| Chain sequence(s) |
A: MSRFRILPLSIFLCFVSLFFCTESFTHQNGVVPSFDPSYSSPLLVKKDQRTSVVATEFGNISAVQIGDGYHIQFITLEPNALLLPLLLHSDMVFFVHTGTGILNWIDEESERKLELRRGDVFRLRSGTVFYVHSNEKLRVYAIFNVGKCLNDPCLGAYSSVRDLLLGFDDRTLRSAFAVPEDILRKIRDATKPPLIVNALPRNRTQGLEEDKWQSRLVRLFVSVEDVTDHLAMKPIVDTNKKKSRTFNVFEEDPDFENNNGRSIVVDEKDLDALKGSRFGVFMVNLTKGSMIGPHWNPSACEISIVLEGEGMVRVVNQQSLSSCKNDRKSESFMVEEGDVFVVPKFHPMAQMSFENSSFVFMGFSTSAKTNHPQFLVGQSSVLKVLDRDVVAVSFNLSNETIKGLLKAQKESVIFECASCAEGELSKLMREIEERKRREEEEIERRRKEEEEARKREEAKRREEEEAKRREEEETERKKREEEEARKREEERKREEEEAKRREEERKKREEEAEQARKREEEREKEEEMAKKREEERQRKEREEVERKRREEQERKRREEEARKREEERKREEEMAKRREQERQRKEREEVERKIREEQERKREEEMAKRREQERQKKEREEMERKKREEEARKREEEMAKIREEERQRKEREDVERKRREEEAMRREEERKREEEAAKRAEEERRKKEEEEEKRRWPPQPKPPEEI
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage |
A: MSRFRILPLSIFLCFVSLFFCTESFTHQNGVVPS FDPSYSSPLLVKKDQRTSVVATEFGNISAVQIGDGYHIQFITLEPNALLLPLLLHSDMVFFVHTGTGILNWIDEESERKLELRRGDVFRLRSGTVFYVHSNEKLRVYAIFNVGKCLNDPCLGAYSSVRDLLLGFDDRTLRSAFAVPEDILRKIRDATKPPLIVNALPRNRTQGLEEDKWQSRLVRLFVSVEDVTDHLAMKPIVDTNKKKSRTFNVFEEDPDFENNNGRSIVVDEKDLDALKGSRFGVFMVNLTKGSMIGPHWNPSACEISIVLEGEGMVRVVNQQSLSSCKNDRKSESFMVEEGDVFVVPKFHPMAQMSFENSSFVFMGFSTSAKTNHPQFLVGQSSVLKVLDRDVVAVSFNLSNETIKGLLKAQKESVIFECASCAEGELSKLMREIEERKRREEEEIERRRKEEEEARKREEAKRREEEEAKRREEEETERKKREEEEARKREEERKREEEEAKRREEERKKREEEAEQARKREEEREKEEEMAKKREEERQRKEREEVERKRREEQERKRREEEARKREEERKREEEMAKRREQERQRKEREEVERKIREEQERKREEEMAKRREQERQKKEREEMERKKREEEARKREEEMAKIREEERQRKEREDVERKRREEEAMRREEERKREEEAAKRAEEERRKKEEEEEKRRWPPQPKPPEEI (Red indicates removed residues) |
| Dynamic mode | No |
| Automated mutations | No |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] PDB: Running AlphaCutter (00:00:03)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:35)
[INFO] FoldX: Starting FoldX energy minimization (00:00:35)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:17:20)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/67b7ea25b55b011/tmp/folded.pdb (00:17:20)
[INFO] Main: Simulation completed successfully. (00:22:28)
|
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 |
|---|---|---|---|---|
| 35 | F | A | 0.9483 | |
| 36 | D | A | -0.9536 | |
| 37 | P | A | -0.6012 | |
| 38 | S | A | -0.7581 | |
| 39 | Y | A | -0.2632 | |
| 40 | S | A | -0.4090 | |
| 41 | S | A | -0.4915 | |
| 42 | P | A | -0.1696 | |
| 43 | L | A | 0.1676 | |
