ID code: '2AD9' 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' --------------------------------------------------------------------------------- 1545 C1' C B 147 alpha beta 1540 1560 1546 1543 1577 C1' U B 148 alpha beta 1572 1592 1578 1575 1607 C1' C B 149 alpha beta 1602 1622 1608 1605 1638 C1' U B 150 alpha beta 1633 1653 1639 1636 1668 C1' C B 151 alpha beta 1663 1683 1669 1666 1699 C1' U B 152 alpha beta 1694 1715 1700 1697 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1543 C2' C B 147 OK OK 1545 1541 1558 1544 1575 C2' U B 148 OK OK 1577 1573 1590 1576 1605 C2' C B 149 OK OK 1607 1603 1620 1606 1636 C2' U B 150 OK OK 1638 1634 1651 1637 1666 C2' C B 151 OK OK 1668 1664 1681 1667 1697 C2' U B 152 OK OK 1699 1695 1713 1698 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1541 C3' C B 147 OK OK 1539 1557 1542 1543 1573 C3' U B 148 OK OK 1571 1589 1574 1575 1603 C3' C B 149 OK OK 1601 1619 1604 1605 1634 C3' U B 150 OK OK 1632 1650 1635 1636 1664 C3' C B 151 OK OK 1662 1680 1665 1666 1695 C3' U B 152 OK OK 1693 1711 1696 1697 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1539 C4' C B 147 OK OK 1541 1556 1538 1540 1571 C4' U B 148 OK OK 1573 1588 1570 1572 1601 C4' C B 149 OK OK 1603 1618 1600 1602 1632 C4' U B 150 OK OK 1634 1649 1631 1633 1662 C4' C B 151 OK OK 1664 1679 1661 1663 1693 C4' U B 152 OK OK 1695 1710 1692 1694 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1538 C5' C B 147 OK OK 1537 1554 1555 1539 1570 C5' U B 148 OK OK 1569 1586 1587 1571 1600 C5' C B 149 OK OK 1599 1616 1617 1601 1631 C5' U B 150 OK OK 1630 1647 1648 1632 1661 C5' C B 151 OK OK 1660 1677 1678 1662 1692 C5' U B 152 OK OK 1691 1708 1709 1693 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1566 P U B 148 distorted distorted 1542 1567 1568 1569 1596 P C B 149 distorted distorted 1574 1597 1598 1599 1627 P U B 150 distorted distorted 1604 1628 1629 1630 1657 P C B 151 distorted distorted 1635 1658 1659 1660 1688 P U B 152 distorted distorted 1665 1689 1690 1691 ---------------------------------------------------------------------------------