ID code: '4ATO' 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' --------------------------------------------------------------------------------- 1401 C1' A G 1 beta 1396 1402 1399 1423 C1' A G 2 beta 1418 1424 1421 1445 C1' A G 3 beta 1440 1446 1443 1467 C1' U G 4 beta 1462 1468 1465 1487 C1' U G 5 beta 1482 1488 1485 1507 C1' G G 6 beta 1502 1508 1505 1530 C1' G G 7 beta 1525 1531 1528 1553 C1' U G 8 beta 1548 1554 1551 1573 C1' G G 9 beta 1568 1574 1571 1596 C1' U G 10 beta 1591 1597 1594 1616 C1' A G 11 beta 1611 1617 1614 1638 C1' A G 12 beta 1633 1639 1636 1660 C1' C G 13 beta 1655 1661 1658 1680 C1' C G 14 beta 1675 1681 1678 1700 C1' U G 15 beta 1695 1701 1698 1720 C1' U G 16 beta 1715 1721 1718 1740 C1' A G 17 beta 1735 1741 1738 1762 C1' C G 18 beta 1757 1763 1760 1782 C1' C G 19 beta 1777 1783 1780 1802 C1' G G 20 beta 1797 1803 1800 1825 C1' U G 21 beta 1820 1826 1823 1845 C1' A G 22 beta 1840 1846 1843 1867 C1' G G 23 beta 1862 1868 1865 1890 C1' U G 24 beta 1885 1891 1888 1910 C1' A G 25 beta 1905 1911 1908 1932 C1' G G 26 beta 1927 1933 1930 1955 C1' G G 27 beta 1950 1956 1953 1978 C1' U G 28 beta 1973 1979 1976 1998 C1' G G 29 beta 1993 1999 1996 2021 C1' C G 30 beta 2016 2022 2019 2041 C1' U G 31 beta 2036 2042 2039 2061 C1' A G 32 beta 2056 2062 2059 2083 C1' A G 33 beta 2078 2084 2081 2108 C1' A23 G 34 beta 2103 2109 2106 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1399 C2' A G 1 OK 1401 1397 1400 1421 C2' A G 2 OK 1423 1419 1422 1443 C2' A G 3 OK 1445 1441 1444 1465 C2' U G 4 OK 1467 1463 1466 1485 C2' U G 5 OK 1487 1483 1486 1505 C2' G G 6 OK 1507 1503 1506 1528 C2' G G 7 OK 1530 1526 1529 1551 C2' U G 8 OK 1553 1549 1552 1571 C2' G G 9 OK 1573 1569 1572 1594 C2' U G 10 OK 1596 1592 1595 1614 C2' A G 11 OK 1616 1612 1615 1636 C2' A G 12 OK 1638 1634 1637 1658 C2' C G 13 OK 1660 1656 1659 1678 C2' C G 14 OK 1680 1676 1679 1698 C2' U G 15 OK 1700 1696 1699 1718 C2' U G 16 OK 1720 1716 1719 1738 C2' A G 17 OK 1740 1736 1739 1760 C2' C G 18 OK 1762 1758 1761 1780 C2' C G 19 OK 1782 1778 1781 1800 C2' G G 20 OK 1802 1798 1801 1823 C2' U G 21 OK 1825 1821 1824 1843 C2' A G 22 OK 1845 1841 1844 1865 C2' G G 23 OK 1867 1863 1866 1888 C2' U G 24 OK 1890 1886 1889 1908 C2' A G 25 OK 1910 1906 1909 1930 C2' G G 26 OK 1932 1928 1931 1953 C2' G G 27 OK 1955 1951 1954 1976 C2' U G 28 OK 1978 1974 1977 1996 C2' G G 29 OK 1998 1994 1997 2019 C2' C G 30 OK 2021 2017 2020 2039 C2' U G 31 OK 2041 2037 2040 2059 C2' A G 32 OK 2061 2057 2060 2081 C2' A G 33 OK 2083 2079 2082 2106 C2' A23 G 34 OK 2108 2104 2107 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1397 