A | -0.2652 | |
| 86 | F | A | 0.5223 | |
| 87 | S | A | 0.1234 | |
| 88 | N | A | -0.9584 | |
| 89 | S | A | -1.2950 | |
| 90 | S | A | -1.6270 | |
| 91 | A | A | -1.6090 | |
| 92 | I | A | 0.0000 | |
| 93 | E | A | -3.6284 | |
| 94 | E | A | -3.2010 | |
| 95 | C | A | -2.7317 | |
| 96 | D | A | -2.8186 | |
| 97 | A | A | 0.0000 | |
| 98 | I | A | 0.0000 | |
| 99 | A | A | 0.0000 | |
| 100 | I | A | 0.0000 | |
| 101 | S | A | 0.0679 | |
| 102 | P | A | 0.0000 | |
| 103 | S | A | 0.0073 | |
| 104 | M | A | 0.0561 | |
| 105 | Y | A | -0.1227 | |
| 106 | G | A | -0.9272 | |
| 107 | G | A | -0.5342 | |
| 108 | A | A | -0.4279 | |
| 109 | F | A | 0.3237 | |
| 110 | A | A | 0.0000 | |
| 111 | D | A | -2.7884 | |
| 112 | K | A | -2.9702 | |
| 113 | L | A | -2.3553 | |
| 114 | L | A | -2.5478 | |
| 115 | E | A | -3.8215 | |
| 116 | K | A | -3.7682 | |
| 117 | G | A | -3.4311 | |
| 118 | K | A | -2.7384 | |
| 119 | L | A | 0.0000 | |
| 120 | L | A | 0.0000 | |
| 121 | S | A | 0.0000 | |
| 122 | N | A | -0.7102 | |
| 123 | V | A | -0.4589 | |
| 124 | V | A | 0.0000 | |
| 125 | T | A | -1.2886 | |
| 126 | K | A | -2.9657 | |
| 127 | H | A | 0.0000 | |
| 128 | K | A | -2.3431 | |
| 129 | D | A | -2.7547 | |
| 130 | I | A | -1.8383 | |
| 131 | F | A | -0.7070 | |
| 132 | T | A | 0.0000 | |
| 133 | I | A | 0.0000 | |
| 134 | G | A | 0.0000 | |
| 135 | I | A | 0.0000 | |
| 136 | T | A | 0.0000 | |
| 137 | G | A | 0.0000 | |
| 138 | T | A | -0.7858 | |
| 139 | N | A | -0.6332 | |
| 140 | G | A | -0.3524 | |
| 141 | K | A | -0.4785 | |
| 142 | T | A | 0.0000 | |
| 143 | T | A | 0.0000 | |
| 144 | S | A | 0.0000 | |
| 145 | V | A | 0.0000 | |
| 146 | H | A | -0.6615 | |
| 147 | M | A | 0.0000 | |
| 148 | L | A | 0.0000 | |
| 149 | K | A | -1.4786 | |
| 150 | S | A | -1.6379 | |
| 151 | I | A | 0.0000 | |
| 152 | L | A | 0.0000 | |
| 153 | E | A | -2.6814 | |
| 154 | N | A | -2.5050 | |
| 155 | A | A | -1.7223 | |
| 156 | G | A | -2.0319 | |
| 157 | K | A | -2.5125 | |
| 158 | K | A | -2.8219 | |
| 159 | V | A | 0.0000 | |
| 160 | L | A | -0.7284 | |
| 161 | V | A | 0.0862 | |
| 162 | G | A | 0.0000 | |
| 163 | G | A | 0.0000 | |
| 164 | N | A | 0.0000 | |
| 165 | G | A | 0.0000 | |
| 166 | G | A | -0.3848 | |
| 167 | G | A | -0.5528 | |
| 168 | G | A | -0.6072 | |
| 169 | F | A | -0.2373 | |
| 170 | S | A | -0.3240 | |
| 171 | G | A | 0.0000 | |
| 172 | Y | A | 0.0000 | |
| 173 | Y | A | 0.0000 | |
| 174 | D | A | -0.6315 | |
| 175 | L | A | 0.0000 | |
| 176 | I | A | 0.0000 | |
| 177 | L | A | 0.0000 | |
| 178 | E | A | -1.7290 | |
| 179 | A | A | 0.0000 | |
| 180 | S | A | -1.8037 | |
