| Chain sequence(s) |
A: MNKAETVLFSVGKDNTCRIGLPPAASGDNYHKRAITVGKLENAGLCFFNPDGKLFVVRGEALYKGPTPTSTTKDWFTDAKCVGRTDWDKFKFLYFHPGGKLFAVTKAGVWYKGPEPENEHVPWLYRQASEIGGSGWERFSILFFDLEGIMYGVTEDRFIKADPLSKKNGSWALAATNIGKQGWEVYSYFMGFSYDGNLWCVSRNDGKLYTASPPTNKDDTWITRATDMGTDYRIYKTIAFGKDKTIKKILKLDFLPDIGKILATNTELVAEQVFDNNKSTIPLKATFMVSETLSAETEFTHEHGFEIGMEAETTFEAGIPFISKGTVRVNASASTSHKWNFTKKNKIEKQVFVSQEFEVGPGQAVTRKAIIKKSTIDLPYSAKVLTIFGYEANISGTWKGVSFYHMHVVQEDI
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 (00:05:47)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/cb6fbc1e108a8ca/tmp/folded.pdb (00:05:47)
[INFO] Main: Simulation completed successfully. (00:07:37)
|
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 | 0.0013 | |
| 2 | N | A | -1.7295 | |
| 3 | K | A | -2.4783 | |
| 4 | A | A | -1.2773 | |
| 5 | E | A | -1.0252 | |
| 6 | T | A | -0.5897 | |
| 7 | V | A | 0.0000 | |
| 8 | L | A | 0.0000 | |
| 9 | F | A | 0.0000 | |
| 10 | S | A | 0.0000 | |
| 11 | V | A | 0.0000 | |
| 12 | G | A | 0.0000 | |
| 13 | K | A | -3.0176 | |
| 14 | D | A | -3.2737 | |
| 15 | N | A | -2.9383 | |
| 16 | T | A | -1.8910 | |
| 17 | C | A | 0.0000 | |
| 18 | R | A | -0.3715 | |
| 19 | I | A | 0.0000 | |
| 20 | G | A | 0.0000 | |
| 21 | L | A | 0.9302 | |
| 22 | P | A | 0.3132 | |
| 23 | P | A | 0.0000 | |
| 24 | A | A | -0.1756 | |
| 25 | A | A | -0.5426 | |
| 26 | S | A | -0.9344 | |
| 27 | G | A | -1.0885 | |
| 28 | D | A | -1.5009 | |
| 29 | N | A | -2.2038 | |
| 30 | Y | A | 0.0000 | |
| 31 | H | A | -1.6442 | |
| 32 | K | A | -2.3881 | |
| 33 | R | A | -1.6447 | |
| 34 | A | A | -0.5967 | |
| 35 | I | A | 0.3209 | |
| 36 | T | A | -0.2863 | |
| 37 | V | A | 0.0000 | |
| 38 | G | A | 0.0000 | |
| 39 | K | A | -2.8242 | |
| 40 | L | A | 0.0000 | |
| 41 | E | A | -3.3263 | |
| 42 | N | A | -2.9013 | |
| 43 | A | A | 0.0000 | |
| 44 | G | A | -1.5554 | |
| 45 | L | A | -0.4369 | |
| 46 | C | A | 0.0000 | |
| 47 | F | A | 0.0000 | |
| 48 | F | A | -0.1085 | |
| 49 | N | A | 0.0000 | |
| 50 | P | A | -1.1620 | |
| 51 | D | A | -2.0166 | |
| 52 | G | A | 0.0000 | |
| 53 | K | A | 0.0000 | |
| 54 | L | A | 0.0000 | |
| 55 | F | A | 0.0000 | |
| 56 | V | A | 0.0000 | |
| 57 | V | A | 0.0000 | |
| 58 | R | A | -2.5459 | |
| 59 | G | A | -2.8518 | |
| 60 | E | A | -3.8551 | |
| 61 | A | A | 0.0000 | |
| 62 | L | A | 0.0000 | |
| 63 | Y | A | -1.3173 | |
| 64 | K | A | -1.2420 | |
| 65 | G | A | -1.0806 | |
| 66 | P | A | -1.0284 | |
| 67 | T | A | 0.0000 | |
| 68 | P | A | 0.0000 | |
| 69 | T | A | -0.4011 | |
