| Chain sequence(s) |
A: GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYDSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLS
B: GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYDSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSP input PDB |
| Selected Chain(s) | A,B |
| 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] (00:00:02)
[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 all chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:11:15)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/f1f32de664b14c3/tmp/folded.pdb (00:11:15)
[INFO] Main: Simulation completed successfully. (00:20:07)
|
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 |
|---|---|---|---|---|
| 236 | G | A | -0.8359 | |
| 237 | G | A | -0.8173 | |
| 238 | P | A | -0.7069 | |
| 239 | S | A | -0.2334 | |
| 240 | V | A | 0.0000 | |
| 241 | F | A | 1.1716 | |
| 242 | L | A | 0.0000 | |
| 243 | F | A | 1.4724 | |
| 244 | P | A | 0.0734 | |
| 245 | P | A | 0.0000 | |
| 246 | K | A | -2.1638 | |
| 247 | P | A | -1.4645 | |
| 248 | K | A | -1.2468 | |
| 249 | D | A | 0.0000 | |
| 250 | T | A | 0.0000 | |
| 251 | L | A | 0.0000 | |
| 252 | M | A | 0.3610 | |
| 253 | I | A | 1.4914 | |
| 254 | S | A | 0.0817 | |
| 255 | R | A | -1.1963 | |
| 256 | T | A | -0.6263 | |
| 257 | P | A | 0.0000 | |
| 258 | E | A | -0.7252 | |
| 259 | V | A | 0.0000 | |
| 260 | T | A | 0.5211 | |
| 261 | C | A | 0.0000 | |
| 262 | V | A | 0.0000 | |
| 263 | V | A | 0.0000 | |
| 264 | V | A | -0.8571 | |
| 265 | D | A | -2.0227 | |
| 266 | V | A | 0.0000 | |
| 267 | S | A | -2.2490 | |
| 268 | H | A | -2.7307 | |
| 269 | E | A | -2.9749 | |
| 270 | D | A | -2.7932 | |
| 271 | P | A | -2.8899 | |
| 272 | E | A | -3.3210 | |
| 273 | V | A | 0.0000 | |
| 274 | K | A | -2.3152 | |
| 275 | F | A | -1.1391 | |
| 276 | N | A | -1.1131 | |
| 277 | W | A | 0.0000 | |
| 278 | Y | A | -0.5432 | |
| 279 | V | A | -0.8540 | |
| 280 | D | A | -2.0755 | |
| 281 | G | A | -0.8299 | |
| 282 | V | A | 0.6620 | |
| 283 | E | A | -0.4525 | |
| 284 | V | A | -0.5158 | |
| 285 | H | A | -1.6816 | |
| 286 | N | A | -1.8540 | |
| 287 | A | A | -1.3474 | |
| 288 | K | A | -1.8355 | |
| 289 | T | A | -1.7812 | |
| 290 | K | A | -2.7978 | |
| 291 | P | A | -2.6272 | |
| 292 | R | A | -3.9530 | |
| 293 | E | A | -3.5831 | |
| 294 | E | A | -2.7504 | |
| 295 | Q | A | -1.9520 | |
| 296 | Y | A | -0.2719 | |
| 297 | D | A | -1.7147 | |
| 298 | S | A | -1.8352 | |
| 299 | T | A | -2.3412 | |
| 300 | Y | A | -2.8776 | |
| 301 | R | A | -2.7184 | |
| 302 | V | A | 0.0000 | |
| 303 | V | A | 0.0000 | |
| 304 | S | A | 0.0000 | |
