ID code: '1IF1' 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' --------------------------------------------------------------------------------- 1725 C1' G C 200 beta 1721 1726 1724 1747 C1' A C 201 beta 1743 1748 1746 1768 C1' G C 202 beta 1764 1769 1767 1790 C1' A C 203 beta 1786 1791 1789 1811 C1' A C 204 beta 1807 1812 1810 1832 C1' G C 205 beta 1828 1833 1831 1854 C1' T C 206 beta 1850 1855 1853 1874 C1' G C 207 beta 1870 1875 1873 1896 C1' A C 208 beta 1892 1897 1895 1917 C1' A C 209 beta 1913 1918 1916 1938 C1' A C 210 beta 1934 1939 1937 1959 C1' G C 211 beta 1955 1960 1958 1981 C1' T C 212 beta 1977 1982 1980 1998 C1' A C 213 beta 1994 1999 1997 2019 C1' C C 214 beta 2015 2020 2018 2038 C1' T C 215 beta 2034 2039 2037 2058 C1' T C 216 beta 2054 2059 2057 2078 C1' T C 217 beta 2074 2079 2077 2098 C1' C C 218 beta 2094 2099 2097 2117 C1' A C 219 beta 2113 2118 2116 2138 C1' C C 220 beta 2134 2139 2137 2157 C1' T C 221 beta 2153 2158 2156 2177 C1' T C 222 beta 2173 2178 2176 2197 C1' C C 223 beta 2193 2198 2196 2216 C1' T C 224 beta 2212 2217 2215 2236 C1' C C 225 beta 2232 2237 2235 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1724 C2' G C 200 1725 1722 1746 C2' A C 201 1747 1744 1767 C2' G C 202 1768 1765 1789 C2' A C 203 1790 1787 1810 C2' A C 204 1811 1808 1831 C2' G C 205 1832 1829 1853 C2' T C 206 1854 1851 1873 C2' G C 207 1874 1871 1895 C2' A C 208 1896 1893 1916 C2' A C 209 1917 1914 1937 C2' A C 210 1938 1935 1958 C2' G C 211 1959 1956 1980 C2' T C 212 1981 1978 1997 C2' A C 213 1998 1995 2018 C2' C C 214 2019 2016 2037 C2' T C 215 2038 2035 2057 C2' T C 216 2058 2055 2077 C2' T C 217 2078 2075 2097 C2' C C 218 2098 2095 2116 C2' A C 219 2117 2114 2137 C2' C C 220 2138 2135 2156 C2' T C 221 2157 2154 2176 C2' T C 222 2177 2174 2196 C2' C C 223 2197 2194 2215 C2' T C 224 2216 2213 2235 C2' C C 225 2236 2233 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1722 C3' G C 200 OK 1720 1723 1724 1744 C3' A C 201 OK 1742 1745 1746 1765 C3' G C 202 OK 1763 1766 1767 1787 C3' A C 203 OK 1785 1788 1789 1808 C3' A C 204 OK 1806 1809 1810 1829 C3' G C 205 OK 1827 1830 1831 1851 C3' T C 206 OK 1849 1852 1853 1871 C3' G C 207 OK 1869 1872 1873 1893 C3' A C 208 OK 1891 1894 1895 1914 C3' A C 209 OK 1912 1915 1916 1935 C3' A C 210 OK 1933 1936 1937 1956 C3' G C 211 OK 1954 1957 1958 1978 C3' T C 212 OK 1976 1979 1980 1995 C3' A C 213 OK 1993 1996 1997 2016 C3' C C 214 OK 2014 2017 2018 2035 C3' T C 215 OK 2033 2036 2037 2055 C3' T C 216 OK 2053 2056 2057 2075 C3' T C 217 OK 2073 2076 2077 2095 C3' C C 218 OK 2093 2096 2097 2114 C3' A C 219 OK 2112 2115 2116 2135 C3' C C 220 OK 2133 2136 2137 2154 C3' T C 221 OK 2152 2155 2156 2174 C3' T C 222 OK 2172 2175 2176 2194 C3' C C 223 OK 2192 2195 2196 2213 C3' T C 224 OK 2211 2214 2215 2233 C3' C C 225 OK 2231 2234 2235 