| Chain sequence(s) |
A: GRSDAYTQVDNFLHAYARGGDELVNGHPSYTVDQAAEQILREQASWQKAPGDSVLTLSYSFLTKPNDFFNTPWKYVSDIYSLGKFSAFSAQQQAQAKLSLQSWSDVTNIHFVDAGQGDQGDLTFGNFSSSVGGAAFAFLPDVPDALKGQSWYLINSSYSANVNPANGNYGRQTLTHEIGHTLGLSHPGDYNAGEGDPTYADATYAEDTRAYSVMSYWEEQNTGQDFKGAYSSAPLLDDIAAIQKLYGANLTTRTGDTVYGFNSNTERDFYSATSSSSKLVFSVWDAGGNDTLDFSGFSQNQKINLNEKALSDVGGLKGNVSIAAGVTVENAIGGSGSDLLIGNDVANVLKGGAGNDILYGGLGADQLWGGAGADTFVYGDIAESSAAAPDTLRDFVSGQDKIDLSGLDAFVNGGLVLQYVDAFAGKAGQAILSYDAASKAGSLAIDFSGDAHADFAINLIGQATQADIVV
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] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:03)
[INFO] FoldX: Starting FoldX energy minimization (00:00:03)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:04:24)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/3db19c9c1f18217/tmp/folded.pdb (00:04:24)
[INFO] Main: Simulation completed successfully. (00:11:34)
|
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 | G | A | -0.9751 | |
| 2 | R | A | -2.0304 | |
| 3 | S | A | -1.6263 | |
| 4 | D | A | -2.5594 | |
| 5 | A | A | 0.0000 | |
| 6 | Y | A | -1.3515 | |
| 7 | T | A | -1.7765 | |
| 8 | Q | A | -1.9262 | |
| 9 | V | A | 0.0000 | |
| 10 | D | A | -1.1812 | |
| 11 | N | A | -1.5944 | |
| 12 | F | A | 0.0000 | |
| 13 | L | A | 0.4490 | |
| 14 | H | A | -0.8349 | |
| 15 | A | A | -0.2138 | |
| 16 | Y | A | 0.0200 | |
| 17 | A | A | -0.0384 | |
| 18 | R | A | -0.1405 | |
| 19 | G | A | -0.7533 | |
| 20 | G | A | -1.5086 | |
| 21 | D | A | -2.3494 | |
| 22 | E | A | -1.8832 | |
| 23 | L | A | 0.4082 | |
| 24 | V | A | 0.6813 | |
| 25 | N | A | -0.2827 | |
| 26 | G | A | -0.4272 | |
| 27 | H | A | 0.0000 | |
| 28 | P | A | -0.1720 | |
| 29 | S | A | -0.2171 | |
| 30 | Y | A | -0.3424 | |
| 31 | T | A | -0.8246 | |
| 32 | V | A | -1.3716 | |
| 33 | D | A | -2.6439 | |
| 34 | Q | A | -2.1661 | |
| 35 | A | A | 0.0000 | |
| 36 | A | A | 0.0000 | |
| 37 | E | A | -3.1155 | |
| 38 | Q | A | -2.0785 | |
| 39 | I | A | 0.0000 | |
| 40 | L | A | -2.2601 | |
| 41 | R | A | -3.1380 | |
| 42 | E | A | -3.5032 | |
| 43 | Q | A | -2.8982 | |
| 44 | A | A | 0.0000 | |
| 45 | S | A | -1.3376 | |
| 46 | W | A | -1.2006 | |
| 47 | Q | A | -2.1988 | |
| 48 | K | A | -2.6044 | |
| 49 | A | A | -1.6653 | |
| 50 | P | A | -1.4079 | |
| 51 | G | A | -1.6807 | |
| 52 | D | A | -2.2920 | |
| 53 | S | A | -1.6208 | |
| 54 | V | A | -0.7147 | |
| 55 | L | A | 0.0000 | |