| 181 | N | A | -2.6760 | |
| 182 | D | A | -3.1572 | |
| 183 | D | A | -3.3446 | |
| 184 | Y | A | -2.4816 | |
| 185 | D | A | -2.5031 | |
| 186 | I | A | 0.0000 | |
| 187 | L | A | 0.0000 | |
| 188 | L | A | 0.0000 | |
| 189 | V | A | 0.0000 | |
| 190 | E | A | 0.0000 | |
| 191 | V | A | 0.0000 | |
| 192 | C | A | 0.0696 | |
| 193 | D | A | -0.1291 | |
| 194 | M | A | 0.6625 | |
| 195 | T | A | 0.0000 | |
| 196 | L | A | 0.0000 | |
| 197 | D | A | -0.9129 | |
| 198 | F | A | 0.0000 | |
| 199 | C | A | 0.0000 | |
| 200 | N | A | -1.1680 | |
| 201 | Y | A | -0.1002 | |
| 202 | C | A | 0.0000 | |
| 203 | F | A | 0.0000 | |
| 204 | D | A | -2.3825 | |
| 205 | F | A | 0.0000 | |
| 206 | D | A | -1.4662 | |
| 207 | M | A | 0.0000 | |
| 208 | V | A | 0.0000 | |
| 209 | G | A | 0.0000 | |
| 210 | L | A | 0.0000 | |
| 211 | T | A | 0.0000 | |
| 212 | N | A | -0.7559 | |
| 213 | I | A | -0.9233 | |
| 214 | G | A | -1.3311 | |
| 215 | N | A | -2.3866 | |
| 216 | D | A | -2.7898 | |
| 217 | H | A | -2.0241 | |
| 218 | M | A | -0.7885 | |
| 219 | D | A | -2.1611 | |
| 220 | V | A | -1.9000 | |
| 221 | H | A | -2.2217 | |
| 222 | K | A | -2.7148 | |
| 223 | T | A | -2.2943 | |
| 224 | I | A | -1.8738 | |
| 225 | A | A | -1.6133 | |
| 226 | N | A | -2.1634 | |
| 227 | Y | A | -1.1358 | |
| 228 | K | A | -1.5986 | |
| 229 | N | A | -1.9363 | |
| 230 | T | A | -1.2908 | |
| 231 | L | A | 0.0000 | |
| 232 | V | A | -1.8141 | |
| 233 | R | A | -1.9038 | |
| 234 | F | A | 0.0000 | |
| 235 | F | A | 0.0000 | |
| 236 | E | A | -2.8550 | |
| 237 | G | A | -2.0463 | |
| 238 | K | A | -1.7810 | |
| 239 | T | A | -1.3940 | |
| 240 | V | A | 0.0000 | |
| 241 | F | A | 0.0000 | |
| 242 | T | A | 0.0000 | |
| 243 | A | A | 0.5401 | |
| 244 | F | A | 1.3702 | |
| 245 | N | A | -0.6693 | |
| 246 | Q | A | -1.1022 | |
| 247 | D | A | -1.9601 | |
| 248 | F | A | -1.3840 | |
| 249 | N | A | -1.5366 | |
| 250 | A | A | -1.5820 | |
| 251 | D | A | -2.0695 | |
| 252 | F | A | 0.0000 | |
| 253 | K | A | -3.1192 | |
| 254 | E | A | -3.1768 | |
| 255 | V | A | -2.3106 | |
| 256 | A | A | -2.3891 | |
| 257 | S | A | -1.9850 | |
| 258 | K | A | -2.0518 | |
| 259 | A | A | -1.3189 | |
| 260 | I | A | -0.0895 | |
| 261 | P | A | 0.8763 | |
| 262 | F | A | 0.0000 | |
| 263 | F | A | 1.5857 | |
| 264 | E | A | -0.5409 | |
| 265 | Y | A | -1.4557 | |
| 266 | D | A | -2.7314 | |
| 267 | E | A | -3.3546 | |
| 268 | K | A | -3.3148 | |
| 269 | L | A | -2.2922 | |
| 270 | Q | A | -2.1364 | |
| 271 | V | A | -1.1789 | |
| 272 | W | A | -0.3890 | |
| 273 | G | A | -1.0019 | |
| 274 | R | A | -1.9132 | |
