| Chain sequence(s) |
A: QVQLVQSGSELKKPGASVKVSCKASGYTFTNYGMNWVRQAPGQGLEWMGWINTYTGEPTYAADFKRRFVFSLDTSVSTAYLQISSLKAEDTAVYYCARYPHYYGSSHWYFDVWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH
B: DIQMTQSPSSLSASVGDRVTITCWASQDISNYLNWYQQKPGKAPKLLIYFTSSLHSGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYSTVPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC input PDB |
| Selected Chain(s) | A,B |
| 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 all 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/f78764ffe2ff075/tmp/folded.pdb (00:00:03)
[INFO] Main: Simulation completed successfully. (00:06:15)
|
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 | Q | A | -1.2889 | |
| 2 | V | A | -0.5425 | |
| 3 | Q | A | -0.9641 | |
| 4 | L | A | 0.0000 | |
| 5 | V | A | 0.2098 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.8042 | |
| 8 | G | A | -1.1002 | |
| 9 | S | A | -1.1610 | |
| 10 | E | A | -1.9627 | |
| 11 | L | A | -1.2667 | |
| 12 | K | A | -1.7872 | |
| 13 | K | A | -2.2518 | |
| 14 | P | A | -1.6619 | |
| 15 | G | A | -1.3436 | |
| 16 | A | A | 0.0000 | |
| 17 | S | A | -1.0577 | |
| 18 | V | A | -1.3143 | |
| 19 | K | A | -1.7180 | |
| 20 | V | A | 0.0000 | |
| 21 | S | A | -0.5116 | |
| 22 | C | A | 0.0000 | |
| 23 | K | A | -0.3980 | |
| 24 | A | A | 0.0000 | |
| 25 | S | A | -0.4546 | |
| 26 | G | A | -0.7893 | |
| 27 | Y | A | -0.3939 | |
| 28 | T | A | -0.3707 | |
| 29 | F | A | 0.0000 | |
| 30 | T | A | -0.1749 | |
| 31 | N | A | -1.0378 | |
| 32 | Y | A | -0.4571 | |
| 33 | G | A | -0.2363 | |
| 34 | M | A | 0.0000 | |
| 35 | N | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | V | A | 0.0000 | |
| 38 | R | A | 0.0000 | |
| 39 | Q | A | -0.7356 | |
| 40 | A | A | -1.0691 | |
| 41 | P | A | -0.8299 | |
| 42 | G | A | -1.2397 | |
| 43 | Q | A | -1.9105 | |
| 44 | G | A | -1.4274 | |
| 45 | L | A | 0.0000 | |
| 46 | E | A | -0.9800 | |
| 47 | W | A | 0.0000 | |
| 48 | M | A | 0.0000 | |
| 49 | G | A | 0.0000 | |
| 50 | W | A | -0.0479 | |
| 51 | I | A | 0.0000 | |
| 52 | N | A | -0.6824 | |
| 53 | T | A | 0.0000 | |
| 54 | Y | A | 0.6010 | |
| 55 | T | A | -0.1275 | |
| 56 | G | A | -0.8390 | |
| 57 | E | A | -1.7456 | |
| 58 | P | A | -0.8105 | |
| 59 | T | A | -0.2846 | |
| 60 | Y | A | -0.4024 | |
| 61 | A | A | 0.0000 | |
| 62 | A | A | -1.6628 | |
| 63 | D | A | -2.6343 | |
| 64 | F | A | 0.0000 | |
| 65 | K | A | -2.9095 | |
| 66 | R | A | -2.9691 | |
| 67 | R | A | -1.7798 | |
| 68 | F | A | 0.0000 | |
| 69 | V | A | 0.0490 | |
| 70 | F | A | 0.0000 | |
| 71 | S | A | -0.2168 | |
| 72 | L | A | -0.1084 | |
| 73 | D | A | -0.4548 | |
| 74 | T | A | 0.0244 | |
| 75 | S | A | 0.0548 | |