| 70 | S | A | -0.9826 | |
| 71 | T | A | -0.9951 | |
| 72 | T | A | -1.3403 | |
| 73 | K | A | -2.5459 | |
| 74 | D | A | -2.7396 | |
| 75 | W | A | 0.0000 | |
| 76 | F | A | -1.7143 | |
| 77 | T | A | -1.6757 | |
| 78 | D | A | -2.5717 | |
| 79 | A | A | -1.8150 | |
| 80 | K | A | -2.3465 | |
| 81 | C | A | -1.8673 | |
| 82 | V | A | 0.0000 | |
| 83 | G | A | 0.0000 | |
| 84 | R | A | -2.9958 | |
| 85 | T | A | -2.6819 | |
| 86 | D | A | -2.9998 | |
| 87 | W | A | 0.0000 | |
| 88 | D | A | -3.6033 | |
| 89 | K | A | -3.3027 | |
| 90 | F | A | 0.0000 | |
| 91 | K | A | -1.8312 | |
| 92 | F | A | 0.0000 | |
| 93 | L | A | 0.0000 | |
| 94 | Y | A | 0.1853 | |
| 95 | F | A | 0.0000 | |
| 96 | H | A | -0.7679 | |
| 97 | P | A | -0.9772 | |
| 98 | G | A | -1.0650 | |
| 99 | G | A | -1.2059 | |
| 100 | K | A | -1.3554 | |
| 101 | L | A | 0.0000 | |
| 102 | F | A | 0.0000 | |
| 103 | A | A | 0.0000 | |
| 104 | V | A | 0.0000 | |
| 105 | T | A | 0.0000 | |
| 106 | K | A | -2.8181 | |
| 107 | A | A | -1.4691 | |
| 108 | G | A | 0.0000 | |
| 109 | V | A | -0.6451 | |
| 110 | W | A | 0.0000 | |
| 111 | Y | A | -0.9649 | |
| 112 | K | A | -1.3459 | |
| 113 | G | A | 0.0000 | |
| 114 | P | A | -1.1685 | |
| 115 | E | A | -1.3241 | |
| 116 | P | A | 0.0000 | |
| 117 | E | A | -2.1876 | |
| 118 | N | A | -2.0342 | |
| 119 | E | A | -2.0788 | |
| 120 | H | A | -1.6491 | |
| 121 | V | A | -1.0707 | |
| 122 | P | A | -0.9082 | |
| 123 | W | A | 0.0000 | |
| 124 | L | A | -0.1657 | |
| 125 | Y | A | 0.2435 | |
| 126 | R | A | -1.3708 | |
| 127 | Q | A | -1.3185 | |
| 128 | A | A | -1.0756 | |
| 129 | S | A | -1.5254 | |
| 130 | E | A | -1.8485 | |
| 131 | I | A | 0.0000 | |
| 132 | G | A | 0.0000 | |
| 133 | G | A | -1.2499 | |
| 134 | S | A | -0.8539 | |
| 135 | G | A | -1.2725 | |
| 136 | W | A | 0.0000 | |
| 137 | E | A | -2.3297 | |
| 138 | R | A | -2.7527 | |
| 139 | F | A | 0.0000 | |
| 140 | S | A | -1.4257 | |
| 141 | I | A | 0.0000 | |
| 142 | L | A | 0.0000 | |
| 143 | F | A | 0.0000 | |
| 144 | F | A | -0.1389 | |
| 145 | D | A | 0.0000 | |
| 146 | L | A | -0.4614 | |
| 147 | E | A | -1.7482 | |
| 148 | G | A | 0.0000 | |
| 149 | I | A | -0.7762 | |
| 150 | M | A | 0.0000 | |
| 151 | Y | A | 0.0000 | |
| 152 | G | A | 0.0000 | |
| 153 | V | A | 0.0000 | |
| 154 | T | A | 0.0000 | |
| 155 | E | A | -3.5053 | |
| 156 | D | A | -3.3680 | |
| 157 | R | A | -3.5979 | |
| 158 | F | A | 0.0000 | |
| 159 | I | A | 0.0000 | |
| 160 | K | A | -0.9033 | |
| 161 | A | A | -0.8368 | |
