| Chain sequence(s) |
A: MARAVGPERRLLAVYTGGTIGMRSELGVLVPGTGLAAILRTLPMFHDEEHARARGLSEDTLVLPPASRNQRILYTVLECQPLFDSSDMTIAEWVCLAQTIKRHYEQYHGFVVIHGTDTMAFAASMLSFMLENLQKTVILTGAQVPIHALWSDGRENLLGALLMAGQYVIPEVCLFFQNQLFRGNRATKVDARRFAAFCSPNLLPLATVGADITINRELVRKVDGKAGLVVHSSMEQDVGLLRLYPGIPAALVRAFLQPPLKGVVMETFGSGNGPTKPDLLQELRVATERGLVIVNCTHCLQGAVTTDYAAGMAMAGAGVISGFDMTSEAALAKLSYVLGQPGLSLDVRKELLTKDLRGEMTPPSVEERRPSLQGNTLGGGVSWLLSLSGSQEADALRNALVPS
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] (00:00:01)
[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 A 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. (00:00:02)
[INFO] FoldX: Starting FoldX energy minimization (00:00:02)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:10:18)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/f9385e2e115a527/tmp/folded.pdb (00:10:18)
[INFO] Main: Simulation completed successfully. (00:16:20)
|
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 | -0.4579 | |
| 2 | A | A | -0.2106 | |
| 3 | R | A | -1.0671 | |
| 4 | A | A | 0.0000 | |
| 5 | V | A | 1.0911 | |
| 6 | G | A | -0.1254 | |
| 7 | P | A | -0.9986 | |
| 8 | E | A | -0.9778 | |
| 9 | R | A | 0.0000 | |
| 10 | R | A | -1.3132 | |
| 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 | -0.4223 | |
| 20 | I | A | 0.0000 | |
| 21 | G | A | 0.0000 | |
| 22 | M | A | 0.0000 | |
| 23 | R | A | -1.4538 | |
| 24 | S | A | -0.5867 | |
| 25 | E | A | -0.6560 | |
| 26 | L | A | 1.0243 | |
| 27 | G | A | 0.5479 | |
| 28 | V | A | 1.5704 | |
| 29 | L | A | 0.7925 | |
| 30 | V | A | 0.1570 | |
| 31 | P | A | -0.5994 | |
| 32 | G | A | 0.0000 | |
| 33 | T | A | -0.5232 | |
| 34 | G | A | -0.3005 | |
| 35 | L | A | 0.0000 | |
| 36 | A | A | -0.6576 | |
| 37 | A | A | -0.4363 | |
| 38 | I | A | 0.1162 | |
| 39 | L | A | 0.0000 | |
| 40 | R | A | -0.7070 | |
| 41 | T | A | -0.1833 | |
| 42 | L | A | -0.0384 | |
| 43 | P | A | -0.2650 | |
| 44 | M | A | -0.0942 | |
| 45 | F | A | 0.0000 | |
| 46 | H | A | 0.0000 | |
| 47 | D | A | -1.5462 | |
| 48 | E | A | -2.3057 | |
| 49 | E | A | -3.0353 | |
| 50 | H | A | -2.2939 | |
| 51 | A | A | 0.0000 | |
| 52 | R | A | -3.1494 | |
| 53 | A | A | -2.0947 | |
| 54 | R | A | -2.2127 | |
| 55 | G | A | -1.7928 | |
| 56 | L | A | -1.4505 | |
| 57 | S | A | -1.6883 | |
| 58 | E | A | -2.3767 | |
| 59 | D | A | -1.8463 | |
| 60 | T | A | -1.1529 | |
| 61 | L | A | 0.0000 | |
| 62 | V | A | 0.0000 | |
| 63 | L | A | 0.0000 | |
| 64 | P | A | -0.6605 | |
| 65 | P | A | -1.1642 | |
| 66 | A | A | -0.8541 | |
| 67 | S | A | -1.6955 | |
| 68 | R | A | -2.7123 | |
| 69 | N | A | -2.5638 | |
| 70 | Q | A | -1.5600 | |
| 71 | R | A | -1.4461 | |
| 72 | I | A | 0.0000 | |
| 73 | L | A | 0.0000 | |
| 74 | Y | A | 0.0000 | |
| 75 | T | A | -0.6302 | |
| 76 | V | A | 0.0000 | |
