| Chain sequence(s) |
A: MARAVGPERRLLAVYTGGTIGMRSELGVLVPGTGLAAILRTLPMFHDEEHARARGLSEDTLVLPPASRNQRILYTVLECQPLFDSSDMTIAEWVCLAQTIKRHYEQYHGFVVIHGTDTMAFAASMLSFMLENLQKTVILTGAQVPIHALWSDGRENLLGALLMAGQYVIPEVCLFFQNQLFRGNRATKVDARRFAAFCSPNLLPLATVGADITINRELVRKVDGKAGLVVHSSMEQDVGLLRLYPGIPAALVRAFLQPPLKGVVMETFGSGNGPTKPDLLQELRVATERGLVIVNCTHCLQGAVTTDYAAGMAMAGAGVISGFDMTSEAALAKLSYVLGQPGLSLDVRKELLTKDLRGEMTPPSVEERRPSLQGNTLGGGVSWLLSLSGSQEADA
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. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:05:17)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/a9bfe8d2619817e/tmp/folded.pdb (00:05:17)
[INFO] Main: Simulation completed successfully. (00:11:36)
|
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 | -0.7116 | |
| 2 | A | A | -0.3725 | |
| 3 | R | A | -1.1447 | |
| 4 | A | A | 0.0000 | |
| 5 | V | A | 0.7907 | |
| 6 | G | A | -0.5044 | |
| 7 | P | A | -1.5794 | |
| 8 | E | A | -2.3325 | |
| 9 | R | A | 0.0000 | |
| 10 | R | A | -1.8773 | |
| 11 | L | A | 0.0000 | |
| 12 | L | A | 0.0000 | |
| 13 | A | A | 0.0000 | |
| 14 | V | A | 0.0000 | |
| 15 | Y | A | 0.0000 | |
| 16 | T | A | 0.0000 | |
| 17 | G | A | 0.0000 | |
| 18 | G | A | 0.0000 | |
| 19 | T | A | -0.4129 | |
| 20 | I | A | 0.0000 | |
| 21 | G | A | 0.0000 | |
| 22 | M | A | 0.0000 | |
| 23 | R | A | -1.4439 | |
| 24 | S | A | -0.5472 | |
| 25 | E | A | -0.6105 | |
| 26 | L | A | 1.0565 | |
| 27 | G | A | 0.5875 | |
| 28 | V | A | 1.6415 | |
| 29 | L | A | 0.9116 | |
| 30 | V | A | 0.1705 | |
| 31 | P | A | -0.6012 | |
| 32 | G | A | 0.0000 | |
| 33 | T | A | -0.5095 | |
| 34 | G | A | -0.3522 | |
| 35 | L | A | 0.0000 | |
| 36 | A | A | 0.0000 | |
| 37 | A | A | -0.5702 | |
| 38 | I | A | 0.0648 | |
| 39 | L | A | 0.0000 | |
| 40 | R | A | -0.8006 | |
| 41 | T | A | -0.1933 | |
| 42 | L | A | -0.0390 | |
| 43 | P | A | -0.2607 | |
| 44 | M | A | -0.1056 | |
| 45 | F | A | 0.0000 | |
| 46 | H | A | 0.0000 | |
| 47 | D | A | -1.5239 | |
| 48 | E | A | -2.3437 | |
| 49 | E | A | -3.1127 | |
| 50 | H | A | -2.4151 | |
| 51 | A | A | 0.0000 | |
| 52 | R | A | -3.3679 | |
| 53 | A | A | -2.4245 | |
| 54 | R | A | -2.9190 | |
| 55 | G | A | -2.1102 | |
| 56 | L | A | -1.7377 | |
| 57 | S | A | -1.9710 | |
| 58 | E | A | -2.6933 | |
| 59 | D | A | -2.4942 | |
| 60 | T | A | -1.4734 | |
| 61 | L | A | 0.0000 | |
| 62 | V | A | 0.0000 | |
| 63 | L | A | 0.0000 | |
| 64 | P | A | -0.6462 | |