| 162 | D | A | -1.9252 | |
| 163 | P | A | -1.1443 | |
| 164 | L | A | -1.4294 | |
| 165 | S | A | -1.8581 | |
| 166 | K | A | -3.0344 | |
| 167 | K | A | -2.9681 | |
| 168 | N | A | -2.5325 | |
| 169 | G | A | -1.5499 | |
| 170 | S | A | -0.4657 | |
| 171 | W | A | 0.0000 | |
| 172 | A | A | 0.5826 | |
| 173 | L | A | 1.4457 | |
| 174 | A | A | 0.4169 | |
| 175 | A | A | -0.0395 | |
| 176 | T | A | -0.5217 | |
| 177 | N | A | -1.6290 | |
| 178 | I | A | 0.0000 | |
| 179 | G | A | 0.0000 | |
| 180 | K | A | -3.9829 | |
| 181 | Q | A | -3.5645 | |
| 182 | G | A | -2.0988 | |
| 183 | W | A | 0.0000 | |
| 184 | E | A | -2.5267 | |
| 185 | V | A | -1.1407 | |
| 186 | Y | A | -0.6209 | |
| 187 | S | A | 0.0000 | |
| 188 | Y | A | -0.4413 | |
| 189 | F | A | 0.0000 | |
| 190 | M | A | 0.0000 | |
| 191 | G | A | 0.1637 | |
| 192 | F | A | -0.0983 | |
| 193 | S | A | 0.0000 | |
| 194 | Y | A | -1.1522 | |
| 195 | D | A | -2.2706 | |
| 196 | G | A | -1.4456 | |
| 197 | N | A | -0.9237 | |
| 198 | L | A | 0.0000 | |
| 199 | W | A | 0.0000 | |
| 200 | C | A | 0.0000 | |
| 201 | V | A | 0.0000 | |
| 202 | S | A | 0.0000 | |
| 203 | R | A | -1.9989 | |
| 204 | N | A | -2.4131 | |
| 205 | D | A | -2.4889 | |
| 206 | G | A | 0.0000 | |
| 207 | K | A | -1.8423 | |
| 208 | L | A | 0.0000 | |
| 209 | Y | A | -0.2066 | |
| 210 | T | A | 0.0000 | |
| 211 | A | A | -0.3259 | |
| 212 | S | A | -0.7094 | |
| 213 | P | A | -0.4264 | |
| 214 | P | A | 0.0000 | |
| 215 | T | A | -1.2062 | |
| 216 | N | A | -2.4361 | |
| 217 | K | A | -3.3259 | |
| 218 | D | A | -3.3018 | |
| 219 | D | A | -2.2524 | |
| 220 | T | A | -1.2197 | |
| 221 | W | A | 0.0000 | |
| 222 | I | A | 0.3366 | |
| 223 | T | A | -0.2431 | |
| 224 | R | A | -0.8504 | |
| 225 | A | A | -0.3351 | |
| 226 | T | A | -0.3714 | |
| 227 | D | A | -0.6903 | |
| 228 | M | A | 0.0000 | |
| 229 | G | A | -1.1491 | |
| 230 | T | A | -1.5465 | |
| 231 | D | A | -1.8424 | |
| 232 | Y | A | 0.0000 | |
| 233 | R | A | -1.5308 | |
| 234 | I | A | -0.7605 | |
| 235 | Y | A | 0.0000 | |
| 236 | K | A | -1.3430 | |
| 237 | T | A | -0.4242 | |
| 238 | I | A | 0.0763 | |
| 239 | A | A | 0.2955 | |
| 240 | F | A | 0.4502 | |
| 241 | G | A | 0.0000 | |
| 242 | K | A | -0.6794 | |
| 243 | D | A | 0.0000 | |
| 244 | K | A | -0.6172 | |
| 245 | T | A | 0.0000 | |
| 246 | I | A | 0.0000 | |
| 247 | K | A | -1.2667 | |
| 248 | K | A | -1.8477 | |
| 249 | I | A | 0.0000 | |
| 250 | L | A | -1.4313 | |
| 251 | K | A | -2.5159 | |
| 252 | L | A | -2.0679 | |
