ID code: '5HJZ' 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' --------------------------------------------------------------------------------- 1765 C1' A C 1 beta 1760 1766 1763 1787 C1' C C 2 beta 1782 1788 1785 1807 C1' C C 3 beta 1802 1808 1805 1827 C1' U C 4 beta 1822 1828 1825 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1763 C2' A C 1 OK 1765 1761 1764 1785 C2' C C 2 OK 1787 1783 1786 1805 C2' C C 3 OK 1807 1803 1806 1825 C2' U C 4 OK 1827 1823 1826 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1761 C3' A C 1 OK 1759 1762 1763 1783 C3' C C 2 OK 1781 1784 1785 1803 C3' C C 3 OK 1801 1804 1805 1823 C3' U C 4 OK 1821 1824 1825 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1759 C4' A C 1 OK 1761 1758 1760 1781 C4' C C 2 OK 1783 1780 1782 1801 C4' C C 3 OK 1803 1800 1802 1821 C4' U C 4 OK 1823 1820 1822 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1758 C5' A C 1 1757 1759 1780 C5' C C 2 1779 1781 1800 C5' C C 3 1799 1801 1820 C5' U C 4 1819 1821 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1754 P A C 1 OK OK 1755 1756 1757 1776 P C C 2 distorted distorted 1762 1777 1778 1779 1796 P C C 3 distorted distorted 1784 1797 1798 1799 1816 P U C 4 distorted distorted 1804 1817 1818 1819 ---------------------------------------------------------------------------------