| 77 | L | A | -0.1361 | |
| 78 | E | A | -0.6171 | |
| 79 | C | A | -0.5188 | |
| 80 | Q | A | -1.2441 | |
| 81 | P | A | -0.9966 | |
| 82 | L | A | -0.5649 | |
| 83 | F | A | -0.9801 | |
| 84 | D | A | -1.9328 | |
| 85 | S | A | 0.0000 | |
| 86 | S | A | -1.9200 | |
| 87 | D | A | -2.4566 | |
| 88 | M | A | 0.0000 | |
| 89 | T | A | -0.5815 | |
| 90 | I | A | 0.0123 | |
| 91 | A | A | 0.0383 | |
| 92 | E | A | -0.2610 | |
| 93 | W | A | 0.0000 | |
| 94 | V | A | 0.1860 | |
| 95 | C | A | 0.2280 | |
| 96 | L | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | Q | A | -1.7113 | |
| 99 | T | A | -1.2764 | |
| 100 | I | A | 0.0000 | |
| 101 | K | A | -2.4626 | |
| 102 | R | A | -3.1601 | |
| 103 | H | A | -2.3533 | |
| 104 | Y | A | 0.0000 | |
| 105 | E | A | -2.8278 | |
| 106 | Q | A | -2.4302 | |
| 107 | Y | A | -1.4113 | |
| 108 | H | A | -1.1668 | |
| 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 | -2.2440 | |
| 118 | T | A | -1.2718 | |
| 119 | M | A | 0.0000 | |
| 120 | A | A | 0.0000 | |
| 121 | F | A | 0.0983 | |
| 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 | -0.3289 | |
| 132 | N | A | -1.1220 | |
| 133 | L | A | 0.0000 | |
| 134 | Q | A | -1.1973 | |
| 135 | K | A | -0.3051 | |
| 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 | -0.6441 | |
| 144 | V | A | 0.4203 | |
| 145 | P | A | 0.0000 | |
| 146 | I | A | 0.0000 | |
| 147 | H | A | -0.1664 | |
| 148 | A | A | 0.6962 | |
| 149 | L | A | 2.0270 | |
| 150 | W | A | 1.8941 | |
| 151 | S | A | 0.0000 | |
| 152 | D | A | 0.0000 | |
| 153 | G | A | 0.0000 | |
| 154 | R | A | -0.9472 | |
| 155 | E | A | -2.1296 | |
| 156 | N | A | 0.0000 | |
| 157 | L | A | 0.0000 | |
| 158 | L | A | -0.3711 | |
| 159 | G | A | -0.6186 | |
| 160 | A | A | 0.0000 | |
| 161 | L | A | 0.0000 | |
| 162 | L | A | 0.3935 | |
| 163 | M | A | 0.0000 | |
| 164 | A | A | 0.0000 | |
| 165 | G | A | 0.0000 | |
| 166 | Q | A | -0.2120 | |
| 167 | Y | A | 0.0197 | |
| 168 | V | A | 0.2792 | |
| 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 | -1.3910 | |
| 178 | N | A | -1.4524 | |
| 179 | Q | A | -0.6484 | |
| 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 | 0.1084 | |
| 188 | K | A | -0.1727 | |
| 189 | V | A | 0.5906 | |
| 190 | D | A | 0.0000 | |
| 191 | A | A | -1.2983 | |
| 192 | R | A | -2.3372 | |
| 193 | R | A | -2.1446 | |
| 194 | F | A | -0.4261 | |
| 195 | A | A | -0.6007 | |
| 196 | A | A | 0.0000 | |
| 197 | F | A | 0.0000 | |
| 198 | C | A | 0.4658 | |
| 199 | S | A | 0.3882 | |
| 200 | P | A | 0.1952 | |
| 201 | N | A | -0.1298 | |
| 202 | L | A | 0.6759 | |
| 203 | L | A | 1.5291 | |
| 204 | P | A | 0.6287 | |
| 205 | L | A | 0.0000 | |
| 206 | A | A | 0.0000 | |
| 207 | T | A | -0.3177 | |
| 208 | V | A | -0.5605 | |
| 209 | G | A | -0.9669 | |