| 253 | D | A | -2.1471 | |
| 254 | F | A | 0.0000 | |
| 255 | L | A | -0.1383 | |
| 256 | P | A | -0.9657 | |
| 257 | D | A | -1.3192 | |
| 258 | I | A | 0.5181 | |
| 259 | G | A | -0.6948 | |
| 260 | K | A | -1.4763 | |
| 261 | I | A | -0.0674 | |
| 262 | L | A | 0.7938 | |
| 263 | A | A | 0.0776 | |
| 264 | T | A | -0.7312 | |
| 265 | N | A | -1.8878 | |
| 266 | T | A | -1.2331 | |
| 267 | E | A | -0.7858 | |
| 268 | L | A | 0.5314 | |
| 269 | V | A | -0.0228 | |
| 270 | A | A | -0.8322 | |
| 271 | E | A | -1.7693 | |
| 272 | Q | A | -1.4018 | |
| 273 | V | A | -0.1326 | |
| 274 | F | A | -0.7625 | |
| 275 | D | A | -2.1614 | |
| 276 | N | A | 0.0000 | |
| 277 | N | A | -2.4469 | |
| 278 | K | A | -2.5229 | |
| 279 | S | A | -1.0796 | |
| 280 | T | A | 0.1040 | |
| 281 | I | A | 1.3825 | |
| 282 | P | A | -0.2253 | |
| 283 | L | A | -1.0736 | |
| 284 | K | A | -2.2775 | |
| 285 | A | A | -1.6071 | |
| 286 | T | A | -1.2182 | |
| 287 | F | A | 0.0000 | |
| 288 | M | A | 0.6360 | |
| 289 | V | A | 0.0000 | |
| 290 | S | A | 0.0317 | |
| 291 | E | A | -1.1291 | |
| 292 | T | A | -1.4605 | |
| 293 | L | A | -1.2793 | |
| 294 | S | A | -2.0131 | |
| 295 | A | A | -2.1743 | |
| 296 | E | A | -3.4622 | |
| 297 | T | A | 0.0000 | |
| 298 | E | A | -2.9961 | |
| 299 | F | A | 0.0000 | |
| 300 | T | A | -1.3044 | |
| 301 | H | A | -1.6051 | |
| 302 | E | A | -2.5725 | |
| 303 | H | A | -2.1892 | |
| 304 | G | A | -1.6642 | |
| 305 | F | A | 0.0000 | |
| 306 | E | A | -0.8823 | |
| 307 | I | A | -0.5450 | |
| 308 | G | A | 0.0000 | |
| 309 | M | A | -0.4864 | |
| 310 | E | A | -2.0209 | |
| 311 | A | A | -1.8094 | |
| 312 | E | A | -2.3128 | |
| 313 | T | A | -1.5717 | |
| 314 | T | A | -1.6641 | |
| 315 | F | A | 0.0000 | |
| 316 | E | A | -2.8583 | |
| 317 | A | A | -1.9716 | |
| 318 | G | A | -0.8219 | |
| 319 | I | A | 0.1232 | |
| 320 | P | A | 0.0000 | |
| 321 | F | A | 0.5472 | |
| 322 | I | A | 0.0000 | |
| 323 | S | A | -1.0372 | |
| 324 | K | A | -1.9143 | |
| 325 | G | A | -1.2423 | |
| 326 | T | A | -0.5269 | |
| 327 | V | A | 0.2311 | |
| 328 | R | A | -1.6368 | |
| 329 | V | A | 0.0000 | |
| 330 | N | A | -0.6195 | |
| 331 | A | A | -0.0128 | |
| 332 | S | A | 0.0834 | |
| 333 | A | A | -0.1081 | |
| 334 | S | A | -0.2214 | |
| 335 | T | A | -0.4141 | |
| 336 | S | A | -1.2104 | |
| 337 | H | A | -1.6684 | |
| 338 | K | A | -2.7886 | |
| 339 | W | A | 0.0000 | |
| 340 | N | A | -2.4566 | |
| 341 | F | A | 0.0000 | |
| 342 | T | A | -1.6995 | |
| 343 | K | A | -3.0754 | |
