ID code: '5A7A' 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' --------------------------------------------------------------------------------- 1445 C1' G R 1 beta 1440 1446 1443 1468 C1' A R 2 beta 1463 1469 1466 1490 C1' A R 3 beta 1485 1491 1488 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1443 C2' G R 1 OK 1445 1441 1444 1466 C2' A R 2 OK 1468 1464 1467 1488 C2' A R 3 OK 1490 1486 1489 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1441 C3' G R 1 OK 1439 1442 1443 1464 C3' A R 2 OK 1462 1465 1466 1486 C3' A R 3 OK 1484 1487 1488 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1439 C4' G R 1 OK 1441 1438 1440 1462 C4' A R 2 OK 1464 1461 1463 1484 C4' A R 3 OK 1486 1483 1485 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1438 C5' G R 1 1437 1439 1461 C5' A R 2 1460 1462 1483 C5' A R 3 1482 1484 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1434 P G R 1 OK OK 1435 1436 1437 1457 P A R 2 distorted distorted 1442 1458 1459 1460 1479 P A R 3 distorted distorted 1465 1480 1481 1482 ---------------------------------------------------------------------------------