ID code: '5ELK' 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' --------------------------------------------------------------------------------- 1858 C1' U R 3 beta 1853 1859 1856 1878 C1' U R 4 beta 1873 1879 1876 1898 C1' A R 5 beta 1893 1899 1896 1920 C1' G R 6 beta 1915 1921 1918 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1856 C2' U R 3 OK 1858 1854 1857 1876 C2' U R 4 OK 1878 1874 1877 1896 C2' A R 5 OK 1898 1894 1897 1918 C2' G R 6 OK 1920 1916 1919 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1854 C3' U R 3 OK 1852 1855 1856 1874 C3' U R 4 OK 1872 1875 1876 1894 C3' A R 5 OK 1892 1895 1896 1916 C3' G R 6 OK 1914 1917 1918 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1852 C4' U R 3 OK 1854 1851 1853 1872 C4' U R 4 OK 1874 1871 1873 1892 C4' A R 5 OK 1894 1891 1893 1914 C4' G R 6 OK 1916 1913 1915 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1851 C5' U R 3 1850 1852 1871 C5' U R 4 1870 1872 1891 C5' A R 5 1890 1892 1913 C5' G R 6 1912 1914 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1847 P U R 3 distorted distorted 1846 1848 1849 1850 1867 P U R 4 distorted distorted 1855 1868 1869 1870 1887 P A R 5 distorted distorted 1875 1888 1889 1890 1909 P G R 6 distorted distorted 1895 1910 1911 1912 1932 P A R 7 distorted distorted 1917 1933 1934 1935 ---------------------------------------------------------------------------------