| 305 | V | A | -0.6391 | |
| 306 | L | A | 0.0000 | |
| 307 | T | A | -0.3812 | |
| 308 | V | A | 0.0000 | |
| 309 | L | A | 0.8169 | |
| 310 | H | A | 0.0000 | |
| 311 | Q | A | -1.0904 | |
| 312 | D | A | -1.2393 | |
| 313 | W | A | 0.0000 | |
| 314 | L | A | -1.0308 | |
| 315 | N | A | -1.8766 | |
| 316 | G | A | -2.1186 | |
| 317 | K | A | -2.2562 | |
| 318 | E | A | -1.8710 | |
| 319 | Y | A | 0.0000 | |
| 320 | K | A | -1.8261 | |
| 321 | C | A | 0.0000 | |
| 322 | K | A | -1.5788 | |
| 323 | V | A | 0.0000 | |
| 324 | S | A | -1.4036 | |
| 325 | N | A | 0.0000 | |
| 326 | K | A | -2.6095 | |
| 327 | A | A | -1.3705 | |
| 328 | L | A | -0.3677 | |
| 329 | P | A | -0.3591 | |
| 330 | A | A | -0.3995 | |
| 331 | P | A | -0.8258 | |
| 332 | I | A | -0.6868 | |
| 333 | E | A | -2.2269 | |
| 334 | K | A | -1.5075 | |
| 335 | T | A | -1.1375 | |
| 336 | I | A | -0.2342 | |
| 337 | S | A | -1.0068 | |
| 338 | K | A | -1.3473 | |
| 339 | A | A | -1.3091 | |
| 340 | K | A | -2.1819 | |
| 341 | G | A | -1.9013 | |
| 342 | Q | A | -1.8563 | |
| 343 | P | A | -1.6337 | |
| 344 | R | A | -1.8824 | |
| 345 | E | A | -2.4087 | |
| 346 | P | A | 0.0000 | |
| 347 | Q | A | -1.0818 | |
| 348 | V | A | 0.0000 | |
| 349 | Y | A | 0.0000 | |
| 350 | T | A | 0.0000 | |
| 351 | L | A | 0.0000 | |
| 352 | P | A | -0.2315 | |
| 353 | P | A | -0.5093 | |
| 354 | S | A | 0.0000 | |
| 355 | R | A | -2.1438 | |
| 356 | E | A | -1.5627 | |
| 357 | E | A | 0.0000 | |
| 358 | M | A | -1.6249 | |
| 359 | T | A | -1.4376 | |
| 360 | K | A | -2.5598 | |
| 361 | N | A | -2.7943 | |
| 362 | Q | A | -2.8082 | |
| 363 | V | A | 0.0000 | |
| 364 | S | A | 0.0000 | |
| 365 | L | A | 0.0000 | |
| 366 | T | A | 0.0000 | |
| 367 | C | A | 0.0000 | |
| 368 | L | A | 0.0000 | |
| 369 | V | A | 0.0000 | |
| 370 | K | A | -0.4253 | |
| 371 | G | A | -0.9750 | |
| 372 | F | A | 0.0000 | |
| 373 | Y | A | -1.1320 | |
| 374 | P | A | 0.0000 | |
| 375 | S | A | -0.4829 | |
| 376 | D | A | -1.5530 | |
| 377 | I | A | -0.7728 | |
| 378 | A | A | -0.5099 | |
| 379 | V | A | -0.2590 | |
| 380 | E | A | -1.0576 | |
| 381 | W | A | 0.0000 | |
| 382 | E | A | -2.1073 | |
| 383 | S | A | 0.0000 | |
| 384 | N | A | -1.9371 | |
| 385 | G | A | -1.9804 | |
| 386 | Q | A | -2.3721 | |
| 387 | P | A | -2.2238 | |
| 388 | E | A | -2.1749 | |
| 389 | N | A | -2.4027 | |
| 390 | N | A | -2.0128 | |
| 391 | Y | A | -1.1314 | |
| 392 | K | A | -0.8527 | |
| 393 | T | A | -0.2237 | |
| 394 | T | A | 0.0000 | |
| 395 | P | A | -0.1138 | |
| 396 | P | A | -0.0423 | |
| 397 | V | A | 0.3523 | |
| 398 | L | A | 0.3401 | |