| 275 | F | A | -0.6627 | |
| 276 | N | A | 0.0000 | |
| 277 | A | A | -0.9844 | |
| 278 | L | A | -0.0553 | |
| 279 | N | A | 0.0000 | |
| 280 | A | A | 0.0000 | |
| 281 | G | A | 0.0000 | |
| 282 | L | A | 0.0000 | |
| 283 | V | A | 0.0000 | |
| 284 | A | A | -0.0512 | |
| 285 | A | A | 0.0493 | |
| 286 | I | A | 0.0000 | |
| 287 | A | A | 0.0000 | |
| 288 | T | A | -1.1700 | |
| 289 | E | A | -0.8797 | |
| 290 | L | A | -0.7849 | |
| 291 | K | A | -2.0276 | |
| 292 | I | A | 0.0000 | |
| 293 | P | A | -1.8174 | |
| 294 | K | A | -2.9618 | |
| 295 | D | A | -2.8677 | |
| 296 | I | A | -1.9672 | |
| 297 | I | A | 0.0000 | |
| 298 | M | A | -2.4061 | |
| 299 | E | A | -3.2723 | |
| 300 | S | A | 0.0000 | |
| 301 | L | A | 0.0000 | |
| 302 | A | A | -2.6169 | |
| 303 | D | A | -3.0803 | |
| 304 | F | A | 0.0000 | |
| 305 | K | A | -2.5857 | |
| 306 | A | A | -1.6601 | |
| 307 | V | A | -1.2709 | |
| 308 | E | A | -2.5278 | |
| 309 | G | A | 0.0000 | |
| 310 | R | A | -1.0563 | |
| 311 | M | A | -0.4990 | |
| 312 | N | A | -0.8837 | |
| 313 | V | A | -0.2319 | |
| 314 | Y | A | 0.0000 | |
| 315 | K | A | -2.4746 | |
| 316 | I | A | 0.0000 | |
| 317 | N | A | -2.5207 | |
| 318 | N | A | -3.1473 | |
| 319 | A | A | 0.0000 | |
| 320 | S | A | -1.6902 | |
| 321 | I | A | 0.0000 | |
| 322 | F | A | 0.0000 | |
| 323 | V | A | 0.0000 | |
| 324 | G | A | 0.0000 | |
| 325 | K | A | -1.0405 | |
| 326 | T | A | 0.0000 | |
| 327 | D | A | -1.0104 | |
| 328 | N | A | 0.0000 | |
| 329 | S | A | -1.3083 | |
| 330 | D | A | -1.3702 | |
| 331 | A | A | -0.7279 | |
| 332 | L | A | 0.0000 | |
| 333 | T | A | -0.8633 | |
| 334 | S | A | -1.0732 | |
| 335 | V | A | 0.0000 | |
| 336 | L | A | 0.0000 | |
| 337 | N | A | -2.1801 | |
| 338 | E | A | -2.0798 | |
| 339 | N | A | -2.2795 | |
| 340 | D | A | -2.6972 | |
| 341 | F | A | 0.0000 | |
| 342 | Y | A | -1.4247 | |
| 343 | A | A | 0.0000 | |
| 344 | L | A | 0.0000 | |
| 345 | F | A | 0.0000 | |
| 346 | I | A | 0.0000 | |
| 347 | G | A | 0.0000 | |
| 348 | T | A | 0.0000 | |
| 349 | P | A | 0.0000 | |
| 350 | R | A | -2.9136 | |
| 351 | A | A | -2.3951 | |
| 352 | N | A | -2.7447 | |
| 353 | E | A | -2.9660 | |
| 354 | E | A | -3.0882 | |
| 355 | H | A | -2.1991 | |
| 356 | R | A | -2.1150 | |
| 357 | L | A | 0.0000 | |
| 358 | S | A | -1.0864 | |
| 359 | I | A | 0.0000 | |
| 360 | L | A | 0.0000 | |
| 361 | D | A | -0.9234 | |
| 362 | E | A | -1.0945 | |
| 363 | A | A | 0.0000 | |
| 364 | V | A | -1.4984 | |
| 365 | K | A | -1.8713 | |
| 366 | Y | A | -1.6211 | |
| 367 | N | A | -2.4588 | |
| 368 | P | A | 0.0000 | |
| 369 | E | A | -2.4508 | |