| 344 | K | A | -3.9107 | |
| 345 | N | A | 0.0000 | |
| 346 | K | A | -3.6757 | |
| 347 | I | A | -2.1147 | |
| 348 | E | A | -3.0022 | |
| 349 | K | A | -2.1366 | |
| 350 | Q | A | -1.8989 | |
| 351 | V | A | 0.0000 | |
| 352 | F | A | 1.5388 | |
| 353 | V | A | 1.0446 | |
| 354 | S | A | 0.0594 | |
| 355 | Q | A | -1.1983 | |
| 356 | E | A | -2.5880 | |
| 357 | F | A | -2.1376 | |
| 358 | E | A | -2.6567 | |
| 359 | V | A | 0.0000 | |
| 360 | G | A | -1.1661 | |
| 361 | P | A | -0.9660 | |
| 362 | G | A | -1.7687 | |
| 363 | Q | A | -2.1793 | |
| 364 | A | A | 0.0000 | |
| 365 | V | A | 0.0000 | |
| 366 | T | A | 0.0000 | |
| 367 | R | A | 0.0000 | |
| 368 | K | A | -1.1656 | |
| 369 | A | A | 0.0000 | |
| 370 | I | A | -0.0342 | |
| 371 | I | A | 0.0000 | |
| 372 | K | A | -1.4560 | |
| 373 | K | A | -1.5498 | |
| 374 | S | A | 0.0000 | |
| 375 | T | A | -0.3574 | |
| 376 | I | A | 0.0000 | |
| 377 | D | A | -0.6254 | |
| 378 | L | A | 0.0000 | |
| 379 | P | A | -0.4606 | |
| 380 | Y | A | 0.0000 | |
| 381 | S | A | -1.3598 | |
| 382 | A | A | 0.0000 | |
| 383 | K | A | -2.2247 | |
| 384 | V | A | 0.0000 | |
| 385 | L | A | -1.1419 | |
| 386 | T | A | 0.0000 | |
| 387 | I | A | 0.0260 | |
| 388 | F | A | 0.2875 | |
| 389 | G | A | -0.5099 | |
| 390 | Y | A | -0.6821 | |
| 391 | E | A | -1.9130 | |
| 392 | A | A | -1.5803 | |
| 393 | N | A | -2.1790 | |
| 394 | I | A | 0.0000 | |
| 395 | S | A | -1.4580 | |
| 396 | G | A | -1.0674 | |
| 397 | T | A | -0.8110 | |
| 398 | W | A | 0.0000 | |
| 399 | K | A | -1.8175 | |
| 400 | G | A | 0.0000 | |
| 401 | V | A | 0.0000 | |
| 402 | S | A | 0.0000 | |
| 403 | F | A | 0.0000 | |
| 404 | Y | A | 0.0000 | |
| 405 | H | A | -1.4884 | |
| 406 | M | A | -0.3222 | |
| 407 | H | A | -0.3210 | |
| 408 | V | A | -0.1555 | |
| 409 | V | A | -0.7348 | |
| 410 | Q | A | -2.0572 | |
| 411 | E | A | -2.1996 | |
| 412 | D | A | -1.9844 | |
| 413 | I | A | 0.3221 |
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 | -0.8906 | 3.4901 | View | CSV | PDB |
| 4.5 | -0.9732 | 3.4555 | View | CSV | PDB |
| 5.0 | -1.0729 | 3.4046 | View | CSV | PDB |
| 5.5 | -1.1717 | 3.3472 | View | CSV | PDB |
| 6.0 | -1.2481 | 3.2952 | View | CSV | PDB |
| 6.5 | -1.2837 | 3.2596 | View | CSV | PDB |
| 7.0 | -1.2764 | 3.2467 | View | CSV | PDB |
| 7.5 | -1.2396 | 3.2525 | View | CSV | PDB |
| 8.0 | -1.1862 | 3.2682 | View | CSV | PDB |
| 8.5 | -1.1211 | 3.2876 | View | CSV | PDB |
| 9.0 | -1.0453 | 3.3925 | 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