| Chain sequence(s) |
A: MDFCWKREMEGKLAHDHRGMTSPRRICVVTGPVIVGAGPSGLATAACLKERGITSVLLERSNCIASLWQLKTYDRLHLHLPKQFCELPIIPFPGDFPTYPTKQQFIEYLEDYARRFDIKPEFNQTVESAAFDENLGMWRVTSVGEEGTTEYVCRWLVAATGENAEPVVPRFEGMDKFAAAGVVKHTCHYKTGGDFAGKRVLVVGCGNSGMEVCLDLCNFGAQPSLVVRDAVHVLPREMLGTSTFGLSMFLLKWLPIRLVDRFLLVVSRFILGDTTLLGLNRPRLGPLELKNISGKTPVLDVGTLAKIKTGDIKVCSGIRRLKRHEVEFDNGKTERFDAIILATGYKSNVPSWLKENKMFSKKDGFPIQEFPEGWRGECGLYAVGFTKRGISGASMDAKRIAEDIHKCWKQDEQVKKI
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. (00:00:02)
[INFO] runJob: FoldX not utilized. Treating input pdb file as it was already optimized. (00:00:02)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:00:03)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/3a427bbbe111a03/tmp/folded.pdb (00:00:03)
[INFO] Main: Simulation completed successfully. (00:03:37)
|
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 | 0.7547 | |
| 2 | D | A | -0.4532 | |
| 3 | F | A | 0.9453 | |
| 4 | C | A | 0.3096 | |
| 5 | W | A | -0.9285 | |
| 6 | K | A | -2.0124 | |
| 7 | R | A | -3.2906 | |
| 8 | E | A | -3.3607 | |
| 9 | M | A | -2.8115 | |
| 10 | E | A | -3.5847 | |
| 11 | G | A | -3.4800 | |
| 12 | K | A | -3.7007 | |
| 13 | L | A | 0.0000 | |
| 14 | A | A | -2.5130 | |
| 15 | H | A | -3.1150 | |
| 16 | D | A | -3.3375 | |
| 17 | H | A | -2.3683 | |
| 18 | R | A | -2.6577 | |
| 19 | G | A | -1.2517 | |
| 20 | M | A | 0.0744 | |
| 21 | T | A | -0.1450 | |
| 22 | S | A | -0.4966 | |
| 23 | P | A | -0.8411 | |
| 24 | R | A | -1.3105 | |
| 25 | R | A | -1.9931 | |
| 26 | I | A | -0.3792 | |
| 27 | C | A | -0.0500 | |
| 28 | V | A | -0.2331 | |
| 29 | V | A | 0.0000 | |
| 30 | T | A | -0.4170 | |
| 31 | G | A | 0.0000 | |
| 32 | P | A | 0.0000 | |
| 33 | V | A | 0.0000 | |
| 34 | I | A | 0.0000 | |
| 35 | V | A | 0.0000 | |
| 36 | G | A | -0.3044 | |
| 37 | A | A | 0.0000 | |
| 38 | G | A | -0.0380 | |
| 39 | P | A | -0.1026 | |
| 40 | S | A | -0.0729 | |
| 41 | G | A | 0.0000 | |
| 42 | L | A | 0.0000 | |
| 43 | A | A | 0.0000 | |
| 44 | T | A | 0.0000 | |
| 45 | A | A | 0.0000 | |
| 46 | A | A | 0.0000 | |
| 47 | C | A | 0.0000 | |
| 48 | L | A | 0.0000 | |
| 49 | K | A | -2.4259 | |
| 50 | E | A | -2.5090 | |
| 51 | R | A | -2.2776 | |
| 52 | G | A | -1.7246 | |
| 53 | I | A | 0.0000 | |
| 54 | T | A | -0.6903 | |
| 55 | S | A | -0.3398 | |
| 56 | V | A | -0.1675 | |
| 57 | L | A | 0.0000 | |
| 58 | L | A | 0.0000 | |
| 59 | E | A | 0.0000 | |
| 60 | R | A | -1.3629 | |
| 61 | S | A | -1.0303 | |
| 62 | N | A | -1.5162 | |
| 63 | C | A | -0.6017 | |
| 64 | I | A | 0.0000 | |
