ID code: '3GIB' 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' --------------------------------------------------------------------------------- 1535 C1' A H 1 beta 1530 1536 1533 1557 C1' A H 2 beta 1552 1558 1555 1579 C1' A H 3 beta 1574 1580 1577 1601 C1' A H 4 beta 1596 1602 1599 1623 C1' A H 5 beta 1618 1624 1621 1645 C1' A H 6 beta 1640 1646 1643 1667 C1' A H 7 beta 1662 1668 1665 1689 C1' A H 8 beta 1684 1690 1687 1711 C1' A H 9 beta 1706 1712 1709 1725 C1' NHE A 70 1724 1738 C1' NHE A 71 1737 1751 C1' NHE C 70 1750 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1533 C2' A H 1 OK 1535 1531 1534 1555 C2' A H 2 OK 1557 1553 1556 1577 C2' A H 3 OK 1579 1575 1578 1599 C2' A H 4 OK 1601 1597 1600 1621 C2' A H 5 OK 1623 1619 1622 1643 C2' A H 6 OK 1645 1641 1644 1665 C2' A H 7 OK 1667 1663 1666 1687 C2' A H 8 OK 1689 1685 1688 1709 C2' A H 9 OK 1711 1707 1710 1724 C2' NHE A 70 1725 1723 1737 C2' NHE A 71 1738 1736 1750 C2' NHE C 70 1751 1749 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1531 C3' A H 1 OK 1529 1532 1533 1553 C3' A H 2 OK 1551 1554 1555 1575 C3' A H 3 OK 1573 1576 1577 1597 C3' A H 4 OK 1595 1598 1599 1619 C3' A H 5 OK 1617 1620 1621 1641 C3' A H 6 OK 1639 1642 1643 1663 C3' A H 7 OK 1661 1664 1665 1685 C3' A H 8 OK 1683 1686 1687 1707 C3' A H 9 OK 1705 1708 1709 1723 C3' NHE A 70 1735 1724 1736 C3' NHE A 71 1748 1737 1749 C3' NHE C 70 1761 1750 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1529 C4' A H 1 OK 1531 1528 1530 1551 C4' A H 2 OK 1553 1550 1552 1573 C4' A H 3 OK 1575 1572 1574 1595 C4' A H 4 OK 1597 1594 1596 1617 C4' A H 5 OK 1619 1616 1618 1639 C4' A H 6 OK 1641 1638 1640 1661 C4' A H 7 OK 1663 1660 1662 1683 C4' A H 8 OK 1685 1682 1684 1705 C4' A H 9 OK 1707 1704 1706 1735 C4' NHE A 70 1723 1747 1748 C4' NHE A 71 1736 1747 1761 C4' NHE C 70 1749 1760 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1528 C5' A H 1 1527 1529 1550 C5' A H 2 1549 1551 1572 C5' A H 3 1571 1573 1594 C5' A H 4 1593 1595 1616 C5' A H 5 1615 1617 1638 C5' A H 6 1637 1639 1660 C5' A H 7 1659 1661 1682 C5' A H 8 1681 1683 1704 C5' A H 9 1703 1705 1734 C5' NHE A 70 1735 1747 C5' NHE A 71 1748 1760 C5' NHE C 70 1761 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1524 P A H 1 distorted distorted 1525 1526 1527 1546 P A H 2 distorted distorted 1532 1547 1548 1549 1568 P A H 3 distorted distorted 1554 1569 1570 1571 1590 P A H 4 distorted distorted 1576 1591 1592 1593 1612 P A H 5 distorted distorted 1598 1613 1614 1615 1634 P A H 6 distorted distorted 1620 1635 1636 1637 1656 P A H 7 distorted distorted 1642 1657 1658 1659 1678 P A H 8 distorted distorted 1664 1679 1680 1681 1700 P A H 9 distorted distorted 1686 1701 1702 1703 ---------------------------------------------------------------------------------