| 65 | P | A | -1.0950 | |
| 66 | A | A | -0.8149 | |
| 67 | S | A | -1.6486 | |
| 68 | R | A | -2.6746 | |
| 69 | N | A | -2.5143 | |
| 70 | Q | A | 0.0000 | |
| 71 | R | A | -1.8545 | |
| 72 | I | A | 0.0000 | |
| 73 | L | A | 0.0000 | |
| 74 | Y | A | 0.0000 | |
| 75 | T | A | -0.8686 | |
| 76 | V | A | 0.0000 | |
| 77 | L | A | -0.1942 | |
| 78 | E | A | -0.6517 | |
| 79 | C | A | -0.4983 | |
| 80 | Q | A | -1.2305 | |
| 81 | P | A | -0.9908 | |
| 82 | L | A | -0.5131 | |
| 83 | F | A | -0.9985 | |
| 84 | D | A | -1.9999 | |
| 85 | S | A | 0.0000 | |
| 86 | S | A | -1.9398 | |
| 87 | D | A | -2.4770 | |
| 88 | M | A | 0.0000 | |
| 89 | T | A | -0.5806 | |
| 90 | I | A | 0.0137 | |
| 91 | A | A | 0.0366 | |
| 92 | E | A | -0.1950 | |
| 93 | W | A | 0.0000 | |
| 94 | V | A | 0.3651 | |
| 95 | C | A | 0.4870 | |
| 96 | L | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | Q | A | -0.9842 | |
| 99 | T | A | 0.0000 | |
| 100 | I | A | 0.0000 | |
| 101 | K | A | -2.0928 | |
| 102 | R | A | -2.9617 | |
| 103 | H | A | -2.3964 | |
| 104 | Y | A | 0.0000 | |
| 105 | E | A | -2.9679 | |
| 106 | Q | A | -2.7427 | |
| 107 | Y | A | 0.0000 | |
| 108 | H | A | -1.5296 | |
| 109 | G | A | 0.0000 | |
| 110 | F | A | 0.0000 | |
| 111 | V | A | 0.0000 | |
| 112 | V | A | 0.0000 | |
| 113 | I | A | 0.0000 | |
| 114 | H | A | 0.0000 | |
| 115 | G | A | 0.0000 | |
| 116 | T | A | 0.0000 | |
| 117 | D | A | -2.2543 | |
| 118 | T | A | -1.2818 | |
| 119 | M | A | 0.0000 | |
| 120 | A | A | 0.0000 | |
| 121 | F | A | 0.0876 | |
| 122 | A | A | 0.0000 | |
| 123 | A | A | 0.0000 | |
| 124 | S | A | 0.0000 | |
| 125 | M | A | 0.0000 | |
| 126 | L | A | 0.0000 | |
| 127 | S | A | 0.0000 | |
| 128 | F | A | 0.0000 | |
| 129 | M | A | 0.0000 | |
| 130 | L | A | 0.0000 | |
| 131 | E | A | -0.4450 | |
| 132 | N | A | -1.2893 | |
| 133 | L | A | 0.0000 | |
| 134 | Q | A | -1.7217 | |
| 135 | K | A | -0.5271 | |
| 136 | T | A | 0.0000 | |
| 137 | V | A | 0.0000 | |
| 138 | I | A | 0.0000 | |
| 139 | L | A | 0.0000 | |
| 140 | T | A | 0.0000 | |
| 141 | G | A | 0.0000 | |
| 142 | A | A | 0.0000 | |
| 143 | Q | A | -0.6507 | |
| 144 | V | A | 0.4276 | |
| 145 | P | A | 0.0000 | |
| 146 | I | A | 0.0000 | |
| 147 | H | A | -0.1521 | |
| 148 | A | A | 0.7304 | |
| 149 | L | A | 2.0318 | |
| 150 | W | A | 1.8936 | |
| 151 | S | A | 0.0000 | |
| 152 | D | A | 0.0000 | |
| 153 | G | A | 0.0000 | |