| 65 | A | A | 0.0000 | |
| 66 | S | A | 0.0653 | |
| 67 | L | A | 0.4511 | |
| 68 | W | A | 0.0440 | |
| 69 | Q | A | 0.0235 | |
| 70 | L | A | 0.8633 | |
| 71 | K | A | -0.2413 | |
| 72 | T | A | -0.6480 | |
| 73 | Y | A | 0.0000 | |
| 74 | D | A | -2.5494 | |
| 75 | R | A | -1.7398 | |
| 76 | L | A | 0.0000 | |
| 77 | H | A | -1.1192 | |
| 78 | L | A | 0.0000 | |
| 79 | H | A | -0.2452 | |
| 80 | L | A | -0.0671 | |
| 81 | P | A | 0.0000 | |
| 82 | K | A | -0.8691 | |
| 83 | Q | A | -1.2960 | |
| 84 | F | A | -0.4899 | |
| 85 | C | A | 0.0000 | |
| 86 | E | A | -0.4566 | |
| 87 | L | A | 0.0000 | |
| 88 | P | A | 0.0000 | |
| 89 | I | A | 1.5593 | |
| 90 | I | A | 0.7355 | |
| 91 | P | A | -0.0807 | |
| 92 | F | A | 0.0000 | |
| 93 | P | A | -0.8757 | |
| 94 | G | A | -1.3926 | |
| 95 | D | A | -1.9660 | |
| 96 | F | A | -0.9593 | |
| 97 | P | A | -0.6562 | |
| 98 | T | A | -0.6387 | |
| 99 | Y | A | 0.0000 | |
| 100 | P | A | 0.0000 | |
| 101 | T | A | -1.2286 | |
| 102 | K | A | -1.5791 | |
| 103 | Q | A | -2.0072 | |
| 104 | Q | A | -1.2608 | |
| 105 | F | A | 0.0000 | |
| 106 | I | A | 0.0000 | |
| 107 | E | A | -1.7875 | |
| 108 | Y | A | 0.0000 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -2.2942 | |
| 111 | D | A | -3.2247 | |
| 112 | Y | A | 0.0000 | |
| 113 | A | A | 0.0000 | |
| 114 | R | A | -4.2253 | |
| 115 | R | A | -3.6396 | |
| 116 | F | A | 0.0000 | |
| 117 | D | A | -3.5588 | |
| 118 | I | A | -2.4806 | |
| 119 | K | A | -2.3841 | |
| 120 | P | A | -1.4507 | |
| 121 | E | A | -1.3199 | |
| 122 | F | A | -1.1558 | |
| 123 | N | A | -1.7612 | |
| 124 | Q | A | -1.5418 | |
| 125 | T | A | -1.0699 | |
| 126 | V | A | -0.9268 | |
| 127 | E | A | -1.6999 | |
| 128 | S | A | -1.2864 | |
| 129 | A | A | 0.0000 | |
| 130 | A | A | -0.7456 | |
| 131 | F | A | -0.8383 | |
| 132 | D | A | -1.2304 | |
| 133 | E | A | -2.3383 | |
| 134 | N | A | -2.0972 | |
| 135 | L | A | -1.3570 | |
| 136 | G | A | -1.2418 | |
| 137 | M | A | -0.7429 | |
| 138 | W | A | 0.0000 | |
| 139 | R | A | -0.1298 | |
| 140 | V | A | 0.0000 | |
| 141 | T | A | -0.5990 | |
| 142 | S | A | 0.0000 | |
| 143 | V | A | -0.7980 | |
| 144 | G | A | -1.6678 | |
| 145 | E | A | -2.7535 | |
| 146 | E | A | -3.0176 | |
| 147 | G | A | -1.9982 | |
| 148 | T | A | -1.3313 | |
| 149 | T | A | -0.8213 | |
| 150 | E | A | 0.0000 | |
| 151 | Y | A | 0.0000 | |
| 152 | V | A | 0.0000 | |
| 153 | C | A | 0.0000 | |
| 154 | R | A | -0.7606 | |
| 155 | W | A | 0.0000 | |
| 156 | L | A | 0.0000 | |
| 157 | V | A | 0.0000 | |
| 158 | A | A | 0.0000 | |
| 159 | A | A | 0.0000 | |