| 399 | D | A | -0.6922 | |
| 400 | S | A | -1.2858 | |
| 401 | D | A | -1.9959 | |
| 402 | G | A | -1.1604 | |
| 403 | S | A | 0.0000 | |
| 404 | F | A | -0.0494 | |
| 405 | F | A | 0.0000 | |
| 406 | L | A | 0.0000 | |
| 407 | Y | A | 0.0000 | |
| 408 | S | A | 0.0000 | |
| 409 | K | A | 0.0000 | |
| 410 | L | A | 0.0000 | |
| 411 | T | A | -1.1335 | |
| 412 | V | A | 0.0000 | |
| 413 | D | A | -2.8439 | |
| 414 | K | A | -3.0480 | |
| 415 | S | A | -2.7689 | |
| 416 | R | A | -3.0133 | |
| 417 | W | A | 0.0000 | |
| 418 | Q | A | -2.4323 | |
| 419 | Q | A | -2.4352 | |
| 420 | G | A | -1.2972 | |
| 421 | N | A | -1.0790 | |
| 422 | V | A | 0.0566 | |
| 423 | F | A | 0.0000 | |
| 424 | S | A | -0.9638 | |
| 425 | C | A | 0.0000 | |
| 426 | S | A | 0.0000 | |
| 427 | V | A | 0.0000 | |
| 428 | M | A | 0.0000 | |
| 429 | H | A | 0.0000 | |
| 430 | E | A | -1.1356 | |
| 431 | A | A | -1.4522 | |
| 432 | L | A | -1.3890 | |
| 433 | H | A | -1.7481 | |
| 434 | N | A | -1.6403 | |
| 435 | H | A | -1.1203 | |
| 436 | Y | A | -0.4704 | |
| 437 | T | A | -0.9111 | |
| 438 | Q | A | -1.4892 | |
| 439 | K | A | -1.2146 | |
| 440 | S | A | -0.6340 | |
| 441 | L | A | 0.0000 | |
| 442 | S | A | 0.0446 | |
| 443 | L | A | 0.1431 | |
| 444 | S | A | 0.2631 | |
| 1236 | G | B | -0.7675 | |
| 1237 | G | B | -0.6856 | |
| 1238 | P | B | 0.0000 | |
| 1239 | S | B | -0.3120 | |
| 1240 | V | B | 0.0000 | |
| 1241 | F | B | 1.4355 | |
| 1242 | L | B | 0.9621 | |
| 1243 | F | B | 1.3872 | |
| 1244 | P | B | 0.0850 | |
| 1245 | P | B | 0.0000 | |
| 1246 | K | B | -1.9920 | |
| 1247 | P | B | -1.2850 | |
| 1248 | K | B | -1.0599 | |
| 1249 | D | B | 0.0000 | |
| 1250 | T | B | 0.0000 | |
| 1251 | L | B | 0.0000 | |
| 1252 | M | B | 0.5542 | |
| 1253 | I | B | 1.5648 | |
| 1254 | S | B | 0.0697 | |
| 1255 | R | B | -1.1883 | |
| 1256 | T | B | -0.6587 | |
| 1257 | P | B | 0.0000 | |
| 1258 | E | B | -0.9400 | |
| 1259 | V | B | 0.0000 | |
| 1260 | T | B | 0.3689 | |
| 1261 | C | B | 0.0000 | |
| 1262 | V | B | 0.0000 | |
| 1263 | V | B | 0.0000 | |
| 1264 | V | B | -0.4823 | |
| 1265 | D | B | -1.6840 | |
| 1266 | V | B | 0.0000 | |
| 1267 | S | B | -2.1888 | |
| 1268 | H | B | -2.8206 | |
| 1269 | E | B | -3.0231 | |
| 1270 | D | B | -2.6328 | |
| 1271 | P | B | -2.5346 | |
| 1272 | E | B | -2.5041 | |
| 1273 | V | B | -1.6433 | |
| 1274 | K | B | -2.0884 | |
| 1275 | F | B | -1.1237 | |
| 1276 | N | B | -1.2682 | |
| 1277 | W | B | 0.0000 | |
| 1278 | Y | B | -0.6126 | |
| 1279 | V | B | -0.9088 | |
| 1280 | D | B | -1.8771 | |
| 1281 | G | B | -0.6962 | |
| 1282 | V | B | 0.8729 | |
| 1283 | E | B | -0.5306 | |
