| Chain sequence(s) |
A: MKITLFWHRRDLRFQDNAGLAAALQSSHPVLPLFIYDQTILEKLPKDDARLTFIFDQVERLAHEAHEAGGGLLARYGHTPDVFKQLLKDYDVAAVYTNEDYEPYATERDTAIAKLLEKNDVAFKSFKDQVIFAKEEVLTKNGKPSKVFGAYSKAWQAKVTPDDFKPHPSSRLLKKENLALPHRADAKRPDLESMGFVRHEQWTPPAHLPPAEVVKRYDKVRDLPAEKRGTTRMSVHLRFGTVSIRQLMQQAQELNNKLLNEMIWRDFFMMLLWHFPNTATEAYDPKMRHLPYRDDPEQYRAWCEGRTGYPLVDAGMRQLNQTGYMHNRARIAAAGFLVKQLFIDWTLGEHYFSEKLLDYDMSNNVGNWQWMAGTGAVAAPWFRVYSPDSQQKQYDPEYAYVKQWVPEFGTDKYPAPIVDHKFGRERAIDLIRKGRTK
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] (00:00:13)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:13)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:13)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:13)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:14)
[INFO] FoldX: Starting FoldX energy minimization (00:00:14)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:07:54)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/b3dceaebb877303/tmp/folded.pdb (00:07:54)
[INFO] Main: Simulation completed successfully. (00:11:08)
|
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 | 0.0798 | |
| 2 | K | A | -1.2680 | |
| 3 | I | A | 0.0000 | |
| 4 | T | A | 0.0000 | |
| 5 | L | A | 0.0000 | |
| 6 | F | A | 0.0000 | |
| 7 | W | A | 0.0000 | |
| 8 | H | A | 0.0000 | |
| 9 | R | A | 0.0000 | |
| 10 | R | A | -0.4949 | |
| 11 | D | A | 0.0000 | |
| 12 | L | A | 0.0000 | |
| 13 | R | A | 0.0000 | |
| 14 | F | A | 0.0000 | |
| 15 | Q | A | -1.1453 | |
| 16 | D | A | 0.0000 | |
| 17 | N | A | 0.0000 | |
| 18 | A | A | 0.0000 | |
| 19 | G | A | 0.0000 | |
| 20 | L | A | 0.0000 | |
| 21 | A | A | 0.0000 | |
| 22 | A | A | -0.4863 | |
| 23 | A | A | 0.0000 | |
| 24 | L | A | 0.0000 | |
| 25 | Q | A | -1.3156 | |
| 26 | S | A | -0.8813 | |
| 27 | S | A | -0.8282 | |
| 28 | H | A | -1.0033 | |
| 29 | P | A | -1.1322 | |
| 30 | V | A | 0.0000 | |
| 31 | L | A | 0.0000 | |
| 32 | P | A | 0.0000 | |
| 33 | L | A | 0.0000 | |
| 34 | F | A | 0.0000 | |
| 35 | I | A | 0.0000 | |
| 36 | Y | A | 0.0000 | |
| 37 | D | A | 0.0000 | |
| 38 | Q | A | -1.1052 | |
| 39 | T | A | -0.8698 | |
| 40 | I | A | -0.5935 | |
| 41 | L | A | 0.0000 | |
| 42 | E | A | -2.7900 | |
| 43 | K | A | -2.7394 | |
| 44 | L | A | -1.9326 | |
| 45 | P | A | -1.9222 | |
| 46 | K | A | -2.8874 | |
| 47 | D | A | -2.1920 | |
| 48 | D | A | 0.0000 | |
| 49 | A | A | -1.2846 | |
| 50 | R | A | -0.9420 | |
| 51 | L | A | 0.0000 | |
| 52 | T | A | 0.0000 | |
| 53 | F | A | -0.5789 | |
| 54 | I | A | 0.0000 | |
| 55 | F | A | -0.6222 | |
| 56 | D | A | -0.9975 | |
| 57 | Q | A | -0.8410 | |
| 58 | V | A | 0.0000 | |
| 59 | E | A | -1.4140 | |
| 60 | R | A | -1.7131 | |
| 61 | L | A | 0.0000 | |
| 62 | A | A | 0.0000 | |
| 63 | H | A | -2.6230 | |