| 154 | R | A | -0.9281 | |
| 155 | E | A | -2.1217 | |
| 156 | N | A | 0.0000 | |
| 157 | L | A | 0.0000 | |
| 158 | L | A | -0.2911 | |
| 159 | G | A | -0.6064 | |
| 160 | A | A | 0.0000 | |
| 161 | L | A | 0.0000 | |
| 162 | L | A | 0.3410 | |
| 163 | M | A | 0.0000 | |
| 164 | A | A | 0.0000 | |
| 165 | G | A | 0.0000 | |
| 166 | Q | A | -0.2144 | |
| 167 | Y | A | -0.0410 | |
| 168 | V | A | 0.1318 | |
| 169 | I | A | 0.0000 | |
| 170 | P | A | 0.0000 | |
| 171 | E | A | 0.0000 | |
| 172 | V | A | 0.0000 | |
| 173 | C | A | 0.0000 | |
| 174 | L | A | 0.0000 | |
| 175 | F | A | 0.0000 | |
| 176 | F | A | 0.0000 | |
| 177 | Q | A | -1.4084 | |
| 178 | N | A | -1.4490 | |
| 179 | Q | A | -0.6562 | |
| 180 | L | A | 0.0000 | |
| 181 | F | A | 0.0000 | |
| 182 | R | A | 0.0000 | |
| 183 | G | A | 0.0000 | |
| 184 | N | A | 0.0000 | |
| 185 | R | A | 0.0000 | |
| 186 | A | A | 0.0000 | |
| 187 | T | A | 0.0953 | |
| 188 | K | A | -0.2397 | |
| 189 | V | A | 0.4996 | |
| 190 | D | A | -0.8009 | |
| 191 | A | A | -1.4510 | |
| 192 | R | A | -2.4342 | |
| 193 | R | A | -2.2501 | |
| 194 | F | A | -0.5219 | |
| 195 | A | A | -0.6721 | |
| 196 | A | A | 0.0000 | |
| 197 | F | A | 0.0000 | |
| 198 | C | A | 0.4419 | |
| 199 | S | A | 0.3914 | |
| 200 | P | A | 0.2071 | |
| 201 | N | A | -0.1691 | |
| 202 | L | A | 0.6455 | |
| 203 | L | A | 1.5071 | |
| 204 | P | A | 0.6722 | |
| 205 | L | A | 0.0000 | |
| 206 | A | A | 0.0000 | |
| 207 | T | A | -0.3406 | |
| 208 | V | A | -0.5615 | |
| 209 | G | A | -0.9625 | |
| 210 | A | A | -0.8516 | |
| 211 | D | A | -1.5686 | |
| 212 | I | A | -0.3901 | |
| 213 | T | A | -0.4750 | |
| 214 | I | A | -0.6188 | |
| 215 | N | A | -1.1852 | |
| 216 | R | A | -2.7920 | |
| 217 | E | A | -2.8306 | |
| 218 | L | A | -1.2714 | |
| 219 | V | A | -1.4122 | |
| 220 | R | A | -2.0162 | |
| 221 | K | A | -2.5994 | |
| 222 | V | A | -1.9908 | |
| 223 | D | A | -3.0046 | |
| 224 | G | A | -2.5074 | |
| 225 | K | A | -2.6283 | |
| 226 | A | A | -1.6286 | |
| 227 | G | A | -1.1051 | |
| 228 | L | A | -0.3575 | |
| 229 | V | A | 0.6001 | |
| 230 | V | A | 0.1670 | |
| 231 | H | A | -0.0055 | |
| 232 | S | A | -0.0199 | |
| 233 | S | A | -0.5140 | |
| 234 | M | A | 0.0000 | |
| 235 | E | A | -1.1500 | |
| 236 | Q | A | -1.6652 | |
| 237 | D | A | -1.4889 | |
| 238 | V | A | -0.6189 | |
| 239 | G | A | 0.0412 | |
| 240 | L | A | 0.2084 | |
| 241 | L | A | 0.0000 | |