| 76 | V | A | 0.5441 | |
| 77 | S | A | 0.0080 | |
| 78 | T | A | 0.0000 | |
| 79 | A | A | 0.0000 | |
| 80 | Y | A | -0.3727 | |
| 81 | L | A | 0.0000 | |
| 82 | Q | A | -0.7322 | |
| 83 | I | A | 0.0000 | |
| 84 | S | A | -0.8845 | |
| 85 | S | A | -1.0647 | |
| 86 | L | A | 0.0000 | |
| 87 | K | A | -1.9019 | |
| 88 | A | A | -1.5525 | |
| 89 | E | A | -2.0420 | |
| 90 | D | A | 0.0000 | |
| 91 | T | A | -0.8302 | |
| 92 | A | A | 0.0000 | |
| 93 | V | A | 0.1181 | |
| 94 | Y | A | 0.0000 | |
| 95 | Y | A | 0.0000 | |
| 96 | C | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | R | A | 0.0000 | |
| 99 | Y | A | 0.0000 | |
| 100 | P | A | -0.0858 | |
| 101 | H | A | -0.3111 | |
| 102 | Y | A | 1.2937 | |
| 103 | Y | A | 1.4021 | |
| 104 | G | A | 0.2745 | |
| 105 | S | A | 0.2755 | |
| 106 | S | A | 0.2974 | |
| 107 | H | A | 0.6132 | |
| 108 | W | A | 0.8068 | |
| 109 | Y | A | 0.0000 | |
| 110 | F | A | 0.0000 | |
| 111 | D | A | -0.3824 | |
| 112 | V | A | -0.1978 | |
| 113 | W | A | -0.5136 | |
| 114 | G | A | 0.0000 | |
| 115 | R | A | -1.9768 | |
| 116 | G | A | -0.9514 | |
| 117 | T | A | 0.0000 | |
| 118 | L | A | -0.2850 | |
| 119 | V | A | 0.0000 | |
| 120 | T | A | -0.9595 | |
| 121 | V | A | -1.3560 | |
| 122 | S | A | -1.1288 | |
| 123 | S | A | -0.9250 | |
| 124 | A | A | -0.6418 | |
| 125 | S | A | -0.8450 | |
| 126 | T | A | -1.2733 | |
| 127 | K | A | -1.9490 | |
| 128 | G | A | -1.7325 | |
| 129 | P | A | -0.8240 | |
| 130 | S | A | -0.4228 | |
| 131 | V | A | 0.0000 | |
| 132 | F | A | 0.0000 | |
| 133 | P | A | -1.2072 | |
| 134 | L | A | 0.0000 | |
| 135 | A | A | -0.9426 | |
| 136 | P | A | 0.0000 | |
| 137 | S | A | -1.0356 | |
| 138 | S | A | -1.5545 | |
| 139 | K | A | -2.1908 | |
| 140 | S | A | -1.2394 | |
| 141 | T | A | -0.9751 | |
| 142 | S | A | -1.0242 | |
| 143 | G | A | -1.2166 | |
| 144 | G | A | -0.8911 | |
| 145 | T | A | -0.6033 | |
| 146 | A | A | -0.3429 | |
| 147 | A | A | 0.0000 | |
| 148 | L | A | 0.0000 | |
| 149 | G | A | 0.0000 | |
| 150 | C | A | 0.0000 | |
| 151 | L | A | 0.0000 | |
| 152 | V | A | 0.0000 | |
| 153 | K | A | -0.3277 | |
| 154 | D | A | -0.6980 | |
| 155 | Y | A | 0.0000 | |
| 156 | F | A | -0.4847 | |
| 157 | P | A | 0.0000 | |
| 158 | E | A | -0.7153 | |
| 159 | P | A | -0.7448 | |
| 160 | V | A | -0.5740 | |
| 161 | T | A | -0.5331 | |
| 162 | V | A | -0.3745 | |
| 163 | S | A | -0.4040 | |
| 164 | W | A | 0.0000 | |
| 165 | N | A | -0.7065 | |
| 166 | S | A | -0.6641 | |
| 167 | G | A | -0.5728 | |
| 168 | A | A | -0.2138 | |
| 169 | L | A | 0.0707 | |
| 170 | T | A | -0.1428 | |
| 171 | S | A | -0.1830 | |
| 172 | G | A | -0.1653 | |
| 173 | V | A | 0.2120 | |
