ID code: '2XC7' 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' --------------------------------------------------------------------------------- 1609 C1' A P 600 alpha beta 1604 1625 1610 1607 1642 C1' U P 601 alpha beta 1637 1656 1643 1640 1671 C1' C P 602 alpha beta 1666 1685 1672 1669 1701 C1' G P 603 alpha beta 1696 1719 1702 1699 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1607 C2' A P 600 OK OK 1609 1605 1624 1608 1640 C2' U P 601 OK OK 1642 1638 1655 1641 1669 C2' C P 602 OK OK 1671 1667 1684 1670 1699 C2' G P 603 OK OK 1701 1697 1718 1700 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1605 C3' A P 600 OK OK 1603 1623 1606 1607 1638 C3' U P 601 OK OK 1636 1654 1639 1640 1667 C3' C P 602 OK OK 1665 1683 1668 1669 1697 C3' G P 603 OK OK 1695 1716 1698 1699 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1603 C4' A P 600 OK OK 1605 1622 1602 1604 1636 C4' U P 601 OK OK 1638 1653 1635 1637 1665 C4' C P 602 OK OK 1667 1682 1664 1666 1695 C4' G P 603 OK OK 1697 1715 1694 1696 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1602 C5' A P 600 distorted distorted 1601 1620 1621 1603 1635 C5' U P 601 distorted distorted 1634 1651 1652 1636 1664 C5' C P 602 OK OK 1663 1680 1681 1665 1694 C5' G P 603 OK OK 1693 1713 1714 1695 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1631 P U P 601 OK OK 1606 1632 1633 1634 1660 P C P 602 distorted distorted 1639 1661 1662 1663 1690 P G P 603 OK OK 1668 1691 1692 1693 ---------------------------------------------------------------------------------