ID code: '2Y8Y' 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' --------------------------------------------------------------------------------- 1603 C1' U B 5 beta 1598 1604 1601 1623 C1' C B 6 beta 1618 1624 1621 1643 C1' C B 7 beta 1638 1644 1641 1663 C1' C B 8 beta 1658 1664 1661 1683 C1' C B 9 beta 1678 1684 1681 1703 C1' A B 10 beta 1698 1704 1701 1725 C1' C B 11 beta 1720 1726 1723 1745 C1' G B 12 beta 1740 1746 1743 1768 C1' C B 13 beta 1763 1769 1766 1788 C1' G B 14 beta 1783 1789 1786 1811 C1' U B 15 beta 1806 1812 1809 1831 C1' G B 16 beta 1826 1832 1829 1854 C1' U B 17 beta 1849 1855 1852 1874 C1' G B 18 beta 1869 1875 1872 1897 C1' G B 19 beta 1892 1898 1895 1920 C1' G B 20 beta 1915 1921 1918 1942 C1' DG B 21 beta 1938 1943 1941 1965 C1' A B 22 beta 1960 1966 1963 1987 C1' U B 23 beta 1982 1988 1985 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1601 C2' U B 5 OK 1603 1599 1602 1621 C2' C B 6 OK 1623 1619 1622 1641 C2' C B 7 OK 1643 1639 1642 1661 C2' C B 8 OK 1663 1659 1662 1681 C2' C B 9 OK 1683 1679 1682 1701 C2' A B 10 OK 1703 1699 1702 1723 C2' C B 11 OK 1725 1721 1724 1743 C2' G B 12 OK 1745 1741 1744 1766 C2' C B 13 OK 1768 1764 1767 1786 C2' G B 14 OK 1788 1784 1787 1809 C2' U B 15 OK 1811 1807 1810 1829 C2' G B 16 OK 1831 1827 1830 1852 C2' U B 17 OK 1854 1850 1853 1872 C2' G B 18 OK 1874 1870 1873 1895 C2' G B 19 OK 1897 1893 1896 1918 C2' G B 20 OK 1920 1916 1919 1941 C2' DG B 21 1942 1939 1963 C2' A B 22 OK 1965 1961 1964 1985 C2' U B 23 OK 1987 1983 1986 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1599 C3' U B 5 OK 1597 1600 1601 1619 C3' C B 6 OK 1617 1620 1621 1639 C3' C B 7 OK 1637 1640 1641 1659 C3' C B 8 OK 1657 1660 1661 1679 C3' C B 9 OK 1677 1680 1681 1699 C3' A B 10 OK 1697 1700 1701 1721 C3' C B 11 OK 1719 1722 1723 1741 C3' G B 12 OK 1739 1742 1743 1764 C3' C B 13 OK 1762 1765 1766 1784 C3' G B 14 OK 1782 1785 1786 1807 C3' U B 15 OK 1805 1808 1809 1827 C3' G B 16 OK 1825 1828 1829 1850 C3' U B 17 OK 1848 1851 1852 1870 C3' G B 18 OK 1868 1871 1872 1893 C3' G B 19 OK 1891 1894 1895 1916 C3' G B 20 OK 1914 1917 1918 1939 C3' DG B 21 OK 1937 1940 1941 1961 C3' A B 22 OK 1959 1962 1963 1983 C3' U B 23 OK 1981 1984 1985 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1597 C4' U B 5 OK 1599 1596 1598 1617 C4' C B 6 OK 1619 1616 1618 1637 C4' C B 7 OK 1639 1636 1638 1657 C4' C B 8 OK 1659 1656 1658 1677 C4' C B 9 OK 1679 1676 1678 1697 C4' A B 10 OK 1699 1696 1698 1719 C4' C B 11 OK 1721 1718 1720 1739 C4' G B 12 OK 1741 1738 1740 1762 C4' C B 13 OK 1764 1761 1763 1782 C4' G B 14 OK 1784 1781 1783 1805 C4' U B 15 OK 1807 1804 1806 1825 C4' G B 16 OK 1827 1824 1826 1848 C4' U B 17 OK 1850 1847 1849 1868 C4' G B 18 OK 1870 1867 1869 1891 C4' G B 19 OK 1893 1890 1892 1914 C4' G B 20 OK 1916 1913 1915 1937 C4' DG B 21 OK 1939 1936 1938 1959 C4' A B 22 OK 1961 1958 1960 1981 C4' U B 23 OK 1983 1980 1982 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1596 C5' U B 5 1595 1597 1616 C5' C B 6 1615 1617 1636 C5' C B 7 1635 1637 1656 C5' C B 8 1655 1657 1676 C5' C B 9 1675 1677 1696 C5' A B 10 1695 1697 1718 C5' C B 11 1717 1719 1738 C5' G B 12 1737 1739 1761 C5' C B 13 1760 1762 1781 C5' G B 14 1780 1782 1804 C5' U B 15 1803 1805 1824 C5' G B 16 1823 1825 1847 C5' U B 17 1846 1848 1867 C5' G B 18 1866 1868 1890 C5' G B 19 1889 1891 1913 C5' G B 20 1912 1914 1936 C5' DG B 21 1935 1937 1958 C5' A B 22 1957 1959 1980 C5' U B 23 1979 1981 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1612 P C B 6 distorted distorted 1600 1613 1614 1615 1632 P C B 7 distorted distorted 1620 1633 1634 1635 1652 P C B 8 distorted distorted 1640 1653 1654 1655 1672 P C B 9 distorted distorted 1660 1673 1674 1675 1692 P A B 10 distorted distorted 1680 1693 1694 1695 1714 P C B 11 distorted distorted 1700 1715 1716 1717 1734 P G B 12 distorted distorted 1722 1735 1736 1737 1757 P C B 13 distorted distorted 1742 1758 1759 1760 1777 P G B 14 OK OK 1765 1778 1779 1780 1800 P U B 15 distorted distorted 1785 1801 1802 1803 1820 P G B 16 distorted distorted 1808 1821 1822 1823 1843 P U B 17 distorted distorted 1828 1844 1845 1846 1863 P G B 18 distorted distorted 1851 1864 1865 1866 1886 P G B 19 distorted distorted 1871 1887 1888 1889 1909 P G B 20 distorted distorted 1894 1910 1911 1912 1932 P DG B 21 distorted distorted 1917 1933 1934 1935 1954 P A B 22 OK OK 1940 1955 1956 1957 1976 P U B 23 distorted distorted 1962 1977 1978 1979 ---------------------------------------------------------------------------------