| 210 | A | A | -0.8456 | |
| 211 | D | A | -1.5431 | |
| 212 | I | A | -0.3449 | |
| 213 | T | A | -0.4219 | |
| 214 | I | A | -0.5090 | |
| 215 | N | A | -1.1827 | |
| 216 | R | A | -2.7849 | |
| 217 | E | A | -2.8722 | |
| 218 | L | A | -1.3887 | |
| 219 | V | A | -1.6403 | |
| 220 | R | A | -2.4736 | |
| 221 | K | A | -2.7833 | |
| 222 | V | A | -2.0388 | |
| 223 | D | A | -3.0185 | |
| 224 | G | A | -2.4387 | |
| 225 | K | A | -2.5966 | |
| 226 | A | A | -1.5861 | |
| 227 | G | A | -1.0330 | |
| 228 | L | A | -0.2843 | |
| 229 | V | A | 0.6187 | |
| 230 | V | A | 0.0475 | |
| 231 | H | A | -0.0500 | |
| 232 | S | A | -0.1004 | |
| 233 | S | A | -0.4923 | |
| 234 | M | A | 0.0000 | |
| 235 | E | A | -1.1019 | |
| 236 | Q | A | -1.6379 | |
| 237 | D | A | -1.4364 | |
| 238 | V | A | -0.6069 | |
| 239 | G | A | 0.0104 | |
| 240 | L | A | 0.1415 | |
| 241 | L | A | 0.0000 | |
| 242 | R | A | -1.5878 | |
| 243 | L | A | 0.0000 | |
| 244 | Y | A | 0.2760 | |
| 245 | P | A | 0.0413 | |
| 246 | G | A | -0.4624 | |
| 247 | I | A | 0.0000 | |
| 248 | P | A | -0.4467 | |
| 249 | A | A | -0.9407 | |
| 250 | A | A | -0.3055 | |
| 251 | L | A | 0.4967 | |
| 252 | V | A | 0.0000 | |
| 253 | R | A | -1.4770 | |
| 254 | A | A | -0.3646 | |
| 255 | F | A | 0.1940 | |
| 256 | L | A | 0.0000 | |
| 257 | Q | A | -1.2542 | |
| 258 | P | A | -0.9585 | |
| 259 | P | A | -0.9349 | |
| 260 | L | A | -0.8734 | |
| 261 | K | A | -1.4242 | |
| 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 | 0.0698 | |
| 269 | G | A | -0.2350 | |
| 270 | S | A | -0.4184 | |
| 271 | G | A | 0.0000 | |
| 272 | N | A | -0.0602 | |
| 273 | G | A | 0.0000 | |
| 274 | P | A | -0.4294 | |
| 275 | T | A | -0.6846 | |
| 276 | K | A | -1.4850 | |
| 277 | P | A | -1.6166 | |
| 278 | D | A | -2.6062 | |
| 279 | L | A | 0.0000 | |
| 280 | L | A | -1.4098 | |
| 281 | Q | A | -2.1571 | |
| 282 | E | A | -1.6753 | |
| 283 | L | A | 0.0000 | |
| 284 | R | A | -2.1775 | |
| 285 | V | A | -1.0050 | |
| 286 | A | A | 0.0000 | |
| 287 | T | A | -1.7100 | |
| 288 | E | A | -2.4638 | |
| 289 | R | A | -2.2195 | |
| 290 | G | A | -1.5184 | |
| 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 | -0.4573 | |
| 298 | H | A | -0.7970 | |
| 299 | C | A | 0.1645 | |
| 300 | L | A | 0.7046 | |
| 301 | Q | A | -0.8263 | |
| 302 | G | A | -0.6976 | |
| 303 | A | A | -0.2822 | |
| 304 | V | A | 0.0000 | |
| 305 | T | A | -0.5193 | |
| 306 | T | A | -0.3060 | |
| 307 | D | A | -1.2807 | |
| 308 | Y | A | 0.4094 | |
| 309 | A | A | 0.4636 | |
| 310 | A | A | 0.2629 | |
| 311 | G | A | 0.0000 | |
| 312 | M | A | 0.6677 | |
| 313 | A | A | 0.3314 | |
| 314 | M | A | 0.0000 | |
| 315 | A | A | -0.0541 | |
| 316 | G | A | -0.3816 | |
| 317 | A | A | 0.0000 | |
| 318 | G | A | -0.8047 | |