| 242 | R | A | -1.4862 | |
| 243 | L | A | 0.0000 | |
| 244 | Y | A | 0.3230 | |
| 245 | P | A | 0.0305 | |
| 246 | G | A | -0.4254 | |
| 247 | I | A | 0.0000 | |
| 248 | P | A | -0.4552 | |
| 249 | A | A | -0.9976 | |
| 250 | A | A | -0.4218 | |
| 251 | L | A | 0.3149 | |
| 252 | V | A | 0.0000 | |
| 253 | R | A | -1.6905 | |
| 254 | A | A | -0.4279 | |
| 255 | F | A | 0.2237 | |
| 256 | L | A | 0.0000 | |
| 257 | Q | A | -1.2127 | |
| 258 | P | A | -0.9446 | |
| 259 | P | A | -0.9362 | |
| 260 | L | A | -0.8592 | |
| 261 | K | A | -1.4934 | |
| 262 | G | A | 0.0000 | |
| 263 | V | A | 0.0000 | |
| 264 | V | A | 0.0000 | |
| 265 | M | A | 0.0000 | |
| 266 | E | A | 0.0000 | |
| 267 | T | A | 0.0000 | |
| 268 | F | A | 0.1052 | |
| 269 | G | A | -0.1716 | |
| 270 | S | A | -0.3842 | |
| 271 | G | A | 0.0000 | |
| 272 | N | A | -0.0727 | |
| 273 | G | A | 0.0000 | |
| 274 | P | A | -0.3634 | |
| 275 | T | A | -0.4799 | |
| 276 | K | A | -1.2806 | |
| 277 | P | A | -1.5583 | |
| 278 | D | A | -2.5067 | |
| 279 | L | A | 0.0000 | |
| 280 | L | A | -1.4850 | |
| 281 | Q | A | -2.3897 | |
| 282 | E | A | -1.9744 | |
| 283 | L | A | 0.0000 | |
| 284 | R | A | -2.4755 | |
| 285 | V | A | -1.6242 | |
| 286 | A | A | 0.0000 | |
| 287 | T | A | -2.0056 | |
| 288 | E | A | -2.7884 | |
| 289 | R | A | -2.6000 | |
| 290 | G | A | -1.7517 | |
| 291 | L | A | 0.0000 | |
| 292 | V | A | 0.0000 | |
| 293 | I | A | 0.0000 | |
| 294 | V | A | 0.0000 | |
| 295 | N | A | 0.0000 | |
| 296 | C | A | 0.0000 | |
| 297 | T | A | 0.0000 | |
| 298 | H | A | -0.2090 | |
| 299 | C | A | 0.4691 | |
| 300 | L | A | 0.9530 | |
| 301 | Q | A | -0.7124 | |
| 302 | G | A | -0.6219 | |
| 303 | A | A | -0.2196 | |
| 304 | V | A | 0.0000 | |
| 305 | T | A | -0.5630 | |
| 306 | T | A | -0.5469 | |
| 307 | D | A | -1.4693 | |
| 308 | Y | A | 0.3976 | |
| 309 | A | A | 0.4759 | |
| 310 | A | A | 0.2847 | |
| 311 | G | A | 0.0000 | |
| 312 | M | A | 0.7196 | |
| 313 | A | A | 0.3914 | |
| 314 | M | A | 0.0000 | |
| 315 | A | A | -0.0507 | |
| 316 | G | A | -0.3684 | |
| 317 | A | A | 0.0000 | |
| 318 | G | A | -0.8947 | |
| 319 | V | A | 0.0000 | |
| 320 | I | A | 0.0000 | |
| 321 | S | A | 0.0421 | |
| 322 | G | A | 0.0000 | |
| 323 | F | A | 0.2160 | |
| 324 | D | A | 0.0000 | |
| 325 | M | A | 0.0000 | |
| 326 | T | A | 0.0490 | |
| 327 | S | A | 0.1679 | |
| 328 | E | A | 0.0580 | |
| 329 | A | A | 0.0000 | |
