ID code: '3AHU' 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' --------------------------------------------------------------------------------- 1641 C1' A X 1 beta 1636 1642 1639 1663 C1' G X 2 beta 1658 1664 1661 1686 C1' A X 3 beta 1681 1687 1684 1708 C1' G X 4 beta 1703 1709 1706 1731 C1' A X 5 beta 1726 1732 1729 1753 C1' G X 6 beta 1748 1754 1751 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1639 C2' A X 1 OK 1641 1637 1640 1661 C2' G X 2 OK 1663 1659 1662 1684 C2' A X 3 OK 1686 1682 1685 1706 C2' G X 4 OK 1708 1704 1707 1729 C2' A X 5 OK 1731 1727 1730 1751 C2' G X 6 OK 1753 1749 1752 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1637 C3' A X 1 OK 1635 1638 1639 1659 C3' G X 2 OK 1657 1660 1661 1682 C3' A X 3 OK 1680 1683 1684 1704 C3' G X 4 OK 1702 1705 1706 1727 C3' A X 5 OK 1725 1728 1729 1749 C3' G X 6 OK 1747 1750 1751 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1635 C4' A X 1 OK 1637 1634 1636 1657 C4' G X 2 OK 1659 1656 1658 1680 C4' A X 3 OK 1682 1679 1681 1702 C4' G X 4 OK 1704 1701 1703 1725 C4' A X 5 OK 1727 1724 1726 1747 C4' G X 6 OK 1749 1746 1748 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1634 C5' A X 1 1633 1635 1656 C5' G X 2 1655 1657 1679 C5' A X 3 1678 1680 1701 C5' G X 4 1700 1702 1724 C5' A X 5 1723 1725 1746 C5' G X 6 1745 1747 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1652 P G X 2 distorted distorted 1638 1653 1654 1655 1675 P A X 3 distorted distorted 1660 1676 1677 1678 1697 P G X 4 distorted distorted 1683 1698 1699 1700 1720 P A X 5 distorted distorted 1705 1721 1722 1723 1742 P G X 6 distorted distorted 1728 1743 1744 1745 ---------------------------------------------------------------------------------