| 174 | H | A | -0.3222 | |
| 175 | T | A | -0.1805 | |
| 176 | F | A | 0.0000 | |
| 177 | P | A | -0.2878 | |
| 178 | A | A | 0.2784 | |
| 179 | V | A | 0.6503 | |
| 180 | L | A | 1.1643 | |
| 181 | Q | A | 0.2058 | |
| 182 | S | A | -0.0969 | |
| 183 | S | A | -0.2665 | |
| 184 | G | A | 0.0015 | |
| 185 | L | A | -0.0012 | |
| 186 | Y | A | 0.3476 | |
| 187 | S | A | 0.1866 | |
| 188 | L | A | 0.0000 | |
| 189 | S | A | 0.0000 | |
| 190 | S | A | 0.0000 | |
| 191 | V | A | 0.0000 | |
| 192 | V | A | 0.0000 | |
| 193 | T | A | -0.1192 | |
| 194 | V | A | 0.0000 | |
| 195 | P | A | -0.6151 | |
| 196 | S | A | -0.6931 | |
| 197 | S | A | -0.6969 | |
| 198 | S | A | -0.5830 | |
| 199 | L | A | -0.7310 | |
| 200 | G | A | -0.8907 | |
| 201 | T | A | -0.6750 | |
| 202 | Q | A | -1.0572 | |
| 203 | T | A | -0.9564 | |
| 204 | Y | A | 0.0000 | |
| 205 | I | A | -1.2493 | |
| 206 | C | A | 0.0000 | |
| 207 | N | A | -1.5629 | |
| 208 | V | A | 0.0000 | |
| 209 | N | A | -1.9187 | |
| 210 | H | A | 0.0000 | |
| 211 | K | A | -2.8063 | |
| 212 | P | A | -2.0051 | |
| 213 | S | A | -2.0309 | |
| 214 | N | A | -2.4850 | |
| 215 | T | A | -2.1621 | |
| 216 | K | A | -2.7109 | |
| 217 | V | A | -1.8231 | |
| 218 | D | A | -2.6012 | |
| 219 | K | A | -2.1515 | |
| 220 | K | A | -2.3497 | |
| 221 | V | A | 0.0000 | |
| 222 | E | A | -2.1094 | |
| 223 | P | A | -1.4727 | |
| 224 | K | A | -2.0612 | |
| 225 | S | A | -1.4742 | |
| 226 | C | A | -1.5484 | |
| 227 | D | A | -2.4805 | |
| 228 | K | A | -2.3961 | |
| 229 | T | A | -1.9327 | |
| 230 | H | A | -1.6128 | |
| 231 | D | B | -2.0061 | |
| 232 | I | B | 0.0000 | |
| 233 | Q | B | -1.8925 | |
| 234 | M | B | 0.0000 | |
| 235 | T | B | -0.6330 | |
| 236 | Q | B | 0.0000 | |
| 237 | S | B | -0.2767 | |
| 238 | P | B | -0.6419 | |
| 239 | S | B | -0.9569 | |
| 240 | S | B | -0.9788 | |
| 241 | L | B | -0.6351 | |
| 242 | S | B | -0.7659 | |
| 243 | A | B | 0.0000 | |
| 244 | S | B | -0.7640 | |
| 245 | V | B | -0.0366 | |
| 246 | G | B | -0.8234 | |
| 247 | D | B | -1.8007 | |
| 248 | R | B | -2.3261 | |
| 249 | V | B | 0.0000 | |
| 250 | T | B | -0.6247 | |
| 251 | I | B | 0.0000 | |
| 252 | T | B | -0.3197 | |
| 253 | C | B | 0.0000 | |
| 254 | W | B | -0.5935 | |
| 255 | A | B | -1.2881 | |
| 256 | S | B | -1.7547 | |
| 257 | Q | B | -2.4925 | |
| 258 | D | B | -2.5927 | |
| 259 | I | B | 0.0000 | |
| 260 | S | B | -1.0647 | |
| 261 | N | B | -0.6021 | |
| 262 | Y | B | 0.4157 | |
| 263 | L | B | 0.0000 | |
| 264 | N | B | 0.0000 | |
| 265 | W | B | 0.0000 | |
| 266 | Y | B | 0.0000 | |
| 267 | Q | B | 0.0000 | |
| 268 | Q | B | 0.0000 | |
| 269 | K | B | -1.4871 | |
| 270 | P | B | -1.4648 | |
| 271 | G | B | -1.7223 | |
