ID code: '2KFY' 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' --------------------------------------------------------------------------------- 1581 C1' A B 1 alpha beta 1576 1598 1582 1579 1615 C1' G B 2 alpha beta 1610 1633 1616 1613 1649 C1' G B 3 alpha beta 1644 1667 1650 1647 1683 C1' G B 4 alpha beta 1678 1701 1684 1681 1717 C1' A B 5 alpha beta 1712 1734 1718 1715 1750 C1' U B 6 alpha beta 1745 1766 1751 1748 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1579 C2' A B 1 OK OK 1581 1577 1596 1580 1613 C2' G B 2 OK OK 1615 1611 1631 1614 1647 C2' G B 3 OK OK 1649 1645 1665 1648 1681 C2' G B 4 OK OK 1683 1679 1699 1682 1715 C2' A B 5 OK OK 1717 1713 1732 1716 1748 C2' U B 6 OK OK 1750 1746 1764 1749 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1577 C3' A B 1 OK OK 1575 1595 1578 1579 1611 C3' G B 2 OK OK 1609 1630 1612 1613 1645 C3' G B 3 OK OK 1643 1664 1646 1647 1679 C3' G B 4 OK OK 1677 1698 1680 1681 1713 C3' A B 5 OK OK 1711 1731 1714 1715 1746 C3' U B 6 OK OK 1744 1762 1747 1748 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1575 C4' A B 1 OK OK 1577 1594 1574 1576 1609 C4' G B 2 OK OK 1611 1629 1608 1610 1643 C4' G B 3 OK OK 1645 1663 1642 1644 1677 C4' G B 4 OK OK 1679 1697 1676 1678 1711 C4' A B 5 OK OK 1713 1730 1710 1712 1744 C4' U B 6 OK OK 1746 1761 1743 1745 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1574 C5' A B 1 OK OK 1573 1592 1593 1575 1608 C5' G B 2 OK OK 1607 1627 1628 1609 1642 C5' G B 3 OK OK 1641 1661 1662 1643 1676 C5' G B 4 OK OK 1675 1695 1696 1677 1710 C5' A B 5 OK OK 1709 1728 1729 1711 1743 C5' U B 6 OK OK 1742 1759 1760 1744 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1604 P G B 2 distorted distorted 1578 1605 1606 1607 1638 P G B 3 distorted distorted 1612 1639 1640 1641 1672 P G B 4 distorted distorted 1646 1673 1674 1675 1706 P A B 5 distorted distorted 1680 1707 1708 1709 1739 P U B 6 distorted distorted 1714 1740 1741 1742 ---------------------------------------------------------------------------------