| 330 | A | A | 0.0000 | |
| 331 | L | A | 0.3137 | |
| 332 | A | A | 0.0000 | |
| 333 | K | A | 0.0000 | |
| 334 | L | A | 0.0000 | |
| 335 | S | A | 0.0000 | |
| 336 | Y | A | 0.0000 | |
| 337 | V | A | 0.0000 | |
| 338 | L | A | 0.0000 | |
| 339 | G | A | -0.6662 | |
| 340 | Q | A | -0.4533 | |
| 341 | P | A | -0.4816 | |
| 342 | G | A | -0.2819 | |
| 343 | L | A | 0.0685 | |
| 344 | S | A | -0.3537 | |
| 345 | L | A | -0.4175 | |
| 346 | D | A | -1.6791 | |
| 347 | V | A | -0.4784 | |
| 348 | R | A | -0.7348 | |
| 349 | K | A | -1.5782 | |
| 350 | E | A | -2.2462 | |
| 351 | L | A | -1.1834 | |
| 352 | L | A | 0.0000 | |
| 353 | T | A | -1.3633 | |
| 354 | K | A | -2.0163 | |
| 355 | D | A | -1.5881 | |
| 356 | L | A | -0.6454 | |
| 357 | R | A | -0.7902 | |
| 358 | G | A | -0.5982 | |
| 359 | E | A | 0.0000 | |
| 360 | M | A | 0.0000 | |
| 361 | T | A | -0.5232 | |
| 362 | P | A | -0.7811 | |
| 363 | P | A | -0.9824 | |
| 364 | S | A | -1.2079 | |
| 365 | V | A | -0.6445 | |
| 366 | E | A | -2.9935 | |
| 367 | E | A | -3.7906 | |
| 368 | R | A | -3.9495 | |
| 369 | R | A | -3.9505 | |
| 370 | P | A | -2.5763 | |
| 371 | S | A | -1.7447 | |
| 372 | L | A | 0.1504 | |
| 373 | Q | A | -1.4323 | |
| 374 | G | A | -1.4414 | |
| 375 | N | A | -1.1113 | |
| 376 | T | A | -0.0754 | |
| 377 | L | A | 1.2706 | |
| 378 | G | A | 0.0000 | |
| 379 | G | A | 0.5103 | |
| 380 | G | A | 1.3304 | |
| 381 | V | A | 2.4462 | |
| 382 | S | A | 1.8714 | |
| 383 | W | A | 2.6035 | |
| 384 | L | A | 2.9148 | |
| 385 | L | A | 2.6260 | |
| 386 | S | A | 1.4453 | |
| 387 | L | A | 1.3059 | |
| 388 | S | A | 0.1644 | |
| 389 | G | A | -0.7118 | |
| 390 | S | A | -1.4707 | |
| 391 | Q | A | -2.6425 | |
| 392 | E | A | -3.0086 | |
| 393 | A | A | -2.1811 | |
| 394 | D | A | -2.6311 | |
| 395 | A | A | -1.5092 |
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 | -0.2537 | 4.5147 | View | CSV | PDB |
| 4.5 | -0.3067 | 4.5147 | View | CSV | PDB |
| 5.0 | -0.3743 | 4.5147 | View | CSV | PDB |
| 5.5 | -0.4476 | 4.5147 | View | CSV | PDB |
| 6.0 | -0.5178 | 4.5147 | View | CSV | PDB |
| 6.5 | -0.577 | 4.5147 | View | CSV | PDB |
| 7.0 | -0.6206 | 4.5147 | View | CSV | PDB |
| 7.5 | -0.6508 | 4.5147 | View | CSV | PDB |
| 8.0 | -0.6719 | 4.5147 | View | CSV | PDB |
| 8.5 | -0.6855 | 4.5147 | View | CSV | PDB |
| 9.0 | -0.6911 | 4.5147 | 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