| 272 | K | B | -2.6116 | |
| 273 | A | B | -1.6518 | |
| 274 | P | B | 0.0000 | |
| 275 | K | B | -1.2640 | |
| 276 | L | B | 0.0000 | |
| 277 | L | B | 0.0000 | |
| 278 | I | B | 0.0000 | |
| 279 | Y | B | 0.7219 | |
| 280 | F | B | 0.8749 | |
| 281 | T | B | 0.0000 | |
| 282 | S | B | 0.0266 | |
| 283 | S | B | 0.3249 | |
| 284 | L | B | 0.3833 | |
| 285 | H | B | -0.1666 | |
| 286 | S | B | -0.4060 | |
| 287 | G | B | -0.5731 | |
| 288 | V | B | 0.0000 | |
| 289 | P | B | -0.4054 | |
| 290 | S | B | -0.4403 | |
| 291 | R | B | -0.7064 | |
| 292 | F | B | 0.0000 | |
| 293 | S | B | -0.2953 | |
| 294 | G | B | -0.1531 | |
| 295 | S | B | -0.6719 | |
| 296 | G | B | -1.0181 | |
| 297 | S | B | -1.1249 | |
| 298 | G | B | -1.6118 | |
| 299 | T | B | -1.7699 | |
| 300 | D | B | -1.9962 | |
| 301 | F | B | 0.0000 | |
| 302 | T | B | -0.5102 | |
| 303 | F | B | 0.0000 | |
| 304 | T | B | -0.5985 | |
| 305 | I | B | 0.0000 | |
| 306 | S | B | -1.3437 | |
| 307 | S | B | -1.1455 | |
| 308 | L | B | 0.0000 | |
| 309 | Q | B | -0.7778 | |
| 310 | P | B | -1.4416 | |
| 311 | E | B | -1.6560 | |
| 312 | D | B | 0.0000 | |
| 313 | I | B | 0.0000 | |
| 314 | A | B | 0.0000 | |
| 315 | T | B | -1.0666 | |
| 316 | Y | B | 0.0000 | |
| 317 | Y | B | 0.0000 | |
| 318 | C | B | 0.0000 | |
| 319 | Q | B | 0.0000 | |
| 320 | Q | B | 0.0000 | |
| 321 | Y | B | 0.0000 | |
| 322 | S | B | -0.0347 | |
| 323 | T | B | 0.2668 | |
| 324 | V | B | 0.8351 | |
| 325 | P | B | 0.0928 | |
| 326 | W | B | 0.0000 | |
| 327 | T | B | -0.6518 | |
| 328 | F | B | -0.5178 | |
| 329 | G | B | 0.0000 | |
| 330 | Q | B | -1.7699 | |
| 331 | G | B | 0.0000 | |
| 332 | T | B | 0.0000 | |
| 333 | K | B | -2.0499 | |
| 334 | V | B | 0.0000 | |
| 335 | E | B | -1.4712 | |
| 336 | I | B | 0.0000 | |
| 337 | K | B | -0.9835 | |
| 338 | R | B | -0.8806 | |
| 339 | T | B | -0.1207 | |
| 340 | V | B | 0.3047 | |
| 341 | A | B | 0.1096 | |
| 342 | A | B | -0.1443 | |
| 343 | P | B | 0.0000 | |
| 344 | S | B | -0.1388 | |
| 345 | V | B | 0.0000 | |
| 346 | F | B | 0.2068 | |
| 347 | I | B | 0.1579 | |
| 348 | F | B | 0.0000 | |
| 349 | P | B | -0.4865 | |
| 350 | P | B | 0.0000 | |
| 351 | S | B | -1.8231 | |
| 352 | D | B | -3.1310 | |
| 353 | E | B | -3.1269 | |
| 354 | Q | B | 0.0000 | |
| 355 | L | B | -2.2283 | |
| 356 | K | B | -2.7754 | |
| 357 | S | B | -1.7264 | |
| 358 | G | B | -1.2058 | |
| 359 | T | B | -0.9529 | |
| 360 | A | B | 0.0000 | |
| 361 | S | B | 0.0000 | |
| 362 | V | B | 0.0000 | |
| 363 | V | B | 0.0000 | |
| 364 | C | B | 0.0000 | |
| 365 | L | B | 0.0000 | |
| 366 | L | B | 0.0000 | |
| 367 | N | B | 0.0000 | |
| 368 | N | B | -0.8868 | |