| 370 | V | A | 0.0000 | |
| 371 | I | A | 0.0000 | |
| 372 | V | A | 0.0000 | |
| 373 | L | A | 0.0000 | |
| 374 | F | A | 0.0000 | |
| 375 | P | A | -1.2959 | |
| 376 | G | A | -1.0733 | |
| 377 | L | A | -0.8600 | |
| 378 | D | A | -2.0022 | |
| 379 | D | A | -2.6619 | |
| 380 | T | A | 0.0000 | |
| 381 | V | A | 0.0000 | |
| 382 | D | A | -1.2304 | |
| 383 | M | A | -0.6486 | |
| 384 | G | A | 0.0000 | |
| 385 | L | A | -0.0032 | |
| 386 | Y | A | 0.1040 | |
| 387 | R | A | -0.9261 | |
| 388 | L | A | 0.0000 | |
| 389 | N | A | -1.9213 | |
| 390 | R | A | -2.1069 | |
| 391 | L | A | -1.2477 | |
| 392 | G | A | -1.7562 | |
| 393 | Y | A | 0.0000 | |
| 394 | E | A | -2.6889 | |
| 395 | G | A | -2.3097 | |
| 396 | R | A | -1.7011 | |
| 397 | I | A | -0.5801 | |
| 398 | E | A | -0.0009 | |
| 399 | V | A | 0.0387 | |
| 400 | A | A | 0.0000 | |
| 401 | N | A | -1.8554 | |
| 402 | S | A | -1.3832 | |
| 403 | L | A | -1.5809 | |
| 404 | D | A | -2.3251 | |
| 405 | E | A | -1.8498 | |
| 406 | I | A | 0.0000 | |
| 407 | I | A | -0.8104 | |
| 408 | A | A | -0.8585 | |
| 409 | L | A | -0.6416 | |
| 410 | I | A | 0.0000 | |
| 411 | A | A | -0.8213 | |
| 412 | E | A | -1.2824 | |
| 413 | F | A | 0.0000 | |
| 414 | S | A | 0.0000 | |
| 415 | H | A | -2.5326 | |
| 416 | E | A | -2.2360 | |
| 417 | D | A | -3.0919 | |
| 418 | A | A | 0.0000 | |
| 419 | L | A | 0.0000 | |
| 420 | F | A | 0.0000 | |
| 421 | I | A | 0.0000 | |
| 422 | G | A | 0.0000 | |
| 423 | G | A | 0.0000 | |
| 424 | N | A | 0.0000 | |
| 425 | G | A | 0.0000 | |
| 426 | Q | A | -1.5688 | |
| 427 | E | A | -2.2728 | |
| 428 | A | A | -1.2459 | |
| 429 | I | A | 0.0000 | |
| 430 | I | A | -1.7224 | |
| 431 | E | A | -2.6508 | |
| 432 | I | A | 0.0000 | |
| 433 | Q | A | 0.0000 | |
| 434 | E | A | -1.8416 | |
| 435 | R | A | -1.4831 | |
| 436 | I | A | 0.0000 | |
| 437 | R | A | -1.7634 | |
| 438 | L | A | -0.5457 | |
| 439 | L | A | -0.5210 | |
| 440 | S | A | -1.4739 | |
| 441 | E | A | -1.9980 | |
| 442 | N | A | -1.1696 | |
| 443 | L | A | 0.1297 |
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 | -0.6517 | 5.2658 | View | CSV | PDB |
| 4.5 | -0.7462 | 5.1488 | View | CSV | PDB |
| 5.0 | -0.862 | 5.0314 | View | CSV | PDB |
| 5.5 | -0.9803 | 4.9481 | View | CSV | PDB |
| 6.0 | -1.082 | 4.8667 | View | CSV | PDB |
| 6.5 | -1.1544 | 4.792 | View | CSV | PDB |
| 7.0 | -1.1976 | 4.7263 | View | CSV | PDB |
| 7.5 | -1.2207 | 4.7411 | View | CSV | PDB |
| 8.0 | -1.2309 | 4.7596 | View | CSV | PDB |
| 8.5 | -1.2288 | 4.7775 | View | CSV | PDB |
| 9.0 | -1.2114 | 4.793 | 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