C3' A G 1 OK 1395 1398 1399 1419 C3' A G 2 OK 1417 1420 1421 1441 C3' A G 3 OK 1439 1442 1443 1463 C3' U G 4 OK 1461 1464 1465 1483 C3' U G 5 OK 1481 1484 1485 1503 C3' G G 6 OK 1501 1504 1505 1526 C3' G G 7 OK 1524 1527 1528 1549 C3' U G 8 OK 1547 1550 1551 1569 C3' G G 9 OK 1567 1570 1571 1592 C3' U G 10 OK 1590 1593 1594 1612 C3' A G 11 OK 1610 1613 1614 1634 C3' A G 12 OK 1632 1635 1636 1656 C3' C G 13 OK 1654 1657 1658 1676 C3' C G 14 OK 1674 1677 1678 1696 C3' U G 15 OK 1694 1697 1698 1716 C3' U G 16 OK 1714 1717 1718 1736 C3' A G 17 OK 1734 1737 1738 1758 C3' C G 18 OK 1756 1759 1760 1778 C3' C G 19 OK 1776 1779 1780 1798 C3' G G 20 OK 1796 1799 1800 1821 C3' U G 21 OK 1819 1822 1823 1841 C3' A G 22 OK 1839 1842 1843 1863 C3' G G 23 OK 1861 1864 1865 1886 C3' U G 24 OK 1884 1887 1888 1906 C3' A G 25 OK 1904 1907 1908 1928 C3' G G 26 OK 1926 1929 1930 1951 C3' G G 27 OK 1949 1952 1953 1974 C3' U G 28 OK 1972 1975 1976 1994 C3' G G 29 OK 1992 1995 1996 2017 C3' C G 30 OK 2015 2018 2019 2037 C3' U G 31 OK 2035 2038 2039 2057 C3' A G 32 OK 2055 2058 2059 2079 C3' A G 33 OK 2077 2080 2081 2104 C3' A23 G 34 OK 2102 2105 2106 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1395 C4' A G 1 OK 1397 1394 1396 1417 C4' A G 2 OK 1419 1416 1418 1439 C4' A G 3 OK 1441 1438 1440 1461 C4' U G 4 OK 1463 1460 1462 1481 C4' U G 5 OK 1483 1480 1482 1501 C4' G G 6 OK 1503 1500 1502 1524 C4' G G 7 OK 1526 1523 1525 1547 C4' U G 8 OK 1549 1546 1548 1567 C4' G G 9 OK 1569 1566 1568 1590 C4' U G 10 OK 1592 1589 1591 1610 C4' A G 11 OK 1612 1609 1611 1632 C4' A G 12 OK 1634 1631 1633 1654 C4' C G 13 OK 1656 1653 1655 1674 C4' C G 14 OK 1676 1673 1675 1694 C4' U G 15 OK 1696 1693 1695 1714 C4' U G 16 OK 1716 1713 1715 1734 C4' A G 17 OK 1736 1733 1735 1756 C4' C G 18 OK 1758 1755 1757 1776 C4' C G 19 OK 1778 1775 1777 1796 C4' G G 20 OK 1798 1795 1797 1819 C4' U G 21 OK 1821 1818 1820 1839 C4' A G 22 OK 1841 1838 1840 1861 C4' G G 23 OK 1863 1860 1862 1884 C4' U G 24 OK 1886 1883 1885 1904 C4' A G 25 OK 1906 1903 1905 1926 C4' G G 26 OK 1928 1925 1927 1949 C4' G G 27 OK 1951 1948 1950 1972 C4' U G 28 OK 1974 1971 1973 1992 C4' G G 29 OK 1994 1991 1993 2015 C4' C G 30 OK 2017 2014 2016 2035 C4' U G 31 OK 2037 2034 2036 2055 C4' A G 32 OK 2057 2054 2056 2077 C4' A G 33 OK 2079 2076 2078 2102 C4' A23 G 34 OK 2104 2101 2103 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1394 C5' A G 1 1393 1395 1416 C5' A G 2 1415 1417 1438 C5' A G 3 1437 1439 1460 C5' U G 4 1459 1461 1480 C5' U G 5 1479 1481 1500 C5' G G 6 1499 1501 1523 C5' G G 7 1522 1524 1546 