ID code: '2LEB' 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' --------------------------------------------------------------------------------- 1614 C1' U B 102 alpha beta 1609 1629 1615 1612 1645 C1' C B 103 alpha beta 1640 1660 1646 1643 1676 C1' C B 104 alpha beta 1671 1691 1677 1674 1707 C1' A B 105 alpha beta 1702 1724 1708 1705 1740 C1' G B 106 alpha beta 1735 1758 1741 1738 1774 C1' U B 107 alpha beta 1769 1790 1775 1772 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1612 C2' U B 102 OK OK 1614 1610 1627 1613 1643 C2' C B 103 OK OK 1645 1641 1658 1644 1674 C2' C B 104 OK OK 1676 1672 1689 1675 1705 C2' A B 105 OK OK 1707 1703 1722 1706 1738 C2' G B 106 OK OK 1740 1736 1756 1739 1772 C2' U B 107 OK OK 1774 1770 1788 1773 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1610 C3' U B 102 OK OK 1608 1626 1611 1612 1641 C3' C B 103 OK OK 1639 1657 1642 1643 1672 C3' C B 104 OK OK 1670 1688 1673 1674 1703 C3' A B 105 OK OK 1701 1721 1704 1705 1736 C3' G B 106 OK OK 1734 1755 1737 1738 1770 C3' U B 107 OK OK 1768 1786 1771 1772 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1608 C4' U B 102 OK OK 1610 1625 1607 1609 1639 C4' C B 103 OK OK 1641 1656 1638 1640 1670 C4' C B 104 OK OK 1672 1687 1669 1671 1701 C4' A B 105 OK OK 1703 1720 1700 1702 1734 C4' G B 106 OK OK 1736 1754 1733 1735 1768 C4' U B 107 OK OK 1770 1785 1767 1769 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1607 C5' U B 102 OK OK 1606 1623 1624 1608 1638 C5' C B 103 OK OK 1637 1654 1655 1639 1669 C5' C B 104 OK OK 1668 1685 1686 1670 1700 C5' A B 105 OK OK 1699 1718 1719 1701 1733 C5' G B 106 OK OK 1732 1752 1753 1734 1767 C5' U B 107 OK OK 1766 1783 1784 1768 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1634 P C B 103 distorted distorted 1611 1635 1636 1637 1665 P C B 104 distorted distorted 1642 1666 1667 1668 1696 P A B 105 distorted distorted 1673 1697 1698 1699 1729 P G B 106 distorted distorted 1704 1730 1731 1732 1763 P U B 107 distorted distorted 1737 1764 1765 1766 ---------------------------------------------------------------------------------