| 1284 | V | B | -0.7444 | |
| 1285 | H | B | -1.9252 | |
| 1286 | N | B | -2.1433 | |
| 1287 | A | B | -1.8332 | |
| 1288 | K | B | -2.2516 | |
| 1289 | T | B | -1.6199 | |
| 1290 | K | B | -2.0571 | |
| 1291 | P | B | -2.2236 | |
| 1292 | R | B | -3.6723 | |
| 1293 | E | B | -3.7610 | |
| 1294 | E | B | -3.2401 | |
| 1295 | Q | B | -2.6883 | |
| 1296 | Y | B | -0.7953 | |
| 1297 | D | B | -2.0324 | |
| 1298 | S | B | -1.9239 | |
| 1299 | T | B | -2.3087 | |
| 1300 | Y | B | -2.8420 | |
| 1301 | R | B | -2.5729 | |
| 1302 | V | B | 0.0000 | |
| 1303 | V | B | 0.0000 | |
| 1304 | S | B | 0.0000 | |
| 1305 | V | B | -0.6221 | |
| 1306 | L | B | 0.0000 | |
| 1307 | T | B | -0.5159 | |
| 1308 | V | B | 0.0000 | |
| 1309 | L | B | 1.0206 | |
| 1310 | H | B | 0.0000 | |
| 1311 | Q | B | -1.3236 | |
| 1312 | D | B | -1.9109 | |
| 1313 | W | B | 0.0000 | |
| 1314 | L | B | -1.3290 | |
| 1315 | N | B | -2.4929 | |
| 1316 | G | B | -2.3354 | |
| 1317 | K | B | -2.7457 | |
| 1318 | E | B | -2.8062 | |
| 1319 | Y | B | 0.0000 | |
| 1320 | K | B | -1.8251 | |
| 1321 | C | B | 0.0000 | |
| 1322 | K | B | -1.5553 | |
| 1323 | V | B | 0.0000 | |
| 1324 | S | B | -1.3837 | |
| 1325 | N | B | 0.0000 | |
| 1326 | K | B | -2.4860 | |
| 1327 | A | B | -1.4195 | |
| 1328 | L | B | -0.5524 | |
| 1329 | P | B | -0.4279 | |
| 1330 | A | B | -0.4447 | |
| 1331 | P | B | -0.9503 | |
| 1332 | I | B | -0.9144 | |
| 1333 | E | B | -2.1969 | |
| 1334 | K | B | -1.3096 | |
| 1335 | T | B | -1.1615 | |
| 1336 | I | B | -0.4272 | |
| 1337 | S | B | -1.3925 | |
| 1338 | K | B | 0.0000 | |
| 1339 | A | B | -1.2410 | |
| 1340 | K | B | -2.2968 | |
| 1341 | G | B | -2.0318 | |
| 1342 | Q | B | -2.3084 | |
| 1343 | P | B | -2.0985 | |
| 1344 | R | B | -2.7473 | |
| 1345 | E | B | -3.0085 | |
| 1346 | P | B | 0.0000 | |
| 1347 | Q | B | -1.2987 | |
| 1348 | V | B | 0.0000 | |
| 1349 | Y | B | 0.0000 | |
| 1350 | T | B | 0.0000 | |
| 1351 | L | B | 0.0000 | |
| 1352 | P | B | -0.3580 | |
| 1353 | P | B | -0.6151 | |
| 1354 | S | B | 0.0000 | |
| 1355 | R | B | -1.8602 | |
| 1356 | E | B | -1.4651 | |
| 1357 | E | B | 0.0000 | |
| 1358 | M | B | -1.2202 | |
| 1359 | T | B | -1.1513 | |
| 1360 | K | B | -1.8510 | |
| 1361 | N | B | -2.4484 | |
| 1362 | Q | B | -2.4266 | |
| 1363 | V | B | 0.0000 | |
| 1364 | S | B | 0.0000 | |
| 1365 | L | B | 0.0000 | |
| 1366 | T | B | 0.0000 | |
| 1367 | C | B | 0.0000 | |
| 1368 | L | B | 0.0000 | |
| 1369 | V | B | 0.0000 | |
| 1370 | K | B | -0.6807 | |
| 1371 | G | B | -1.2206 | |
| 1372 | F | B | 0.0000 | |
| 1373 | Y | B | -1.3072 | |
| 1374 | P | B | 0.0000 | |