| 44 | L | A | -0.0299 | |
| 45 | V | A | -1.0348 | |
| 46 | K | A | -2.3219 | |
| 47 | K | A | -3.4255 | |
| 48 | D | A | -3.3261 | |
| 49 | Q | A | -2.7729 | |
| 50 | R | A | -1.9934 | |
| 51 | T | A | -0.8541 | |
| 52 | S | A | -0.1516 | |
| 53 | V | A | 0.9709 | |
| 54 | V | A | 0.5349 | |
| 55 | A | A | -0.2389 | |
| 56 | T | A | -1.0522 | |
| 57 | E | A | -2.0417 | |
| 58 | F | A | -1.4315 | |
| 59 | G | A | 0.0000 | |
| 60 | N | A | -0.8387 | |
| 61 | I | A | 0.0000 | |
| 62 | S | A | -0.2468 | |
| 63 | A | A | 0.0000 | |
| 64 | V | A | 0.0000 | |
| 65 | Q | A | -1.3177 | |
| 66 | I | A | 0.0000 | |
| 67 | G | A | -1.2729 | |
| 68 | D | A | -2.3883 | |
| 69 | G | A | -1.4175 | |
| 70 | Y | A | -0.5359 | |
| 71 | H | A | -0.6913 | |
| 72 | I | A | 0.0000 | |
| 73 | Q | A | 0.0000 | |
| 74 | F | A | 0.0000 | |
| 75 | I | A | 0.0000 | |
| 76 | T | A | 0.0000 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.7310 | |
| 79 | P | A | -2.5744 | |
| 80 | N | A | -2.1090 | |
| 81 | A | A | 0.0000 | |
| 82 | L | A | 0.0228 | |
| 83 | L | A | 0.0000 | |
| 84 | L | A | 0.4836 | |
| 85 | P | A | 0.3715 | |
| 86 | L | A | 0.0000 | |
| 87 | L | A | 0.3547 | |
| 88 | L | A | 0.0000 | |
| 89 | H | A | -0.3394 | |
| 90 | S | A | -0.6655 | |
| 91 | D | A | -1.5729 | |
| 92 | M | A | 0.0000 | |
| 93 | V | A | 0.0000 | |
| 94 | F | A | 0.0000 | |
| 95 | F | A | 0.0000 | |
| 96 | V | A | 0.0000 | |
| 97 | H | A | -1.1134 | |
| 98 | T | A | -1.7053 | |
| 99 | G | A | -2.3260 | |
| 100 | T | A | -2.3931 | |
| 101 | G | A | 0.0000 | |
| 102 | I | A | -1.1323 | |
| 103 | L | A | 0.0000 | |
| 104 | N | A | 0.0000 | |
| 105 | W | A | 0.0000 | |
| 106 | I | A | -1.3587 | |
| 107 | D | A | -3.0184 | |
| 108 | E | A | -3.1702 | |
| 109 | E | A | -2.7849 | |
| 110 | S | A | -2.0225 | |
| 111 | E | A | -1.5424 | |
| 112 | R | A | -1.8034 | |
| 113 | K | A | -1.9208 | |
| 114 | L | A | 0.0000 | |
| 115 | E | A | -2.4602 | |
| 116 | L | A | 0.0000 | |
| 117 | R | A | -2.4017 | |
| 118 | R | A | -2.3631 | |
| 119 | G | A | 0.0000 | |
| 120 | D | A | 0.0000 | |
| 121 | V | A | 0.0000 | |
| 122 | F | A | 0.0000 | |
| 123 | R | A | -1.1417 | |
| 124 | L | A | 0.0000 | |
| 125 | R | A | -2.4166 | |
| 126 | S | A | -1.3799 | |
| 127 | G | A | -1.1213 | |
| 128 | T | A | -1.2343 | |
| 129 | V | A | 0.0000 | |
| 130 | F | A | 0.0000 | |
