ID code: '2RRA' 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' --------------------------------------------------------------------------------- 1543 C1' G B 1 alpha beta 1538 1561 1544 1541 1578 C1' A B 2 alpha beta 1573 1595 1579 1576 1611 C1' A B 3 alpha beta 1606 1628 1612 1609 1644 C1' G B 4 alpha beta 1639 1662 1645 1642 1678 C1' A B 5 alpha beta 1673 1695 1679 1676 1711 C1' A B 6 alpha beta 1706 1729 1712 1709 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1541 C2' G B 1 OK OK 1543 1539 1559 1542 1576 C2' A B 2 OK OK 1578 1574 1593 1577 1609 C2' A B 3 OK OK 1611 1607 1626 1610 1642 C2' G B 4 OK OK 1644 1640 1660 1643 1676 C2' A B 5 OK OK 1678 1674 1693 1677 1709 C2' A B 6 OK OK 1711 1707 1727 1710 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1539 C3' G B 1 OK OK 1537 1558 1540 1541 1574 C3' A B 2 OK OK 1572 1592 1575 1576 1607 C3' A B 3 OK OK 1605 1625 1608 1609 1640 C3' G B 4 OK OK 1638 1659 1641 1642 1674 C3' A B 5 OK OK 1672 1692 1675 1676 1707 C3' A B 6 OK OK 1705 1725 1708 1709 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1537 C4' G B 1 OK OK 1539 1557 1536 1538 1572 C4' A B 2 OK OK 1574 1591 1571 1573 1605 C4' A B 3 OK OK 1607 1624 1604 1606 1638 C4' G B 4 OK OK 1640 1658 1637 1639 1672 C4' A B 5 OK OK 1674 1691 1671 1673 1705 C4' A B 6 OK OK 1707 1724 1704 1706 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1536 C5' G B 1 OK OK 1535 1555 1556 1537 1571 C5' A B 2 OK OK 1570 1589 1590 1572 1604 C5' A B 3 OK OK 1603 1622 1623 1605 1637 C5' G B 4 OK OK 1636 1656 1657 1638 1671 C5' A B 5 OK OK 1670 1689 1690 1672 1704 C5' A B 6 OK OK 1703 1722 1723 1705 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1567 P A B 2 distorted distorted 1540 1568 1569 1570 1600 P A B 3 distorted distorted 1575 1601 1602 1603 1633 P G B 4 distorted distorted 1608 1634 1635 1636 1667 P A B 5 distorted distorted 1641 1668 1669 1670 1700 P A B 6 distorted distorted 1675 1701 1702 1703 ---------------------------------------------------------------------------------