| 1375 | S | B | -0.2579 | |
| 1376 | D | B | -1.0333 | |
| 1377 | I | B | -0.5705 | |
| 1378 | A | B | 0.0000 | |
| 1379 | V | B | 0.0000 | |
| 1380 | E | B | -0.9093 | |
| 1381 | W | B | 0.0000 | |
| 1382 | E | B | -1.6105 | |
| 1383 | S | B | -1.3675 | |
| 1384 | N | B | -1.8664 | |
| 1385 | G | B | -1.7990 | |
| 1386 | Q | B | -2.1409 | |
| 1387 | P | B | -1.8185 | |
| 1388 | E | B | 0.0000 | |
| 1389 | N | B | -2.0766 | |
| 1390 | N | B | -1.6697 | |
| 1391 | Y | B | -1.0340 | |
| 1392 | K | B | -0.9065 | |
| 1393 | T | B | -0.3048 | |
| 1394 | T | B | 0.0000 | |
| 1395 | P | B | -0.0770 | |
| 1396 | P | B | 0.1093 | |
| 1397 | V | B | 0.4645 | |
| 1398 | L | B | 0.6633 | |
| 1399 | D | B | -0.5824 | |
| 1400 | S | B | -1.2649 | |
| 1401 | D | B | -1.9637 | |
| 1402 | G | B | -1.0604 | |
| 1403 | S | B | 0.0000 | |
| 1404 | F | B | 0.0155 | |
| 1405 | F | B | 0.0000 | |
| 1406 | L | B | 0.0000 | |
| 1407 | Y | B | 0.0000 | |
| 1408 | S | B | 0.0000 | |
| 1409 | K | B | 0.0000 | |
| 1410 | L | B | 0.0000 | |
| 1411 | T | B | -0.9785 | |
| 1412 | V | B | 0.0000 | |
| 1413 | D | B | -2.4731 | |
| 1414 | K | B | -2.4161 | |
| 1415 | S | B | -2.0566 | |
| 1416 | R | B | -1.8305 | |
| 1417 | W | B | 0.0000 | |
| 1418 | Q | B | -1.9212 | |
| 1419 | Q | B | -1.8890 | |
| 1420 | G | B | -1.1135 | |
| 1421 | N | B | -0.8571 | |
| 1422 | V | B | 0.1062 | |
| 1423 | F | B | 0.0000 | |
| 1424 | S | B | -0.6901 | |
| 1425 | C | B | 0.0000 | |
| 1426 | S | B | 0.0000 | |
| 1427 | V | B | 0.0000 | |
| 1428 | M | B | 0.0000 | |
| 1429 | H | B | 0.0000 | |
| 1430 | E | B | -1.2534 | |
| 1431 | A | B | -1.8626 | |
| 1432 | L | B | 0.0000 | |
| 1433 | H | B | -1.8412 | |
| 1434 | N | B | -1.6264 | |
| 1435 | H | B | -1.1034 | |
| 1436 | Y | B | -0.2941 | |
| 1437 | T | B | -0.6868 | |
| 1438 | Q | B | -1.0752 | |
| 1439 | K | B | -0.8697 | |
| 1440 | S | B | -0.4542 | |
| 1441 | L | B | 0.0000 | |
| 1442 | S | B | -0.1426 | |
| 1443 | L | B | -0.2768 | |
| 1444 | S | B | -0.3092 | |
| 1445 | P | B | -0.3805 |
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 | -0.7676 | 4.1007 | View | CSV | PDB |
| 4.5 | -0.8323 | 4.0862 | View | CSV | PDB |
| 5.0 | -0.9113 | 4.0734 | View | CSV | PDB |
| 5.5 | -0.9878 | 4.0741 | View | CSV | PDB |
| 6.0 | -1.0446 | 4.0974 | View | CSV | PDB |
| 6.5 | -1.0706 | 4.1532 | View | CSV | PDB |
| 7.0 | -1.0671 | 4.2285 | View | CSV | PDB |
| 7.5 | -1.0456 | 4.3155 | View | CSV | PDB |
| 8.0 | -1.0152 | 4.4074 | View | CSV | PDB |
| 8.5 | -0.9782 | 4.5004 | View | CSV | PDB |
| 9.0 | -0.9341 | 4.5914 | 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