| 131 | Y | A | 0.2302 | |
| 132 | V | A | 0.0000 | |
| 133 | H | A | -0.8987 | |
| 134 | S | A | 0.0000 | |
| 135 | N | A | -2.6473 | |
| 136 | E | A | -3.3336 | |
| 137 | K | A | -2.9627 | |
| 138 | L | A | 0.0000 | |
| 139 | R | A | -1.6797 | |
| 140 | V | A | 0.0000 | |
| 141 | Y | A | 0.0000 | |
| 142 | A | A | 0.0000 | |
| 143 | I | A | 0.0000 | |
| 144 | F | A | 0.0000 | |
| 145 | N | A | -0.9703 | |
| 146 | V | A | -0.5632 | |
| 147 | G | A | -1.0175 | |
| 148 | K | A | -1.9637 | |
| 149 | C | A | -0.2729 | |
| 150 | L | A | 0.1309 | |
| 151 | N | A | -1.6481 | |
| 152 | D | A | -1.9421 | |
| 153 | P | A | -1.0084 | |
| 154 | C | A | -0.1523 | |
| 155 | L | A | 0.9559 | |
| 156 | G | A | 0.3560 | |
| 157 | A | A | 0.0000 | |
| 158 | Y | A | 0.3093 | |
| 159 | S | A | 0.0591 | |
| 160 | S | A | -0.1568 | |
| 161 | V | A | 0.0720 | |
| 162 | R | A | -0.9261 | |
| 163 | D | A | -1.4439 | |
| 164 | L | A | 0.2398 | |
| 165 | L | A | 0.5520 | |
| 166 | L | A | 0.0988 | |
| 167 | G | A | 0.1338 | |
| 168 | F | A | 0.9231 | |
| 169 | D | A | -0.9628 | |
| 170 | D | A | -2.5747 | |
| 171 | R | A | -2.7911 | |
| 172 | T | A | -1.1003 | |
| 173 | L | A | 0.0000 | |
| 174 | R | A | -1.7290 | |
| 175 | S | A | -0.8049 | |
| 176 | A | A | 0.0435 | |
| 177 | F | A | 1.3432 | |
| 178 | A | A | 0.3156 | |
| 179 | V | A | 0.0805 | |
| 180 | P | A | -1.1821 | |
| 181 | E | A | -3.1953 | |
| 182 | D | A | -2.6844 | |
| 183 | I | A | -1.5301 | |
| 184 | L | A | 0.0000 | |
| 185 | R | A | -3.9301 | |
| 186 | K | A | -3.3541 | |
| 187 | I | A | -1.9538 | |
| 188 | R | A | -2.7403 | |
| 189 | D | A | -3.1924 | |
| 190 | A | A | -2.0912 | |
| 191 | T | A | -1.5981 | |
| 192 | K | A | -2.3351 | |
| 193 | P | A | -0.9354 | |
| 194 | P | A | -0.6564 | |
| 195 | L | A | 0.0799 | |
| 196 | I | A | 0.0000 | |
| 197 | V | A | -0.3455 | |
| 198 | N | A | -1.0038 | |
| 199 | A | A | -0.2288 | |
| 200 | L | A | 0.5188 | |
| 201 | P | A | -1.1220 | |
| 202 | R | A | -2.7972 | |
| 203 | N | A | -3.0717 | |
| 204 | R | A | -3.3574 | |
| 205 | T | A | -2.0291 | |
| 206 | Q | A | -2.5916 | |
| 207 | G | A | -2.0202 | |
| 208 | L | A | -0.9005 | |
| 209 | E | A | -2.7961 | |
| 210 | E | A | -2.9243 | |
| 211 | D | A | -2.9436 | |
| 212 | K | A | -2.9417 | |
| 213 | W | A | -1.6675 | |
| 214 | Q | A | -2.0037 | |
| 215 | S | A | -1.7841 | |