| 56 | T | A | -0.3014 | |
| 57 | L | A | 0.0000 | |
| 58 | S | A | -0.7192 | |
| 59 | Y | A | 0.0000 | |
| 60 | S | A | 0.0000 | |
| 61 | F | A | 0.0000 | |
| 62 | L | A | 0.0000 | |
| 63 | T | A | -1.5126 | |
| 64 | K | A | -2.1252 | |
| 65 | P | A | -2.0388 | |
| 66 | N | A | -2.0638 | |
| 67 | D | A | -2.4009 | |
| 68 | F | A | 0.0000 | |
| 69 | F | A | -1.1770 | |
| 70 | N | A | -1.9711 | |
| 71 | T | A | -0.9776 | |
| 72 | P | A | 0.0000 | |
| 73 | W | A | 0.0955 | |
| 74 | K | A | -1.2681 | |
| 75 | Y | A | -0.3488 | |
| 76 | V | A | -0.1687 | |
| 77 | S | A | -0.7439 | |
| 78 | D | A | -1.3836 | |
| 79 | I | A | 0.0000 | |
| 80 | Y | A | 1.0000 | |
| 81 | S | A | 0.0320 | |
| 82 | L | A | 0.0000 | |
| 83 | G | A | -0.9451 | |
| 84 | K | A | -1.7027 | |
| 85 | F | A | -1.0377 | |
| 86 | S | A | -0.6661 | |
| 87 | A | A | -0.5248 | |
| 88 | F | A | 0.0000 | |
| 89 | S | A | -0.3702 | |
| 90 | A | A | -0.4348 | |
| 91 | Q | A | -0.9403 | |
| 92 | Q | A | 0.0000 | |
| 93 | Q | A | -0.6667 | |
| 94 | A | A | -0.4494 | |
| 95 | Q | A | 0.0000 | |
| 96 | A | A | 0.0000 | |
| 97 | K | A | -1.0227 | |
| 98 | L | A | -0.6132 | |
| 99 | S | A | 0.0000 | |
| 100 | L | A | 0.0000 | |
| 101 | Q | A | -1.3435 | |
| 102 | S | A | 0.0000 | |
| 103 | W | A | 0.0000 | |
| 104 | S | A | -0.8037 | |
| 105 | D | A | -0.5371 | |
| 106 | V | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | N | A | -0.7523 | |
| 109 | I | A | 0.0000 | |
| 110 | H | A | -0.4323 | |
| 111 | F | A | -0.1185 | |
| 112 | V | A | 0.3084 | |
| 113 | D | A | -1.4779 | |
| 114 | A | A | -1.5713 | |
| 115 | G | A | -1.5822 | |
| 116 | Q | A | -2.1185 | |
| 117 | G | A | -2.2903 | |
| 118 | D | A | -3.2296 | |
| 119 | Q | A | -2.8644 | |
| 120 | G | A | -2.1674 | |
| 121 | D | A | -2.1688 | |
| 122 | L | A | 0.0000 | |
| 123 | T | A | -1.2654 | |
| 124 | F | A | 0.0000 | |
| 125 | G | A | 0.0000 | |
| 126 | N | A | 0.0000 | |
| 127 | F | A | 0.0000 | |
| 128 | S | A | 0.0000 | |
| 129 | S | A | -0.5643 | |
| 130 | S | A | -0.2767 | |
| 131 | V | A | 0.0359 | |
| 132 | G | A | -0.3708 | |
| 133 | G | A | -0.7305 | |
| 134 | A | A | -0.0930 | |
| 135 | A | A | 0.0298 | |
| 136 | F | A | 0.2496 | |
| 137 | A | A | 0.2505 | |
| 138 | F | A | 0.0870 | |
| 139 | L | A | -0.6270 | |
| 140 | P | A | 0.0000 | |
| 141 | D | A | -2.4996 | |
| 142 | V | A | -1.1239 | |
| 143 | P | A | -1.3365 | |