| 64 | E | A | -2.6297 | |
| 65 | A | A | 0.0000 | |
| 66 | H | A | -2.7456 | |
| 67 | E | A | -3.3404 | |
| 68 | A | A | -2.8324 | |
| 69 | G | A | -2.5585 | |
| 70 | G | A | 0.0000 | |
| 71 | G | A | 0.0000 | |
| 72 | L | A | 0.0000 | |
| 73 | L | A | 0.0000 | |
| 74 | A | A | 0.0000 | |
| 75 | R | A | -0.5174 | |
| 76 | Y | A | -0.0847 | |
| 77 | G | A | -0.6757 | |
| 78 | H | A | -1.2160 | |
| 79 | T | A | 0.0000 | |
| 80 | P | A | -1.4860 | |
| 81 | D | A | -2.5474 | |
| 82 | V | A | 0.0000 | |
| 83 | F | A | 0.0000 | |
| 84 | K | A | -2.4234 | |
| 85 | Q | A | -2.4033 | |
| 86 | L | A | 0.0000 | |
| 87 | L | A | -2.0672 | |
| 88 | K | A | -2.7191 | |
| 89 | D | A | -2.2526 | |
| 90 | Y | A | 0.0000 | |
| 91 | D | A | -2.2954 | |
| 92 | V | A | 0.0000 | |
| 93 | A | A | -1.0080 | |
| 94 | A | A | 0.0000 | |
| 95 | V | A | 0.0000 | |
| 96 | Y | A | 0.0000 | |
| 97 | T | A | 0.0000 | |
| 98 | N | A | 0.0000 | |
| 99 | E | A | -0.7288 | |
| 100 | D | A | -0.6699 | |
| 101 | Y | A | 0.0000 | |
| 102 | E | A | -0.6710 | |
| 103 | P | A | -0.7584 | |
| 104 | Y | A | -0.5403 | |
| 105 | A | A | 0.0000 | |
| 106 | T | A | -1.1238 | |
| 107 | E | A | -1.8822 | |
| 108 | R | A | 0.0000 | |
| 109 | D | A | -1.0031 | |
| 110 | T | A | -1.0594 | |
| 111 | A | A | -1.0114 | |
| 112 | I | A | 0.0000 | |
| 113 | A | A | -1.6373 | |
| 114 | K | A | -2.5884 | |
| 115 | L | A | -2.1948 | |
| 116 | L | A | 0.0000 | |
| 117 | E | A | -3.9998 | |
| 118 | K | A | -3.9373 | |
| 119 | N | A | -3.5658 | |
| 120 | D | A | -3.3804 | |
| 121 | V | A | 0.0000 | |
| 122 | A | A | -1.3849 | |
| 123 | F | A | -0.8128 | |
| 124 | K | A | -0.6939 | |
| 125 | S | A | -0.4977 | |
| 126 | F | A | -0.1612 | |
| 127 | K | A | -0.5287 | |
| 128 | D | A | 0.0000 | |
| 129 | Q | A | -0.4172 | |
| 130 | V | A | 0.0000 | |
| 131 | I | A | 0.0000 | |
| 132 | F | A | 0.0000 | |
| 133 | A | A | 0.0000 | |
| 134 | K | A | -1.6173 | |
| 135 | E | A | -2.7061 | |
| 136 | E | A | -1.9610 | |
| 137 | V | A | 0.0000 | |
| 138 | L | A | -1.8871 | |
| 139 | T | A | -2.0308 | |
| 140 | K | A | -2.6971 | |
| 141 | N | A | -2.7665 | |
| 142 | G | A | -2.6655 | |
| 143 | K | A | -2.9763 | |
| 144 | P | A | -1.7374 | |
| 145 | S | A | 0.0000 | |
| 146 | K | A | -0.3274 | |
| 147 | V | A | 1.3953 | |
| 148 | F | A | 0.6356 | |
| 149 | G | A | -0.0305 | |
| 150 | A | A | -0.0865 | |
| 151 | Y | A | 0.0000 | |
| 152 | S | A | 0.0000 | |
| 153 | K | A | -2.0735 | |
| 154 | A | A | -1.3663 | |
| 155 | W | A | 0.0000 | |
| 156 | Q | A | -1.6073 | |
| 157 | A | A | -1.2166 | |
| 158 | K | A | -1.6440 | |
| 159 | V | A | -0.9929 | |
| 160 | T | A | -1.3518 | |
| 161 | P | A | -1.6844 | |
| 162 | D | A | -2.7345 | |