| 216 | R | A | -2.0632 | |
| 217 | L | A | -0.2943 | |
| 218 | V | A | -0.4957 | |
| 219 | R | A | -0.9952 | |
| 220 | L | A | 1.0989 | |
| 221 | F | A | 0.9723 | |
| 222 | V | A | -0.2189 | |
| 223 | S | A | -0.0285 | |
| 224 | V | A | 0.2967 | |
| 225 | E | A | -1.6463 | |
| 226 | D | A | -1.6176 | |
| 227 | V | A | 0.2734 | |
| 228 | T | A | -0.7242 | |
| 229 | D | A | -1.6019 | |
| 230 | H | A | -0.5731 | |
| 231 | L | A | 0.7676 | |
| 232 | A | A | 0.2004 | |
| 233 | M | A | 0.2504 | |
| 234 | K | A | -0.2892 | |
| 235 | P | A | 0.0589 | |
| 236 | I | A | 1.8800 | |
| 237 | V | A | 1.8476 | |
| 238 | D | A | -0.6980 | |
| 239 | T | A | -0.8567 | |
| 240 | N | A | -2.8857 | |
| 241 | K | A | -3.7596 | |
| 242 | K | A | -4.0189 | |
| 243 | K | A | -3.8352 | |
| 244 | S | A | -2.3909 | |
| 245 | R | A | -1.7631 | |
| 246 | T | A | 0.0000 | |
| 247 | F | A | -1.0199 | |
| 248 | N | A | -1.4711 | |
| 249 | V | A | 0.0000 | |
| 250 | F | A | -1.0707 | |
| 251 | E | A | -2.4971 | |
| 252 | E | A | -3.0840 | |
| 253 | D | A | -3.4769 | |
| 254 | P | A | -2.7556 | |
| 255 | D | A | -2.7057 | |
| 256 | F | A | -2.0439 | |
| 257 | E | A | -3.2885 | |
| 258 | N | A | -2.2023 | |
| 259 | N | A | -2.3362 | |
| 260 | N | A | -2.3297 | |
| 261 | G | A | 0.0000 | |
| 262 | R | A | -2.8090 | |
| 263 | S | A | -1.6115 | |
| 264 | I | A | 0.0000 | |
| 265 | V | A | 0.0841 | |
| 266 | V | A | 0.0000 | |
| 267 | D | A | 0.0000 | |
| 268 | E | A | -3.2045 | |
| 269 | K | A | -3.2292 | |
| 270 | D | A | -2.5632 | |
| 271 | L | A | 0.0000 | |
| 272 | D | A | -2.9019 | |
| 273 | A | A | -1.9628 | |
| 274 | L | A | 0.0000 | |
| 275 | K | A | -3.3510 | |
| 276 | G | A | -2.3676 | |
| 277 | S | A | 0.0000 | |
| 278 | R | A | -2.5855 | |
| 279 | F | A | 0.0000 | |
| 280 | G | A | 0.0000 | |
| 281 | V | A | 0.0000 | |
| 282 | F | A | 0.0000 | |
| 283 | M | A | 0.0000 | |
| 284 | V | A | 0.0000 | |
| 285 | N | A | -1.3971 | |
| 286 | L | A | 0.0000 | |
| 287 | T | A | -2.0135 | |
| 288 | K | A | -2.9066 | |
| 289 | G | A | -2.1809 | |
| 290 | S | A | 0.0000 | |
| 291 | M | A | 0.0000 | |
| 292 | I | A | 0.0000 | |
| 293 | G | A | 0.0000 | |
| 294 | P | A | 0.2279 | |
| 295 | H | A | 0.0000 | |
| 296 | W | A | 0.2995 | |
| 297 | N | A | 0.0000 | |
| 298 | P | A | -0.1932 | |
| 299 | S | A | -0.6117 | |
| 300 | A | A | 0.0000 | |
