ID code: '2LEC' 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' G B 103 alpha beta 1640 1663 1646 1643 1679 C1' G B 104 alpha beta 1674 1697 1680 1677 1713 C1' A B 105 alpha beta 1708 1730 1714 1711 1746 C1' G B 106 alpha beta 1741 1764 1747 1744 1780 C1' U B 107 alpha beta 1775 1796 1781 1778 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G B 103 OK OK 1645 1641 1661 1644 1677 C2' G B 104 OK OK 1679 1675 1695 1678 1711 C2' A B 105 OK OK 1713 1709 1728 1712 1744 C2' G B 106 OK OK 1746 1742 1762 1745 1778 C2' U B 107 OK OK 1780 1776 1794 1779 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1610 C3' U B 102 OK OK 1608 1626 1611 1612 1641 C3' G B 103 OK OK 1639 1660 1642 1643 1675 C3' G B 104 OK OK 1673 1694 1676 1677 1709 C3' A B 105 OK OK 1707 1727 1710 1711 1742 C3' G B 106 OK OK 1740 1761 1743 1744 1776 C3' U B 107 OK OK 1774 1792 1777 1778 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1608 C4' U B 102 OK OK 1610 1625 1607 1609 1639 C4' G B 103 OK OK 1641 1659 1638 1640 1673 C4' G B 104 OK OK 1675 1693 1672 1674 1707 C4' A B 105 OK OK 1709 1726 1706 1708 1740 C4' G B 106 OK OK 1742 1760 1739 1741 1774 C4' U B 107 OK OK 1776 1791 1773 1775 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G B 103 OK OK 1637 1657 1658 1639 1672 C5' G B 104 OK OK 1671 1691 1692 1673 1706 C5' A B 105 OK OK 1705 1724 1725 1707 1739 C5' G B 106 OK OK 1738 1758 1759 1740 1773 C5' U B 107 OK OK 1772 1789 1790 1774 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1634 P G B 103 distorted distorted 1611 1635 1636 1637 1668 P G B 104 distorted distorted 1642 1669 1670 1671 1702 P A B 105 distorted distorted 1676 1703 1704 1705 1735 P G B 106 distorted distorted 1710 1736 1737 1738 1769 P U B 107 distorted distorted 1743 1770 1771 1772 ---------------------------------------------------------------------------------