| 163 | D | A | -2.0970 | |
| 164 | F | A | 0.0000 | |
| 165 | K | A | -2.8740 | |
| 166 | P | A | -1.7960 | |
| 167 | H | A | -1.2512 | |
| 168 | P | A | -1.3370 | |
| 169 | S | A | 0.0000 | |
| 170 | S | A | -1.4992 | |
| 171 | R | A | -2.1744 | |
| 172 | L | A | -1.7494 | |
| 173 | L | A | -2.1680 | |
| 174 | K | A | -3.2260 | |
| 175 | K | A | -3.5429 | |
| 176 | E | A | -3.1737 | |
| 177 | N | A | -2.3356 | |
| 178 | L | A | 0.0000 | |
| 179 | A | A | 0.0000 | |
| 180 | L | A | 0.3220 | |
| 181 | P | A | -0.4901 | |
| 182 | H | A | -1.4577 | |
| 183 | R | A | -2.3156 | |
| 184 | A | A | -1.6177 | |
| 185 | D | A | -1.6599 | |
| 186 | A | A | -1.6124 | |
| 187 | K | A | -2.3355 | |
| 188 | R | A | -1.4870 | |
| 189 | P | A | -1.2364 | |
| 190 | D | A | -1.6305 | |
| 191 | L | A | 0.0000 | |
| 192 | E | A | -2.5331 | |
| 193 | S | A | -1.3936 | |
| 194 | M | A | 0.0000 | |
| 195 | G | A | -1.8393 | |
| 196 | F | A | 0.0000 | |
| 197 | V | A | -1.7862 | |
| 198 | R | A | -2.2985 | |
| 199 | H | A | -2.2260 | |
| 200 | E | A | -2.1817 | |
| 201 | Q | A | -0.8010 | |
| 202 | W | A | 0.6293 | |
| 203 | T | A | 0.1462 | |
| 204 | P | A | -0.1562 | |
| 205 | P | A | -0.4170 | |
| 206 | A | A | -0.5002 | |
| 207 | H | A | -0.9392 | |
| 208 | L | A | -0.2668 | |
| 209 | P | A | 0.0000 | |
| 210 | P | A | -1.0117 | |
| 211 | A | A | -1.4332 | |
| 212 | E | A | -2.5783 | |
| 213 | V | A | 0.0000 | |
| 214 | V | A | 0.0000 | |
| 215 | K | A | -3.6202 | |
| 216 | R | A | -3.5989 | |
| 217 | Y | A | 0.0000 | |
| 218 | D | A | -3.7704 | |
| 219 | K | A | -3.2178 | |
| 220 | V | A | -2.3056 | |
| 221 | R | A | -2.0114 | |
| 222 | D | A | -1.3082 | |
| 223 | L | A | -0.8342 | |
| 224 | P | A | 0.0000 | |
| 225 | A | A | -1.4156 | |
| 226 | E | A | -1.9611 | |
| 227 | K | A | -2.8488 | |
| 228 | R | A | -3.1942 | |
| 229 | G | A | 0.0000 | |
| 230 | T | A | -1.6378 | |
| 231 | T | A | -0.7937 | |
| 232 | R | A | -0.9518 | |
| 233 | M | A | 0.0000 | |
| 234 | S | A | -0.3062 | |
| 235 | V | A | 0.0000 | |
| 236 | H | A | 0.0000 | |
| 237 | L | A | 0.0000 | |
| 238 | R | A | -0.4637 | |
| 239 | F | A | 0.0000 | |
| 240 | G | A | 0.0000 | |
| 241 | T | A | 0.0000 | |
| 242 | V | A | 0.0000 | |
| 243 | S | A | 0.0000 | |
| 244 | I | A | 0.0000 | |
| 245 | R | A | 0.0000 | |
| 246 | Q | A | -1.1816 | |
| 247 | L | A | 0.0000 | |
| 248 | M | A | 0.0000 | |
| 249 | Q | A | -1.7416 | |
| 250 | Q | A | -1.5510 | |
| 251 | A | A | 0.0000 | |
| 252 | Q | A | -2.3606 | |
| 253 | E | A | -2.6219 | |
| 254 | L | A | -2.1488 | |
| 255 | N | A | 0.0000 | |
| 256 | N | A | -2.7485 | |
| 257 | K | A | -2.7145 | |
| 258 | L | A | 0.0000 | |
| 259 | L | A | 0.0000 | |
| 260 | N | A | -1.3459 | |
| 261 | E | A | -0.7972 | |
