ID code: '5A79' 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' --------------------------------------------------------------------------------- 1461 C1' G R 1 beta 1456 1462 1459 1484 C1' A R 2 beta 1479 1485 1482 1506 C1' A R 3 beta 1501 1507 1504 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1459 C2' G R 1 OK 1461 1457 1460 1482 C2' A R 2 OK 1484 1480 1483 1504 C2' A R 3 OK 1506 1502 1505 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1457 C3' G R 1 OK 1455 1458 1459 1480 C3' A R 2 OK 1478 1481 1482 1502 C3' A R 3 OK 1500 1503 1504 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1455 C4' G R 1 OK 1457 1454 1456 1478 C4' A R 2 OK 1480 1477 1479 1500 C4' A R 3 OK 1502 1499 1501 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1454 C5' G R 1 1453 1455 1477 C5' A R 2 1476 1478 1499 C5' A R 3 1498 1500 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1450 P G R 1 OK OK 1451 1452 1453 1473 P A R 2 distorted distorted 1458 1474 1475 1476 1495 P A R 3 distorted distorted 1481 1496 1497 1498 ---------------------------------------------------------------------------------