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1720 C4' G C 200 OK 1722 1719 1721 1742 C4' A C 201 OK 1744 1741 1743 1763 C4' G C 202 OK 1765 1762 1764 1785 C4' A C 203 OK 1787 1784 1786 1806 C4' A C 204 OK 1808 1805 1807 1827 C4' G C 205 OK 1829 1826 1828 1849 C4' T C 206 OK 1851 1848 1850 1869 C4' G C 207 OK 1871 1868 1870 1891 C4' A C 208 OK 1893 1890 1892 1912 C4' A C 209 OK 1914 1911 1913 1933 C4' A C 210 OK 1935 1932 1934 1954 C4' G C 211 OK 1956 1953 1955 1976 C4' T C 212 OK 1978 1975 1977 1993 C4' A C 213 OK 1995 1992 1994 2014 C4' C C 214 OK 2016 2013 2015 2033 C4' T C 215 OK 2035 2032 2034 2053 C4' T C 216 OK 2055 2052 2054 2073 C4' T C 217 OK 2075 2072 2074 2093 C4' C C 218 OK 2095 2092 2094 2112 C4' A C 219 OK 2114 2111 2113 2133 C4' C C 220 OK 2135 2132 2134 2152 C4' T C 221 OK 2154 2151 2153 2172 C4' T C 222 OK 2174 2171 2173 2192 C4' C C 223 OK 2194 2191 2193 2211 C4' T C 224 OK 2213 2210 2212 2231 C4' C C 225 OK 2233 2230 2232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1719 C5' G C 200 1718 1720 1741 C5' A C 201 1740 1742 1762 C5' G C 202 1761 1763 1784 C5' A C 203 1783 1785 1805 C5' A C 204 1804 1806 1826 C5' G C 205 1825 1827 1848 C5' T C 206 1847 1849 1868 C5' G C 207 1867 1869 1890 C5' A C 208 1889 1891 1911 C5' A C 209 1910 1912 1932 C5' A C 210 1931 1933 1953 C5' G C 211 1952 1954 1975 C5' T C 212 1974 1976 1992 C5' A C 213 1991 1993 2013 C5' C C 214 2012 2014 2032 C5' T C 215 2031 2033 2052 C5' T C 216 2051 2053 2072 C5' T C 217 2071 2073 2092 C5' C C 218 2091 2093 2111 C5' A C 219 2110 2112 2132 C5' C C 220 2131 2133 2151 C5' T C 221 2150 2152 2171 C5' T C 222 2170 2172 2191 C5' C C 223 2190 2192 2210 C5' T C 224 2209 2211 2230 C5' C C 225 2229 2231 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1737 P A C 201 OK OK 1723 1738 1739 1740 1758 P G C 202 OK OK 1745 1759 1760 1761 1780 P A C 203 OK OK 1766 1781 1782 1783 1801 P A C 204 OK OK 1788 1802 1803 1804 1822 P G C 205 OK OK 1809 1823 1824 1825 1844 P T C 206 OK OK 1830 1845 1846 1847 1864 P G C 207 OK OK 1852 1865 1866 1867 1886 P A C 208 OK OK 1872 1887 1888 1889 1907 P A C 209 OK OK 1894 1908 1909 1910 1928 P A C 210 OK OK 1915 1929 1930 1931 1949 P G C 211 OK OK 1936 1950 1951 1952 1971 P T C 212 OK OK 1957 1972 1973 1974 2009 P C C 214 OK OK 1996 2010 2011 2012 2028 P T C 215 OK OK 2017 2029 2030 2031 2048 P T C 216 OK OK 2036 2049 2050 2051 2068 P T C 217 OK OK 2056 2069 2070 2071 2088 P C C 218 OK OK 2076 2089 2090 2091 2107 P A C 219 OK OK 2096 2108 2109 2110 2128 P C C 220 OK OK 2115 2129 2130 2131 2147 P T C 221 OK OK 2136 2148 2149 2150 2167 P T C 222 OK OK 2155 2168 2169 2170 2187 P C C 223 OK OK 2175 2188 2189 2190 2206 P T C 224 OK OK 2195 2207 2208 2209 2226 P C C 225 OK OK 2214 2227 2228 2229 ---------------------------------------------------------------------------------