| 144 | D | A | -2.3715 | |
| 145 | A | A | -1.3653 | |
| 146 | L | A | 0.0000 | |
| 147 | K | A | -1.5498 | |
| 148 | G | A | 0.0000 | |
| 149 | Q | A | 0.0000 | |
| 150 | S | A | 0.0000 | |
| 151 | W | A | 0.0000 | |
| 152 | Y | A | 0.0000 | |
| 153 | L | A | 0.0000 | |
| 154 | I | A | 0.1634 | |
| 155 | N | A | -0.4737 | |
| 156 | S | A | -0.3690 | |
| 157 | S | A | -0.2392 | |
| 158 | Y | A | 0.2804 | |
| 159 | S | A | 0.1183 | |
| 160 | A | A | 0.2309 | |
| 161 | N | A | 0.0000 | |
| 162 | V | A | 0.6269 | |
| 163 | N | A | -0.6307 | |
| 164 | P | A | 0.0000 | |
| 165 | A | A | -0.9239 | |
| 166 | N | A | -1.6159 | |
| 167 | G | A | -0.9910 | |
| 168 | N | A | -0.6405 | |
| 169 | Y | A | 0.1307 | |
| 170 | G | A | 0.0000 | |
| 171 | R | A | 0.0000 | |
| 172 | Q | A | 0.0000 | |
| 173 | T | A | 0.0000 | |
| 174 | L | A | 0.0000 | |
| 175 | T | A | 0.0000 | |
| 176 | H | A | 0.0000 | |
| 177 | E | A | 0.0000 | |
| 178 | I | A | 0.0000 | |
| 179 | G | A | 0.0000 | |
| 180 | H | A | 0.0000 | |
| 181 | T | A | 0.0000 | |
| 182 | L | A | 0.0000 | |
| 183 | G | A | 0.0000 | |
| 184 | L | A | 0.0000 | |
| 185 | S | A | 0.0000 | |
| 186 | H | A | -0.9831 | |
| 187 | P | A | -0.6924 | |
| 188 | G | A | -1.4672 | |
| 189 | D | A | -2.3126 | |
| 190 | Y | A | -1.5759 | |
| 191 | N | A | -1.9577 | |
| 192 | A | A | -1.8493 | |
| 193 | G | A | -2.0591 | |
| 194 | E | A | -2.8133 | |
| 195 | G | A | -2.3903 | |
| 196 | D | A | -2.6155 | |
| 197 | P | A | -1.5395 | |
| 198 | T | A | -1.1905 | |
| 199 | Y | A | -0.8300 | |
| 200 | A | A | -1.0294 | |
| 201 | D | A | -2.1687 | |
| 202 | A | A | 0.0000 | |
| 203 | T | A | -0.8342 | |
| 204 | Y | A | 0.0000 | |
| 205 | A | A | 0.0000 | |
| 206 | E | A | -0.1706 | |
| 207 | D | A | 0.0000 | |
| 208 | T | A | 0.0000 | |
| 209 | R | A | -0.8000 | |
| 210 | A | A | 0.0000 | |
| 211 | Y | A | 0.0000 | |
| 212 | S | A | 0.0000 | |
| 213 | V | A | 0.0000 | |
| 214 | M | A | 0.0000 | |
| 215 | S | A | 0.0000 | |
| 216 | Y | A | -0.5373 | |
| 217 | W | A | 0.0000 | |
| 218 | E | A | -2.3229 | |
| 219 | E | A | 0.0000 | |
| 220 | Q | A | -2.8172 | |
| 221 | N | A | -2.3414 | |
| 222 | T | A | -1.4155 | |
| 223 | G | A | -1.5959 | |
| 224 | Q | A | 0.0000 | |
| 225 | D | A | -2.1334 | |
| 226 | F | A | 0.0000 | |
| 227 | K | A | -2.2420 | |
| 228 | G | A | -1.7052 | |
| 229 | A | A | 0.0000 | |
| 230 | Y | A | -0.4696 | |