| 160 | T | A | -0.3693 | |
| 161 | G | A | -0.8802 | |
| 162 | E | A | -1.5521 | |
| 163 | N | A | -1.3327 | |
| 164 | A | A | -0.9467 | |
| 165 | E | A | -0.8313 | |
| 166 | P | A | -0.1832 | |
| 167 | V | A | 0.5649 | |
| 168 | V | A | 1.2278 | |
| 169 | P | A | -0.0061 | |
| 170 | R | A | -1.9655 | |
| 171 | F | A | -2.0031 | |
| 172 | E | A | -3.2432 | |
| 173 | G | A | -3.1529 | |
| 174 | M | A | -2.5719 | |
| 175 | D | A | -3.2774 | |
| 176 | K | A | -3.6574 | |
| 177 | F | A | 0.0000 | |
| 178 | A | A | -1.2014 | |
| 179 | A | A | -1.1099 | |
| 180 | A | A | -1.0404 | |
| 181 | G | A | -0.5187 | |
| 182 | V | A | 0.9778 | |
| 183 | V | A | 0.3412 | |
| 184 | K | A | 0.0957 | |
| 185 | H | A | 0.0000 | |
| 186 | T | A | 0.0000 | |
| 187 | C | A | 0.0000 | |
| 188 | H | A | -1.1178 | |
| 189 | Y | A | 0.0000 | |
| 190 | K | A | -1.7194 | |
| 191 | T | A | -1.2715 | |
| 192 | G | A | 0.0000 | |
| 193 | G | A | -0.9670 | |
| 194 | D | A | -1.9216 | |
| 195 | F | A | 0.0000 | |
| 196 | A | A | -1.0870 | |
| 197 | G | A | -1.4065 | |
| 198 | K | A | -2.0829 | |
| 199 | R | A | -2.1883 | |
| 200 | V | A | 0.0000 | |
| 201 | L | A | 0.0000 | |
| 202 | V | A | 0.0000 | |
| 203 | V | A | 0.0000 | |
| 204 | G | A | -0.7171 | |
| 205 | C | A | -0.5336 | |
| 206 | G | A | -0.5648 | |
| 207 | N | A | -0.3658 | |
| 208 | S | A | -0.2691 | |
| 209 | G | A | 0.0000 | |
| 210 | M | A | 0.0000 | |
| 211 | E | A | 0.0000 | |
| 212 | V | A | 0.0000 | |
| 213 | C | A | 0.0000 | |
| 214 | L | A | 0.0000 | |
| 215 | D | A | 0.0000 | |
| 216 | L | A | 0.0000 | |
| 217 | C | A | -0.8927 | |
| 218 | N | A | -0.9568 | |
| 219 | F | A | 0.1971 | |
| 220 | G | A | -0.8389 | |
| 221 | A | A | 0.0000 | |
| 222 | Q | A | -2.3262 | |
| 223 | P | A | 0.0000 | |
| 224 | S | A | 0.0000 | |
| 225 | L | A | 0.0000 | |
| 226 | V | A | 0.0000 | |
| 227 | V | A | -1.2123 | |
| 228 | R | A | -2.8023 | |
| 229 | D | A | -2.5676 | |
| 230 | A | A | -1.8607 | |
| 231 | V | A | -1.3000 | |
| 232 | H | A | 0.0000 | |
| 233 | V | A | 0.0000 | |
| 234 | L | A | 0.0000 | |
| 235 | P | A | 0.0000 | |
| 236 | R | A | -1.0360 | |
| 237 | E | A | -1.0299 | |
| 238 | M | A | 0.0000 | |
| 239 | L | A | 1.2355 | |
| 240 | G | A | -0.0332 | |
| 241 | T | A | -0.1895 | |
| 242 | S | A | -0.3593 | |
| 243 | T | A | 0.0000 | |
| 244 | F | A | 0.6485 | |
| 245 | G | A | 0.7217 | |
| 246 | L | A | 1.1686 | |
| 247 | S | A | 0.0000 | |
| 248 | M | A | 1.4313 | |
| 249 | F | A | 2.2482 | |
| 250 | L | A | 1.8581 | |
| 251 | L | A | 1.1771 | |
| 252 | K | A | 0.0490 | |
