ID code: '4NHA' 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' --------------------------------------------------------------------------------- 1788 C1' G B 1 beta 1783 1789 1786 1811 C1' C B 2 beta 1806 1812 1809 1831 C1' G B 3 beta 1826 1832 1829 1854 C1' U B 4 beta 1849 1855 1852 1874 C1' U B 5 beta 1869 1875 1872 1894 C1' G B 6 beta 1889 1895 1892 1917 C1' G B 7 beta 1912 1918 1915 1940 C1' C B 8 beta 1935 1941 1938 1960 C1' C B 9 beta 1955 1961 1958 1980 C1' A B 10 beta 1975 1981 1978 2002 C1' A B 11 beta 1997 2003 2000 2024 C1' C B 12 beta 2019 2025 2022 2044 C1' G B 13 beta 2039 2045 2042 2067 C1' C B 14 beta 2062 2068 2065 2087 C1' U B 15 beta 2082 2088 2085 2107 C1' U B 16 beta 2102 2108 2105 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1786 C2' G B 1 OK 1788 1784 1787 1809 C2' C B 2 OK 1811 1807 1810 1829 C2' G B 3 OK 1831 1827 1830 1852 C2' U B 4 OK 1854 1850 1853 1872 C2' U B 5 OK 1874 1870 1873 1892 C2' G B 6 OK 1894 1890 1893 1915 C2' G B 7 OK 1917 1913 1916 1938 C2' C B 8 OK 1940 1936 1939 1958 C2' C B 9 OK 1960 1956 1959 1978 C2' A B 10 OK 1980 1976 1979 2000 C2' A B 11 OK 2002 1998 2001 2022 C2' C B 12 OK 2024 2020 2023 2042 C2' G B 13 OK 2044 2040 2043 2065 C2' C B 14 OK 2067 2063 2066 2085 C2' U B 15 OK 2087 2083 2086 2105 C2' U B 16 OK 2107 2103 2106 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1784 C3' G B 1 OK 1782 1785 1786 1807 C3' C B 2 OK 1805 1808 1809 1827 C3' G B 3 OK 1825 1828 1829 1850 C3' U B 4 OK 1848 1851 1852 1870 C3' U B 5 OK 1868 1871 1872 1890 C3' G B 6 OK 1888 1891 1892 1913 C3' G B 7 OK 1911 1914 1915 1936 C3' C B 8 OK 1934 1937 1938 1956 C3' C B 9 OK 1954 1957 1958 1976 C3' A B 10 OK 1974 1977 1978 1998 C3' A B 11 OK 1996 1999 2000 2020 C3' C B 12 OK 2018 2021 2022 2040 C3' G B 13 OK 2038 2041 2042 2063 C3' C B 14 OK 2061 2064 2065 2083 C3' U B 15 OK 2081 2084 2085 2103 C3' U B 16 OK 2101 2104 2105 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1782 C4' G B 1 OK 1784 1781 1783 1805 C4' C B 2 OK 1807 1804 1806 1825 C4' G B 3 OK 1827 1824 1826 1848 C4' U B 4 OK 1850 1847 1849 1868 C4' U B 5 OK 1870 1867 1869 1888 C4' G B 6 OK 1890 1887 1889 1911 C4' G B 7 OK 1913 1910 1912 1934 C4' C B 8 OK 1936 1933 1935 1954 C4' C B 9 OK 1956 1953 1955 1974 C4' A B 10 OK 1976 1973 1975 1996 C4' A B 11 OK 1998 1995 1997 2018 C4' C B 12 OK 2020 2017 2019 2038 C4' G B 13 OK 2040 2037 2039 2061 C4' C B 14 OK 2063 2060 2062 2081 C4' U B 15 OK 2083 2080 2082 2101 C4' U B 16 OK 2103 2100 2102 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1781 C5' G B 1 1780 1782 1804 C5' C B 2 1803 1805 1824 C5' G B 3 1823 1825 1847 C5' U B 4 1846 1848 1867 C5' U B 5 1866 1868 1887 C5' G B 6 1886 1888 1910 C5' G B 7 1909 1911 1933 C5' C B 8 1932 1934 1953 C5' C B 9 1952 1954 1973 C5' A B 10 1972 1974 1995 C5' A B 11 1994 1996 2017 C5' C B 12 2016 2018 2037 C5' G B 13 2036 2038 2060 C5' C B 14 2059 2061 2080 C5' U B 15 2079 2081 2100 C5' U B 16 2099 2101 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1777 P G B 1 distorted distorted 1778 1779 1780 1800 P C B 2 distorted distorted 1785 1801 1802 1803 1820 P G B 3 distorted distorted 1808 1821 1822 1823 1843 P U B 4 distorted distorted 1828 1844 1845 1846 1863 P U B 5 distorted distorted 1851 1864 1865 1866 1883 P G B 6 distorted distorted 1871 1884 1885 1886 1906 P G B 7 distorted distorted 1891 1907 1908 1909 1929 P C B 8 distorted distorted 1914 1930 1931 1932 1949 P C B 9 distorted distorted 1937 1950 1951 1952 1969 P A B 10 distorted distorted 1957 1970 1971 1972 1991 P A B 11 distorted distorted 1977 1992 1993 1994 2013 P C B 12 distorted distorted 1999 2014 2015 2016 2033 P G B 13 distorted distorted 2021 2034 2035 2036 2056 P C B 14 distorted distorted 2041 2057 2058 2059 2076 P U B 15 distorted distorted 2064 2077 2078 2079 2096 P U B 16 distorted distorted 2084 2097 2098 2099 ---------------------------------------------------------------------------------