| 301 | C | A | -0.0461 | |
| 302 | E | A | 0.0000 | |
| 303 | I | A | 0.0000 | |
| 304 | S | A | 0.0000 | |
| 305 | I | A | 0.0000 | |
| 306 | V | A | 0.0000 | |
| 307 | L | A | -1.4051 | |
| 308 | E | A | -2.3754 | |
| 309 | G | A | -2.2201 | |
| 310 | E | A | -2.1347 | |
| 311 | G | A | 0.0000 | |
| 312 | M | A | 0.0000 | |
| 313 | V | A | 0.0000 | |
| 314 | R | A | -0.6347 | |
| 315 | V | A | 0.0000 | |
| 316 | V | A | -0.5681 | |
| 317 | N | A | 0.0000 | |
| 318 | Q | A | -0.8450 | |
| 319 | Q | A | -1.7889 | |
| 320 | S | A | -1.9755 | |
| 321 | L | A | 0.4050 | |
| 322 | S | A | -0.2718 | |
| 323 | S | A | -0.6161 | |
| 324 | C | A | -1.4424 | |
| 325 | K | A | -2.9121 | |
| 326 | N | A | -3.4174 | |
| 327 | D | A | -4.0786 | |
| 328 | R | A | -4.1271 | |
| 329 | K | A | -3.3482 | |
| 330 | S | A | -2.0674 | |
| 331 | E | A | -1.1250 | |
| 332 | S | A | -0.6409 | |
| 333 | F | A | 0.0000 | |
| 334 | M | A | -0.1768 | |
| 335 | V | A | 0.0000 | |
| 336 | E | A | -2.5804 | |
| 337 | E | A | -2.9104 | |
| 338 | G | A | -2.1530 | |
| 339 | D | A | 0.0000 | |
| 340 | V | A | 0.0000 | |
| 341 | F | A | 0.0000 | |
| 342 | V | A | 0.0000 | |
| 343 | V | A | 0.0000 | |
| 344 | P | A | 0.0000 | |
| 345 | K | A | 0.0776 | |
| 346 | F | A | 0.8825 | |
| 347 | H | A | 0.0000 | |
| 348 | P | A | 0.1951 | |
| 349 | M | A | 0.0000 | |
| 350 | A | A | 0.0000 | |
| 351 | Q | A | 0.0000 | |
| 352 | M | A | 0.0000 | |
| 353 | S | A | 0.0000 | |
| 354 | F | A | 0.0000 | |
| 355 | E | A | -2.4818 | |
| 356 | N | A | -2.4320 | |
| 357 | S | A | -1.9809 | |
| 358 | S | A | -1.8021 | |
| 359 | F | A | 0.0000 | |
| 360 | V | A | 0.0000 | |
| 361 | F | A | 0.0000 | |
| 362 | M | A | 0.0000 | |
| 363 | G | A | 0.0000 | |
| 364 | F | A | 0.0000 | |
| 365 | S | A | 0.0000 | |
| 366 | T | A | -0.8609 | |
| 367 | S | A | -1.3953 | |
| 368 | A | A | 0.0000 | |
| 369 | K | A | -2.8693 | |
| 370 | T | A | -1.5738 | |
| 371 | N | A | -1.1125 | |
| 372 | H | A | -1.4032 | |
| 373 | P | A | -0.5106 | |
| 374 | Q | A | -0.1284 | |
| 375 | F | A | 0.0000 | |
| 376 | L | A | 0.7060 | |
| 377 | V | A | 0.3272 | |
| 378 | G | A | 0.0000 | |
| 379 | Q | A | -1.7351 | |
| 380 | S | A | -0.4865 | |
| 381 | S | A | 0.0000 | |
| 382 | V | A | 1.2011 | |
| 383 | L | A | 1.0443 | |
| 384 | K | A | 0.2579 | |
| 385 | V | A | 1.6732 | |
| 386 | L | A | 0.9731 | |