| 319 | V | A | 0.0000 | |
| 320 | I | A | 0.0000 | |
| 321 | S | A | 0.0396 | |
| 322 | G | A | 0.0000 | |
| 323 | F | A | 0.2162 | |
| 324 | D | A | 0.0000 | |
| 325 | M | A | 0.0000 | |
| 326 | T | A | -0.0646 | |
| 327 | S | A | 0.0661 | |
| 328 | E | A | 0.0594 | |
| 329 | A | A | 0.0000 | |
| 330 | A | A | 0.0000 | |
| 331 | L | A | 0.2831 | |
| 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 | -0.6472 | |
| 340 | Q | A | -0.4294 | |
| 341 | P | A | -0.4614 | |
| 342 | G | A | -0.2596 | |
| 343 | L | A | 0.1025 | |
| 344 | S | A | -0.3485 | |
| 345 | L | A | -0.3816 | |
| 346 | D | A | -1.6901 | |
| 347 | V | A | -0.5532 | |
| 348 | R | A | -0.7540 | |
| 349 | K | A | -1.6386 | |
| 350 | E | A | -2.3822 | |
| 351 | L | A | -1.3317 | |
| 352 | L | A | 0.0000 | |
| 353 | T | A | -1.5547 | |
| 354 | K | A | -2.3840 | |
| 355 | D | A | -1.4548 | |
| 356 | L | A | 0.0000 | |
| 357 | R | A | -0.9064 | |
| 358 | G | A | -0.6699 | |
| 359 | E | A | 0.0000 | |
| 360 | M | A | 0.0000 | |
| 361 | T | A | -0.4659 | |
| 362 | P | A | -0.7567 | |
| 363 | P | A | -0.9649 | |
| 364 | S | A | -1.2396 | |
| 365 | V | A | -0.8118 | |
| 366 | E | A | -3.1394 | |
| 367 | E | A | -3.7664 | |
| 368 | R | A | -3.7307 | |
| 369 | R | A | -3.5236 | |
| 370 | P | A | -2.7576 | |
| 371 | S | A | -1.8178 | |
| 372 | L | A | 0.3089 | |
| 373 | Q | A | -0.9628 | |
| 374 | G | A | -1.5549 | |
| 375 | N | A | -0.9821 | |
| 376 | T | A | -0.0598 | |
| 377 | L | A | 1.2245 | |
| 378 | G | A | 0.0000 | |
| 379 | G | A | 0.1917 | |
| 380 | G | A | 0.7299 | |
| 381 | V | A | 0.8702 | |
| 382 | S | A | 0.9484 | |
| 383 | W | A | 1.5943 | |
| 384 | L | A | 0.4976 | |
| 385 | L | A | 0.1018 | |
| 386 | S | A | 0.6460 | |
| 387 | L | A | 0.3042 | |
| 388 | S | A | -0.5057 | |
| 389 | G | A | -1.2800 | |
| 390 | S | A | -1.7514 | |
| 391 | Q | A | -2.9283 | |
| 392 | E | A | -3.1280 | |
| 393 | A | A | 0.0000 | |
| 394 | D | A | -3.2812 | |
| 395 | A | A | -2.2785 | |
| 396 | L | A | -1.1798 | |
| 397 | R | A | -1.7924 | |
| 398 | N | A | -1.5612 | |
| 399 | A | A | -0.0036 | |
| 400 | L | A | 1.3069 | |
| 401 | V | A | 1.5341 | |
| 402 | P | A | 0.2405 | |
| 403 | S | A | -0.0948 |
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 | -0.2759 | 4.1338 | View | CSV | PDB |
| 4.5 | -0.3264 | 4.1409 | View | CSV | PDB |
| 5.0 | -0.3899 | 4.1563 | View | CSV | PDB |
| 5.5 | -0.458 | 4.1792 | View | CSV | PDB |
| 6.0 | -0.5215 | 4.201 | View | CSV | PDB |
| 6.5 | -0.5734 | 4.2143 | View | CSV | PDB |
| 7.0 | -0.6103 | 4.2201 | View | CSV | PDB |
| 7.5 | -0.6348 | 4.2222 | View | CSV | PDB |
| 8.0 | -0.6508 | 4.2228 | View | CSV | PDB |
| 8.5 | -0.6595 | 4.2231 | View | CSV | PDB |
| 9.0 | -0.6604 | 4.2231 | 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