| 262 | M | A | 0.0000 | |
| 263 | I | A | 0.0000 | |
| 264 | W | A | -0.0003 | |
| 265 | R | A | 0.0000 | |
| 266 | D | A | 0.0000 | |
| 267 | F | A | 0.0000 | |
| 268 | F | A | 0.0000 | |
| 269 | M | A | 0.0000 | |
| 270 | M | A | 0.0000 | |
| 271 | L | A | 0.0000 | |
| 272 | L | A | 0.0000 | |
| 273 | W | A | -0.3885 | |
| 274 | H | A | -0.6785 | |
| 275 | F | A | -0.2397 | |
| 276 | P | A | -0.7294 | |
| 277 | N | A | -1.4559 | |
| 278 | T | A | 0.0000 | |
| 279 | A | A | -0.6803 | |
| 280 | T | A | -0.9659 | |
| 281 | E | A | -1.7044 | |
| 282 | A | A | 0.0000 | |
| 283 | Y | A | -0.7730 | |
| 284 | D | A | -1.1909 | |
| 285 | P | A | -1.6759 | |
| 286 | K | A | -2.7265 | |
| 287 | M | A | 0.0000 | |
| 288 | R | A | -2.0880 | |
| 289 | H | A | -2.1193 | |
| 290 | L | A | 0.0000 | |
| 291 | P | A | -1.0389 | |
| 292 | Y | A | -0.8428 | |
| 293 | R | A | -1.6101 | |
| 294 | D | A | -2.5218 | |
| 295 | D | A | -2.2176 | |
| 296 | P | A | -2.2401 | |
| 297 | E | A | -2.8238 | |
| 298 | Q | A | -2.1967 | |
| 299 | Y | A | -2.0707 | |
| 300 | R | A | -3.1639 | |
| 301 | A | A | -2.3286 | |
| 302 | W | A | 0.0000 | |
| 303 | C | A | 0.0000 | |
| 304 | E | A | -2.7599 | |
| 305 | G | A | 0.0000 | |
| 306 | R | A | -1.8410 | |
| 307 | T | A | 0.0000 | |
| 308 | G | A | 0.0000 | |
| 309 | Y | A | 0.0000 | |
| 310 | P | A | -0.5809 | |
| 311 | L | A | 0.0000 | |
| 312 | V | A | 0.0000 | |
| 313 | D | A | 0.0000 | |
| 314 | A | A | 0.0000 | |
| 315 | G | A | 0.0000 | |
| 316 | M | A | 0.0000 | |
| 317 | R | A | -1.3312 | |
| 318 | Q | A | 0.0000 | |
| 319 | L | A | 0.0000 | |
| 320 | N | A | -1.7557 | |
| 321 | Q | A | -1.5593 | |
| 322 | T | A | -0.8161 | |
| 323 | G | A | 0.0000 | |
| 324 | Y | A | -0.3124 | |
| 325 | M | A | 0.0000 | |
| 326 | H | A | 0.0000 | |
| 327 | N | A | -1.1450 | |
| 328 | R | A | -0.7959 | |
| 329 | A | A | 0.0000 | |
| 330 | R | A | -0.7641 | |
| 331 | I | A | 0.0000 | |
| 332 | A | A | 0.0000 | |
| 333 | A | A | 0.0000 | |
| 334 | A | A | 0.0000 | |
| 335 | G | A | -0.0855 | |
| 336 | F | A | 0.0000 | |
| 337 | L | A | 0.0000 | |
| 338 | V | A | 0.0000 | |
| 339 | K | A | 0.0000 | |
| 340 | Q | A | 0.0000 | |
| 341 | L | A | 0.0000 | |
| 342 | F | A | 0.0000 | |
| 343 | I | A | 0.0000 | |
| 344 | D | A | -0.4450 | |
| 345 | W | A | 0.0000 | |
| 346 | T | A | -0.1247 | |
| 347 | L | A | 0.5012 | |
| 348 | G | A | 0.0000 | |
| 349 | E | A | 0.0000 | |
| 350 | H | A | -1.1155 | |
| 351 | Y | A | -0.8175 | |
| 352 | F | A | 0.0000 | |
| 353 | S | A | -1.2118 | |
| 354 | E | A | -2.4245 | |
| 355 | K | A | -1.6468 | |
| 356 | L | A | 0.0000 | |
| 357 | L | A | 0.0000 | |
| 358 | D | A | 0.0000 | |
| 359 | Y | A | -0.3820 | |
| 360 | D | A | -0.2861 | |