| 387 | D | A | -1.1870 | |
| 388 | R | A | -1.4739 | |
| 389 | D | A | -1.1252 | |
| 390 | V | A | 0.6787 | |
| 391 | V | A | 0.0000 | |
| 392 | A | A | 0.0000 | |
| 393 | V | A | 1.7083 | |
| 394 | S | A | 1.1226 | |
| 395 | F | A | 1.4235 | |
| 396 | N | A | 0.4858 | |
| 397 | L | A | 0.5061 | |
| 398 | S | A | -0.7997 | |
| 399 | N | A | -1.6223 | |
| 400 | E | A | -2.2908 | |
| 401 | T | A | -1.1668 | |
| 402 | I | A | 0.0000 | |
| 403 | K | A | -2.2030 | |
| 404 | G | A | -1.4199 | |
| 405 | L | A | 0.1026 | |
| 406 | L | A | 0.0000 | |
| 407 | K | A | -2.3522 | |
| 408 | A | A | -1.2577 | |
| 409 | Q | A | -1.6482 | |
| 410 | K | A | -2.7629 | |
| 411 | E | A | -2.2255 | |
| 412 | S | A | -1.2101 | |
| 413 | V | A | -0.4150 | |
| 414 | I | A | 0.0000 | |
| 415 | F | A | 0.0000 | |
| 416 | E | A | -2.3179 | |
| 417 | C | A | -1.1478 | |
| 418 | A | A | -1.0642 | |
| 419 | S | A | -0.8954 | |
| 420 | C | A | -0.4599 | |
| 421 | A | A | 0.0000 | |
| 422 | E | A | -1.0144 | |
| 423 | G | A | -0.7218 | |
| 424 | E | A | 0.0000 | |
| 425 | L | A | -0.7396 | |
| 426 | S | A | -1.3675 | |
| 427 | K | A | -2.6053 | |
| 428 | L | A | -1.6704 | |
| 429 | M | A | -1.7689 | |
| 430 | R | A | -3.8780 | |
| 431 | E | A | -4.1762 | |
| 432 | I | A | -2.9486 | |
| 433 | E | A | -4.5004 | |
| 434 | E | A | -5.5795 | |
| 435 | R | A | -6.1263 | |
| 436 | K | A | -6.4288 | |
| 437 | R | A | -6.5948 | |
| 438 | R | A | -6.8379 | |
| 439 | E | A | -6.7995 | |
| 440 | E | A | -6.6829 | |
| 441 | E | A | -6.8153 | |
| 442 | E | A | -6.3818 | |
| 443 | I | A | -4.7498 | |
| 444 | E | A | -6.0743 | |
| 445 | R | A | -6.4387 | |
| 446 | R | A | -5.8678 | |
| 447 | R | A | -5.4819 | |
| 448 | K | A | -5.1353 | |
| 449 | E | A | -4.5634 |
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 | -1.0915 | 4.2466 | View | CSV | PDB |
| 4.5 | -1.1983 | 4.0512 | View | CSV | PDB |
| 5.0 | -1.3318 | 3.8474 | View | CSV | PDB |
| 5.5 | -1.469 | 3.6441 | View | CSV | PDB |
| 6.0 | -1.5849 | 3.4462 | View | CSV | PDB |
| 6.5 | -1.6589 | 3.2553 | View | CSV | PDB |
| 7.0 | -1.6861 | 3.2104 | View | CSV | PDB |
| 7.5 | -1.6792 | 3.3568 | View | CSV | PDB |
| 8.0 | -1.6529 | 3.5155 | View | CSV | PDB |
| 8.5 | -1.6126 | 3.6879 | View | CSV | PDB |
| 9.0 | -1.5577 | 3.8702 | 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