C5' U G 8 1545 1547 1566 C5' G G 9 1565 1567 1589 C5' U G 10 1588 1590 1609 C5' A G 11 1608 1610 1631 C5' A G 12 1630 1632 1653 C5' C G 13 1652 1654 1673 C5' C G 14 1672 1674 1693 C5' U G 15 1692 1694 1713 C5' U G 16 1712 1714 1733 C5' A G 17 1732 1734 1755 C5' C G 18 1754 1756 1775 C5' C G 19 1774 1776 1795 C5' G G 20 1794 1796 1818 C5' U G 21 1817 1819 1838 C5' A G 22 1837 1839 1860 C5' G G 23 1859 1861 1883 C5' U G 24 1882 1884 1903 C5' A G 25 1902 1904 1925 C5' G G 26 1924 1926 1948 C5' G G 27 1947 1949 1971 C5' U G 28 1970 1972 1991 C5' G G 29 1990 1992 2014 C5' C G 30 2013 2015 2034 C5' U G 31 2033 2035 2054 C5' A G 32 2053 2055 2076 C5' A G 33 2075 2077 2101 C5' A23 G 34 2100 2102 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1412 P A G 2 distorted distorted 1398 1413 1414 1415 1434 P A G 3 distorted distorted 1420 1435 1436 1437 1456 P U G 4 distorted distorted 1442 1457 1458 1459 1476 P U G 5 distorted distorted 1464 1477 1478 1479 1496 P G G 6 distorted distorted 1484 1497 1498 1499 1519 P G G 7 distorted distorted 1504 1520 1521 1522 1542 P U G 8 distorted distorted 1527 1543 1544 1545 1562 P G G 9 distorted distorted 1550 1563 1564 1565 1585 P U G 10 distorted distorted 1570 1586 1587 1588 1605 P A G 11 distorted distorted 1593 1606 1607 1608 1627 P A G 12 distorted distorted 1613 1628 1629 1630 1649 P C G 13 distorted distorted 1635 1650 1651 1652 1669 P C G 14 distorted distorted 1657 1670 1671 1672 1689 P U G 15 distorted distorted 1677 1690 1691 1692 1709 P U G 16 distorted distorted 1697 1710 1711 1712 1729 P A G 17 distorted distorted 1717 1730 1731 1732 1751 P C G 18 distorted distorted 1737 1752 1753 1754 1771 P C G 19 distorted distorted 1759 1772 1773 1774 1791 P G G 20 distorted distorted 1779 1792 1793 1794 1814 P U G 21 distorted distorted 1799 1815 1816 1817 1834 P A G 22 distorted distorted 1822 1835 1836 1837 1856 P G G 23 distorted distorted 1842 1857 1858 1859 1879 P U G 24 distorted distorted 1864 1880 1881 1882 1899 P A G 25 distorted distorted 1887 1900 1901 1902 1921 P G G 26 distorted distorted 1907 1922 1923 1924 1944 P G G 27 distorted distorted 1929 1945 1946 1947 1967 P U G 28 distorted distorted 1952 1968 1969 1970 1987 P G G 29 distorted distorted 1975 1988 1989 1990 2010 P C G 30 distorted distorted 1995 2011 2012 2013 2030 P U G 31 distorted distorted 2018 2031 2032 2033 2050 P A G 32 distorted distorted 2038 2051 2052 2053 2072 P A G 33 distorted distorted 2058 2073 2074 2075 2097 P A23 G 34 distorted distorted 2080 2098 2099 2100 ---------------------------------------------------------------------------------