| 231 | S | A | 0.0000 | |
| 232 | S | A | 0.0000 | |
| 233 | A | A | 0.0000 | |
| 234 | P | A | 0.0000 | |
| 235 | L | A | 0.0000 | |
| 236 | L | A | 0.0000 | |
| 237 | D | A | 0.0000 | |
| 238 | D | A | 0.0000 | |
| 239 | I | A | 0.0000 | |
| 240 | A | A | -1.0084 | |
| 241 | A | A | 0.0000 | |
| 242 | I | A | 0.0000 | |
| 243 | Q | A | -0.9590 | |
| 244 | K | A | -1.7571 | |
| 245 | L | A | -0.7311 | |
| 246 | Y | A | -0.3418 | |
| 247 | G | A | -0.5187 | |
| 248 | A | A | -0.2245 | |
| 249 | N | A | 0.1694 | |
| 250 | L | A | 1.2019 | |
| 251 | T | A | 0.3549 | |
| 252 | T | A | 0.0000 | |
| 253 | R | A | -0.7535 | |
| 254 | T | A | -0.8705 | |
| 255 | G | A | -1.7629 | |
| 256 | D | A | -2.7261 | |
| 257 | T | A | 0.0000 | |
| 258 | V | A | -0.8172 | |
| 259 | Y | A | 0.0000 | |
| 260 | G | A | 0.0000 | |
| 261 | F | A | -0.6498 | |
| 262 | N | A | -1.4737 | |
| 263 | S | A | -1.4296 | |
| 264 | N | A | -2.1258 | |
| 265 | T | A | -1.7658 | |
| 266 | E | A | -2.3398 | |
| 267 | R | A | -1.4769 | |
| 268 | D | A | -1.0397 | |
| 269 | F | A | -0.5870 | |
| 270 | Y | A | 0.0000 | |
| 271 | S | A | -0.8328 | |
| 272 | A | A | 0.0000 | |
| 273 | T | A | -0.7511 | |
| 274 | S | A | -0.5298 | |
| 275 | S | A | -0.7650 | |
| 276 | S | A | -0.8317 | |
| 277 | S | A | -1.1576 | |
| 278 | K | A | -2.0807 | |
| 279 | L | A | 0.0000 | |
| 280 | V | A | 0.0000 | |
| 281 | F | A | 0.0000 | |
| 282 | S | A | 0.0000 | |
| 283 | V | A | 0.0000 | |
| 284 | W | A | 0.0000 | |
| 285 | D | A | 0.0000 | |
| 286 | A | A | -0.0703 | |
| 287 | G | A | -0.9215 | |
| 288 | G | A | -1.9386 | |
| 289 | N | A | -2.1356 | |
| 290 | D | A | 0.0000 | |
| 291 | T | A | -0.4870 | |
| 292 | L | A | 0.0000 | |
| 293 | D | A | -0.3928 | |
| 294 | F | A | 0.0000 | |
| 295 | S | A | -0.4840 | |
| 296 | G | A | -0.5822 | |
| 297 | F | A | 0.0000 | |
| 298 | S | A | -1.0988 | |
| 299 | Q | A | -1.5663 | |
| 300 | N | A | -2.0209 | |
| 301 | Q | A | 0.0000 | |
| 302 | K | A | -1.2042 | |
| 303 | I | A | 0.0000 | |
| 304 | N | A | -0.5671 | |
| 305 | L | A | 0.0000 | |
| 306 | N | A | -1.7194 | |
| 307 | E | A | -1.9893 | |
| 308 | K | A | -1.6236 | |
| 309 | A | A | -0.6634 | |
| 310 | L | A | 0.0000 | |
| 311 | S | A | 0.0000 | |
| 312 | D | A | -1.1179 | |
| 313 | V | A | 0.0000 | |
| 314 | G | A | 0.0000 | |
| 315 | G | A | -1.4823 | |
| 316 | L | A | 0.0000 | |
| 317 | K | A | -1.7676 | |