| 369 | F | B | 0.0000 | |
| 370 | Y | B | -1.0738 | |
| 371 | P | B | -1.6676 | |
| 372 | R | B | -3.0814 | |
| 373 | E | B | -3.2193 | |
| 374 | A | B | -2.4229 | |
| 375 | K | B | -2.5537 | |
| 376 | V | B | 0.0000 | |
| 377 | Q | B | -0.6803 | |
| 378 | W | B | 0.0000 | |
| 379 | K | B | -0.5402 | |
| 380 | V | B | 0.0000 | |
| 381 | D | B | -1.5444 | |
| 382 | N | B | -1.4180 | |
| 383 | A | B | -0.2439 | |
| 384 | L | B | 0.7135 | |
| 385 | Q | B | -0.1511 | |
| 386 | S | B | -0.4321 | |
| 387 | G | B | -0.9032 | |
| 388 | N | B | -0.8199 | |
| 389 | S | B | -1.0390 | |
| 390 | Q | B | -1.0579 | |
| 391 | E | B | -1.3722 | |
| 392 | S | B | -0.7433 | |
| 393 | V | B | -0.8964 | |
| 394 | T | B | -1.1406 | |
| 395 | E | B | -2.2253 | |
| 396 | Q | B | 0.0000 | |
| 397 | D | B | -1.9008 | |
| 398 | S | B | -2.0802 | |
| 399 | K | B | -2.5398 | |
| 400 | D | B | -1.9964 | |
| 401 | S | B | 0.0000 | |
| 402 | T | B | 0.0000 | |
| 403 | Y | B | -1.3060 | |
| 404 | S | B | 0.0000 | |
| 405 | L | B | 0.0000 | |
| 406 | S | B | 0.0000 | |
| 407 | S | B | 0.0000 | |
| 408 | T | B | -0.5210 | |
| 409 | L | B | 0.0000 | |
| 410 | T | B | -0.4228 | |
| 411 | L | B | -0.6520 | |
| 412 | S | B | -0.9743 | |
| 413 | K | B | -1.7579 | |
| 414 | A | B | -1.7484 | |
| 415 | D | B | -2.5409 | |
| 416 | Y | B | 0.0000 | |
| 417 | E | B | -3.1982 | |
| 418 | K | B | -3.3613 | |
| 419 | H | B | -2.6980 | |
| 420 | K | B | -2.0544 | |
| 421 | V | B | -0.9324 | |
| 422 | Y | B | 0.0000 | |
| 423 | A | B | 0.0000 | |
| 424 | C | B | 0.0000 | |
| 425 | E | B | -0.8932 | |
| 426 | V | B | 0.0000 | |
| 427 | T | B | -1.2781 | |
| 428 | H | B | 0.0000 | |
| 429 | Q | B | -1.7884 | |
| 430 | G | B | -0.4797 | |
| 431 | L | B | -0.2760 | |
| 432 | S | B | -0.4848 | |
| 433 | S | B | -0.3956 | |
| 434 | P | B | -0.4925 | |
| 435 | V | B | 0.0928 | |
| 436 | T | B | -0.3774 | |
| 437 | K | B | -0.5388 | |
| 438 | S | B | -0.4117 | |
| 439 | F | B | -0.4444 | |
| 440 | N | B | -1.0803 | |
| 441 | R | B | -1.7405 | |
| 442 | G | B | -1.6410 | |
| 443 | E | B | -1.6842 | |
| 444 | C | B | -1.5993 |
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 | -0.7246 | 1.8161 | View | CSV | PDB |
| 4.5 | -0.771 | 1.8155 | View | CSV | PDB |
| 5.0 | -0.8231 | 1.8142 | View | CSV | PDB |
| 5.5 | -0.8692 | 1.8132 | View | CSV | PDB |
| 6.0 | -0.8968 | 1.8155 | View | CSV | PDB |
| 6.5 | -0.8979 | 1.8216 | View | CSV | PDB |
| 7.0 | -0.8761 | 1.8266 | View | CSV | PDB |
| 7.5 | -0.8411 | 1.8256 | View | CSV | PDB |
| 8.0 | -0.7994 | 1.8195 | View | CSV | PDB |
| 8.5 | -0.7518 | 1.8107 | View | CSV | PDB |
| 9.0 | -0.6972 | 1.8003 | 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