| 253 | W | A | 1.3285 | |
| 254 | L | A | 1.3610 | |
| 255 | P | A | 0.2931 | |
| 256 | I | A | -0.0623 | |
| 257 | R | A | -1.2391 | |
| 258 | L | A | 0.3165 | |
| 259 | V | A | 0.0000 | |
| 260 | D | A | 0.0000 | |
| 261 | R | A | -0.9246 | |
| 262 | F | A | 0.3976 | |
| 263 | L | A | 0.0000 | |
| 264 | L | A | 0.6342 | |
| 265 | V | A | 1.3384 | |
| 266 | V | A | 1.5458 | |
| 267 | S | A | 0.0000 | |
| 268 | R | A | 0.2380 | |
| 269 | F | A | 2.1805 | |
| 270 | I | A | 2.1323 | |
| 271 | L | A | 0.6843 | |
| 272 | G | A | 0.4268 | |
| 273 | D | A | -0.2254 | |
| 274 | T | A | 0.0000 | |
| 275 | T | A | 0.0207 | |
| 276 | L | A | 1.0708 | |
| 277 | L | A | 0.0915 | |
| 278 | G | A | -0.3414 | |
| 279 | L | A | 0.0000 | |
| 280 | N | A | -1.9150 | |
| 281 | R | A | -1.5165 | |
| 282 | P | A | -1.2951 | |
| 283 | R | A | -1.6960 | |
| 284 | L | A | -0.4912 | |
| 285 | G | A | -0.6675 | |
| 286 | P | A | 0.0000 | |
| 287 | L | A | -0.3658 | |
| 288 | E | A | -0.4186 | |
| 289 | L | A | -0.2717 | |
| 290 | K | A | -1.2020 | |
| 291 | N | A | -1.0326 | |
| 292 | I | A | 0.8039 | |
| 293 | S | A | -0.2548 | |
| 294 | G | A | -1.4071 | |
| 295 | K | A | -1.8855 | |
| 296 | T | A | -1.4301 | |
| 297 | P | A | -0.5302 | |
| 298 | V | A | 0.0000 | |
| 299 | L | A | 0.0000 | |
| 300 | D | A | -0.3937 | |
| 301 | V | A | -0.0020 | |
| 302 | G | A | -0.1282 | |
| 303 | T | A | 0.0000 | |
| 304 | L | A | 0.0000 | |
| 305 | A | A | -0.9485 | |
| 306 | K | A | -1.8693 | |
| 307 | I | A | 0.0000 | |
| 308 | K | A | -2.0597 | |
| 309 | T | A | -1.7338 | |
| 310 | G | A | -2.0182 | |
| 311 | D | A | -2.5717 | |
| 312 | I | A | 0.0000 | |
| 313 | K | A | -2.3004 | |
| 314 | V | A | -0.4693 | |
| 315 | C | A | -1.0029 | |
| 316 | S | A | -1.7866 | |
| 317 | G | A | 0.0000 | |
| 318 | I | A | -2.2199 | |
| 319 | R | A | -3.4823 | |
| 320 | R | A | -2.8246 | |
| 321 | L | A | 0.0000 | |
| 322 | K | A | -3.2629 | |
| 323 | R | A | -3.5897 | |
| 324 | H | A | -2.6123 | |
| 325 | E | A | -2.9600 | |
| 326 | V | A | 0.0000 | |
| 327 | E | A | 0.0000 | |
| 328 | F | A | 0.0000 | |
| 329 | D | A | -3.8019 | |
| 330 | N | A | -3.1254 | |
| 331 | G | A | -2.7551 | |
| 332 | K | A | -2.9405 | |
| 333 | T | A | -2.4361 | |
| 334 | E | A | -2.0193 | |
| 335 | R | A | -2.9899 | |
| 336 | F | A | 0.0000 | |
| 337 | D | A | -1.6776 | |
| 338 | A | A | 0.0000 | |
| 339 | I | A | 0.0000 | |
| 340 | I | A | 0.0000 | |
| 341 | L | A | 0.0000 | |
| 342 | A | A | 0.0979 | |
| 343 | T | A | 0.2163 | |
| 344 | G | A | -0.2847 | |
| 345 | Y | A | -0.6281 | |