| 318 | G | A | 0.0000 | |
| 319 | N | A | 0.0000 | |
| 320 | V | A | 0.0000 | |
| 321 | S | A | 0.0000 | |
| 322 | I | A | 0.0000 | |
| 323 | A | A | 0.0000 | |
| 324 | A | A | -0.9699 | |
| 325 | G | A | -0.8874 | |
| 326 | V | A | 0.0000 | |
| 327 | T | A | -0.6787 | |
| 328 | V | A | 0.0000 | |
| 329 | E | A | -0.6779 | |
| 330 | N | A | -0.2407 | |
| 331 | A | A | 0.0000 | |
| 332 | I | A | -0.0260 | |
| 333 | G | A | 0.0000 | |
| 334 | G | A | 0.0000 | |
| 335 | S | A | -0.9912 | |
| 336 | G | A | -1.2929 | |
| 337 | S | A | -1.3469 | |
| 338 | D | A | 0.0000 | |
| 339 | L | A | 0.0000 | |
| 340 | L | A | 0.0000 | |
| 341 | I | A | 0.0000 | |
| 342 | G | A | 0.0000 | |
| 343 | N | A | -0.8837 | |
| 344 | D | A | -1.1826 | |
| 345 | V | A | 0.1022 | |
| 346 | A | A | 0.1415 | |
| 347 | N | A | 0.0000 | |
| 348 | V | A | 0.2841 | |
| 349 | L | A | 0.0000 | |
| 350 | K | A | -0.6288 | |
| 351 | G | A | 0.0000 | |
| 352 | G | A | -0.7502 | |
| 353 | A | A | -0.7508 | |
| 354 | G | A | -1.2606 | |
| 355 | N | A | -1.7343 | |
| 356 | D | A | 0.0000 | |
| 357 | I | A | -0.3579 | |
| 358 | L | A | 0.0000 | |
| 359 | Y | A | 0.3256 | |
| 360 | G | A | 0.0000 | |
| 361 | G | A | 0.0000 | |
| 362 | L | A | 0.1956 | |
| 363 | G | A | -0.0579 | |
| 364 | A | A | 0.0642 | |
| 365 | D | A | 0.0000 | |
| 366 | Q | A | -0.3811 | |
| 367 | L | A | 0.0000 | |
| 368 | W | A | -0.3806 | |
| 369 | G | A | 0.0000 | |
| 370 | G | A | -0.5839 | |
| 371 | A | A | -0.4943 | |
| 372 | G | A | -0.9119 | |
| 373 | A | A | -0.9691 | |
| 374 | D | A | 0.0000 | |
| 375 | T | A | -0.4519 | |
| 376 | F | A | 0.0000 | |
| 377 | V | A | 0.0000 | |
| 378 | Y | A | 0.0000 | |
| 379 | G | A | -0.9602 | |
| 380 | D | A | -1.4520 | |
| 381 | I | A | -0.2037 | |
| 382 | A | A | 0.0541 | |
| 383 | E | A | 0.0000 | |
| 384 | S | A | 0.0000 | |
| 385 | S | A | 0.0127 | |
| 386 | A | A | -0.3500 | |
| 387 | A | A | -0.0566 | |
| 388 | A | A | -0.0876 | |
| 389 | P | A | -0.2650 | |
| 390 | D | A | 0.0000 | |
| 391 | T | A | -0.3847 | |
| 392 | L | A | 0.0000 | |
| 393 | R | A | -0.6984 | |
| 394 | D | A | -0.4233 | |
| 395 | F | A | 0.0000 | |
| 396 | V | A | 0.7840 | |
| 397 | S | A | -0.3816 | |
| 398 | G | A | -0.7025 | |
| 399 | Q | A | -1.1652 | |
| 400 | D | A | 0.0000 | |
| 401 | K | A | -0.5475 | |
| 402 | I | A | 0.0000 | |
| 403 | D | A | 0.0000 | |
| 404 | L | A | 0.0000 | |
| 405 | S | A | 0.4486 | |
