ID code: '5DNO' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 1314 C1' C B 1 beta 1309 1315 1312 1334 C1' U B 2 beta 1329 1335 1332 1354 C1' U B 3 beta 1349 1355 1352 1374 C1' A B 4 beta 1369 1375 1372 1396 C1' A B 5 beta 1391 1397 1394 1418 C1' A B 6 beta 1413 1419 1416 1440 C1' C B 7 beta 1435 1441 1438 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1312 C2' C B 1 OK 1314 1310 1313 1332 C2' U B 2 OK 1334 1330 1333 1352 C2' U B 3 OK 1354 1350 1353 1372 C2' A B 4 OK 1374 1370 1373 1394 C2' A B 5 OK 1396 1392 1395 1416 C2' A B 6 OK 1418 1414 1417 1438 C2' C B 7 OK 1440 1436 1439 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1310 C3' C B 1 OK 1308 1311 1312 1330 C3' U B 2 OK 1328 1331 1332 1350 C3' U B 3 OK 1348 1351 1352 1370 C3' A B 4 OK 1368 1371 1372 1392 C3' A B 5 OK 1390 1393 1394 1414 C3' A B 6 OK 1412 1415 1416 1436 C3' C B 7 OK 1434 1437 1438 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1308 C4' C B 1 OK 1310 1307 1309 1328 C4' U B 2 OK 1330 1327 1329 1348 C4' U B 3 OK 1350 1347 1349 1368 C4' A B 4 OK 1370 1367 1369 1390 C4' A B 5 OK 1392 1389 1391 1412 C4' A B 6 OK 1414 1411 1413 1434 C4' C B 7 OK 1436 1433 1435 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1307 C5' C B 1 1306 1308 1327 C5' U B 2 1326 1328 1347 C5' U B 3 1346 1348 1367 C5' A B 4 1366 1368 1389 C5' A B 5 1388 1390 1411 C5' A B 6 1410 1412 1433 C5' C B 7 1432 1434 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1323 P U B 2 distorted distorted 1311 1324 1325 1326 1343 P U B 3 distorted distorted 1331 1344 1345 1346 1363 P A B 4 distorted distorted 1351 1364 1365 1366 1385 P A B 5 distorted distorted 1371 1386 1387 1388 1407 P A B 6 distorted distorted 1393 1408 1409 1410 1429 P C B 7 distorted distorted 1415 1430 1431 1432 ---------------------------------------------------------------------------------