| 346 | K | A | -2.0718 | |
| 347 | S | A | 0.0000 | |
| 348 | N | A | -1.2236 | |
| 349 | V | A | 0.0000 | |
| 350 | P | A | -1.8184 | |
| 351 | S | A | -1.1489 | |
| 352 | W | A | 0.0000 | |
| 353 | L | A | 0.0000 | |
| 354 | K | A | -2.2538 | |
| 355 | E | A | -2.4961 | |
| 356 | N | A | -2.7437 | |
| 357 | K | A | -2.6490 | |
| 358 | M | A | 0.0000 | |
| 359 | F | A | 0.0000 | |
| 360 | S | A | -1.8571 | |
| 361 | K | A | -3.3489 | |
| 362 | K | A | -3.0748 | |
| 363 | D | A | -2.6319 | |
| 364 | G | A | 0.0000 | |
| 365 | F | A | -0.9552 | |
| 366 | P | A | -0.8302 | |
| 367 | I | A | 0.0491 | |
| 368 | Q | A | -1.8647 | |
| 369 | E | A | -1.9690 | |
| 370 | F | A | -1.4844 | |
| 371 | P | A | -1.4328 | |
| 372 | E | A | -2.6347 | |
| 373 | G | A | -1.8181 | |
| 374 | W | A | -1.5973 | |
| 375 | R | A | -2.5209 | |
| 376 | G | A | -2.0438 | |
| 377 | E | A | -2.1636 | |
| 378 | C | A | -0.8620 | |
| 379 | G | A | -0.8265 | |
| 380 | L | A | 0.0000 | |
| 381 | Y | A | 0.0000 | |
| 382 | A | A | 0.0000 | |
| 383 | V | A | 0.0000 | |
| 384 | G | A | -0.5939 | |
| 385 | F | A | 0.0000 | |
| 386 | T | A | -1.5555 | |
| 387 | K | A | -1.9723 | |
| 388 | R | A | -1.9734 | |
| 389 | G | A | -1.2323 | |
| 390 | I | A | -0.4112 | |
| 391 | S | A | -0.6026 | |
| 392 | G | A | 0.0000 | |
| 393 | A | A | 0.0000 | |
| 394 | S | A | 0.0000 | |
| 395 | M | A | -0.2737 | |
| 396 | D | A | 0.0000 | |
| 397 | A | A | 0.0000 | |
| 398 | K | A | -1.5898 | |
| 399 | R | A | -1.7187 | |
| 400 | I | A | 0.0000 | |
| 401 | A | A | 0.0000 | |
| 402 | E | A | -2.2701 | |
| 403 | D | A | -1.7903 | |
| 404 | I | A | 0.0000 | |
| 405 | H | A | -2.1277 | |
| 406 | K | A | -2.7188 | |
| 407 | C | A | -1.9101 | |
| 408 | W | A | -2.0822 | |
| 409 | K | A | -3.2072 | |
| 410 | Q | A | -2.9518 | |
| 411 | D | A | -2.5584 | |
| 412 | E | A | -2.9637 | |
| 413 | Q | A | -2.4579 | |
| 414 | V | A | -0.5224 | |
| 415 | K | A | -2.1154 | |
| 416 | K | A | -1.7281 | |
| 417 | I | A | 0.8184 |
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 | -0.7689 | 4.5634 | View | CSV | PDB |
| 4.5 | -0.8292 | 4.5651 | View | CSV | PDB |
| 5.0 | -0.902 | 4.5705 | View | CSV | PDB |
| 5.5 | -0.9726 | 4.5862 | View | CSV | PDB |
| 6.0 | -1.0238 | 4.6264 | View | CSV | PDB |
| 6.5 | -1.0427 | 4.7063 | View | CSV | PDB |
| 7.0 | -1.0298 | 4.8243 | View | CSV | PDB |
| 7.5 | -0.9962 | 4.964 | View | CSV | PDB |
| 8.0 | -0.9519 | 5.1124 | View | CSV | PDB |
| 8.5 | -0.8998 | 5.2635 | View | CSV | PDB |
| 9.0 | -0.8395 | 5.4148 | 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