| 406 | G | A | -0.6266 | |
| 407 | L | A | 0.0000 | |
| 408 | D | A | -1.6920 | |
| 409 | A | A | -0.5474 | |
| 410 | F | A | 0.6691 | |
| 411 | V | A | 0.3932 | |
| 412 | N | A | -1.0668 | |
| 413 | G | A | -0.6746 | |
| 414 | G | A | -0.1655 | |
| 415 | L | A | 0.8668 | |
| 416 | V | A | 1.8771 | |
| 417 | L | A | 1.0194 | |
| 418 | Q | A | -0.3756 | |
| 419 | Y | A | -0.0743 | |
| 420 | V | A | -0.3101 | |
| 421 | D | A | -1.2804 | |
| 422 | A | A | -0.4816 | |
| 423 | F | A | -0.7662 | |
| 424 | A | A | -1.1001 | |
| 425 | G | A | -1.8549 | |
| 426 | K | A | -2.2603 | |
| 427 | A | A | -0.9388 | |
| 428 | G | A | 0.0000 | |
| 429 | Q | A | -0.4639 | |
| 430 | A | A | 0.0000 | |
| 431 | I | A | 0.1818 | |
| 432 | L | A | -0.1068 | |
| 433 | S | A | -0.5451 | |
| 434 | Y | A | -1.0441 | |
| 435 | D | A | -1.8966 | |
| 436 | A | A | -1.4111 | |
| 437 | A | A | -0.9444 | |
| 438 | S | A | -1.2400 | |
| 439 | K | A | -2.1423 | |
| 440 | A | A | -1.4021 | |
| 441 | G | A | 0.0000 | |
| 442 | S | A | -0.3868 | |
| 443 | L | A | 0.0000 | |
| 444 | A | A | -0.1019 | |
| 445 | I | A | 0.0000 | |
| 446 | D | A | 0.0000 | |
| 447 | F | A | -0.6187 | |
| 448 | S | A | -1.2909 | |
| 449 | G | A | -1.9785 | |
| 450 | D | A | -2.5960 | |
| 451 | A | A | -1.7516 | |
| 452 | H | A | -1.6412 | |
| 453 | A | A | -0.9764 | |
| 454 | D | A | -0.9910 | |
| 455 | F | A | 0.0000 | |
| 456 | A | A | 0.0000 | |
| 457 | I | A | 0.0000 | |
| 458 | N | A | -0.6344 | |
| 459 | L | A | 0.0000 | |
| 460 | I | A | -0.3957 | |
| 461 | G | A | -0.8078 | |
| 462 | Q | A | -1.1307 | |
| 463 | A | A | 0.0000 | |
| 464 | T | A | -0.8242 | |
| 465 | Q | A | -1.0420 | |
| 466 | A | A | -0.3089 | |
| 467 | D | A | 0.0000 | |
| 468 | I | A | 0.0000 | |
| 469 | V | A | 1.3483 | |
| 470 | V | A | 2.2721 |
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 | -0.2703 | 2.2488 | View | CSV | PDB |
| 4.5 | -0.3291 | 2.0578 | View | CSV | PDB |
| 5.0 | -0.3961 | 2.0578 | View | CSV | PDB |
| 5.5 | -0.4621 | 2.0578 | View | CSV | PDB |
| 6.0 | -0.5188 | 2.0578 | View | CSV | PDB |
| 6.5 | -0.5615 | 2.0578 | View | CSV | PDB |
| 7.0 | -0.5919 | 2.0578 | View | CSV | PDB |
| 7.5 | -0.615 | 2.0578 | View | CSV | PDB |
| 8.0 | -0.6329 | 2.0578 | View | CSV | PDB |
| 8.5 | -0.6428 | 2.0578 | View | CSV | PDB |
| 9.0 | -0.6402 | 2.0578 | 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