| 361 | M | A | -0.2653 | |
| 362 | S | A | 0.0000 | |
| 363 | N | A | -0.3918 | |
| 364 | N | A | 0.0000 | |
| 365 | V | A | 0.0000 | |
| 366 | G | A | -0.2510 | |
| 367 | N | A | -0.5274 | |
| 368 | W | A | 0.0000 | |
| 369 | Q | A | 0.0000 | |
| 370 | W | A | 0.0340 | |
| 371 | M | A | 0.0000 | |
| 372 | A | A | 0.0000 | |
| 373 | G | A | 0.1606 | |
| 374 | T | A | 0.0000 | |
| 375 | G | A | -0.2850 | |
| 376 | A | A | 0.1017 | |
| 377 | V | A | 0.3430 | |
| 378 | A | A | 0.2008 | |
| 379 | A | A | 0.0766 | |
| 380 | P | A | 0.2424 | |
| 381 | W | A | 0.5216 | |
| 382 | F | A | 0.8785 | |
| 383 | R | A | -0.1402 | |
| 384 | V | A | -0.3285 | |
| 385 | Y | A | -0.1083 | |
| 386 | S | A | -1.0010 | |
| 387 | P | A | 0.0000 | |
| 388 | D | A | -2.5184 | |
| 389 | S | A | -1.9044 | |
| 390 | Q | A | 0.0000 | |
| 391 | Q | A | 0.0000 | |
| 392 | K | A | -3.1095 | |
| 393 | Q | A | -2.4725 | |
| 394 | Y | A | -1.1481 | |
| 395 | D | A | 0.0000 | |
| 396 | P | A | -2.1144 | |
| 397 | E | A | -2.3874 | |
| 398 | Y | A | -1.5233 | |
| 399 | A | A | -1.3356 | |
| 400 | Y | A | 0.0000 | |
| 401 | V | A | 0.0000 | |
| 402 | K | A | -2.4542 | |
| 403 | Q | A | -1.9518 | |
| 404 | W | A | -1.1641 | |
| 405 | V | A | 0.0000 | |
| 406 | P | A | -1.2386 | |
| 407 | E | A | -1.3672 | |
| 408 | F | A | -1.0266 | |
| 409 | G | A | -1.2107 | |
| 410 | T | A | -1.6114 | |
| 411 | D | A | -2.6424 | |
| 412 | K | A | -2.5733 | |
| 413 | Y | A | -1.4945 | |
| 414 | P | A | -0.9472 | |
| 415 | A | A | -0.4830 | |
| 416 | P | A | -0.4086 | |
| 417 | I | A | -0.2420 | |
| 418 | V | A | 0.0000 | |
| 419 | D | A | -1.2510 | |
| 420 | H | A | -1.7990 | |
| 421 | K | A | -2.2002 | |
| 422 | F | A | -0.6388 | |
| 423 | G | A | 0.0000 | |
| 424 | R | A | -2.2934 | |
| 425 | E | A | -2.5917 | |
| 426 | R | A | -2.5226 | |
| 427 | A | A | 0.0000 | |
| 428 | I | A | -1.5222 | |
| 429 | D | A | -2.3805 | |
| 430 | L | A | -1.8764 | |
| 431 | I | A | 0.0000 | |
| 432 | R | A | -2.9823 | |
| 433 | K | A | -3.1400 | |
| 434 | G | A | 0.0000 | |
| 435 | R | A | -2.8690 | |
| 436 | T | A | -2.2641 | |
| 437 | K | A | -2.8117 |
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 | -0.9203 | 3.5291 | View | CSV | PDB |
| 4.5 | -0.979 | 3.4819 | View | CSV | PDB |
| 5.0 | -1.0495 | 3.4032 | View | CSV | PDB |
| 5.5 | -1.117 | 3.3038 | View | CSV | PDB |
| 6.0 | -1.1638 | 3.2001 | View | CSV | PDB |
| 6.5 | -1.1773 | 3.1082 | View | CSV | PDB |
| 7.0 | -1.1581 | 3.0435 | View | CSV | PDB |
| 7.5 | -1.1169 | 3.0098 | View | CSV | PDB |
| 8.0 | -1.0632 | 2.9964 | View | CSV | PDB |
| 8.5 | -1.0004 | 2.9918 | View | CSV | PDB |
| 9.0 | -0.9289 | 2.9902 | 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