ID code: '2GLI' 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' --------------------------------------------------------------------------------- 1299 C1' T C 2 beta 1295 1300 1298 1319 C1' T C 3 beta 1315 1320 1318 1339 C1' C C 4 beta 1335 1340 1338 1358 C1' G C 5 beta 1354 1359 1357 1380 C1' T C 6 beta 1376 1381 1379 1400 C1' C C 7 beta 1396 1401 1399 1419 C1' T C 8 beta 1415 1420 1418 1439 C1' T C 9 beta 1435 1440 1438 1459 C1' G C 10 beta 1455 1460 1458 1481 C1' G C 11 beta 1477 1482 1480 1503 C1' G C 12 beta 1499 1504 1502 1525 C1' T C 13 beta 1521 1526 1524 1545 C1' G C 14 beta 1541 1546 1544 1567 C1' G C 15 beta 1563 1568 1566 1589 C1' T C 16 beta 1585 1590 1588 1609 C1' C C 17 beta 1605 1610 1608 1628 C1' C C 18 beta 1624 1629 1627 1647 C1' A C 19 beta 1643 1648 1646 1668 C1' C C 20 beta 1664 1669 1667 1687 C1' G C 21 beta 1683 1688 1686 1728 C1' C D 52 beta 1724 1729 1727 1747 C1' G D 53 beta 1743 1748 1746 1769 C1' T D 54 beta 1765 1770 1768 1789 C1' G D 55 beta 1785 1790 1788 1811 C1' G D 56 beta 1807 1812 1810 1833 C1' A D 57 beta 1829 1834 1832 1854 C1' C D 58 beta 1850 1855 1853 1873 C1' C D 59 beta 1869 1874 1872 1892 C1' A D 60 beta 1888 1893 1891 1913 C1' C D 61 beta 1909 1914 1912 1932 C1' C D 62 beta 1928 1933 1931 1951 C1' C D 63 beta 1947 1952 1950 1970 C1' A D 64 beta 1966 1971 1969 1991 C1' A D 65 beta 1987 1992 1990 2012 C1' G D 66 beta 2008 2013 2011 2034 C1' A D 67 beta 2030 2035 2033 2055 C1' C D 68 beta 2051 2056 2054 2074 C1' G D 69 beta 2070 2075 2073 2096 C1' A D 70 beta 2092 2097 2095 2117 C1' A D 71 beta 2113 2118 2116 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1298 C2' T C 2 1299 1296 1318 C2' T C 3 1319 1316 1338 C2' C C 4 1339 1336 1357 C2' G C 5 1358 1355 1379 C2' T C 6 1380 1377 1399 C2' C C 7 1400 1397 1418 C2' T C 8 1419 1416 1438 C2' T C 9 1439 1436 1458 C2' G C 10 1459 1456 1480 C2' G C 11 1481 1478 1502 C2' G C 12 1503 1500 1524 C2' T C 13 1525 1522 1544 C2' G C 14 1545 1542 1566 C2' G C 15 1567 1564 1588 C2' T C 16 1589 1586 1608 C2' C C 17 1609 1606 1627 C2' C C 18 1628 1625 1646 C2' A C 19 1647 1644 1667 C2' C C 20 1668 1665 1686 C2' G C 21 1687 1684 1727 C2' C D 52 1728 1725 1746 C2' G D 53 1747 1744 1768 C2' T D 54 1769 1766 1788 C2' G D 55 1789 1786 1810 C2' G D 56 1811 1808 1832 C2' A D 57 1833 1830 1853 C2' C D 58 1854 1851 1872 C2' C D 59 1873 1870 1891 C2' A D 60 1892 1889 1912 C2' C D 61 1913 1910 1931 C2' C D 62 1932 1929 1950 C2' C D 63 1951 1948 1969 C2' A D 64 1970 1967 1990 C2' A D 65 1991 1988 2011 C2' G D 66 2012 2009 2033 C2' A D 67 2034 2031 2054 C2' C D 68 2055 2052 2073 C2' G D 69 2074 2071 2095 C2' A D 70 2096 2093 2116 C2' A D 71 2117 2114 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1296 C3' T C 2 OK 1294 1297 1298 1316 C3' T C 3 OK 1314 1317 1318 1336 C3' C C 4 OK 1334 1337 1338 1355 C3' G C 5 OK 1353 1356 1357 1377 C3' T C 6 OK 1375 1378 1379 1397 C3' C C 7 OK 1395 1398 1399 1416 C3' T C 8 OK 1414 1417 1418 1436 C3' T C 9 OK 1434 1437 1438 1456 C3' G C 10 OK 1454 1457 1458 1478 C3' G C 11 OK 1476 1479 1480 1500 C3' G C 12 OK 1498 1501 1502 1522 C3' T C 13 OK 1520 1523 1524 1542 C3' G C 14 OK 1540 1543 1544 1564 C3' G C 15 OK 1562 1565 1566 1586 C3' T C 16 OK 1584 1587 1588 1606 C3' C C 17 OK 1604 1607 1608 1625 C3' C C 18 OK 1623 1626 1627 1644 C3' A C 19 OK 1642 1645 1646 1665 C3' C C 20 OK 1663 1666 1667 1684 C3' G C 21 OK 1682 1685 1686 1725 C3' C D 52 OK 1723 1726 1727 1744 C3' G D 53 OK 1742 1745 1746 1766 C3' T D 54 OK 1764 1767 1768 1786 C3' G D 55 OK 1784 1787 1788 1808 C3' G D 56 OK 1806 1809 1810 1830 C3' A D 57 OK 1828 1831 1832 1851 C3' C D 58 OK 1849 1852 1853 1870 C3' C D 59 OK 1868 1871 1872 1889 C3' A D 60 OK 1887 1890 1891 1910 C3' C D 61 OK 1908 1911 1912 1929 C3' C D 62 OK 1927 1930 1931 1948 C3' C D 63 OK 1946 1949 1950 1967 C3' A D 64 OK 1965 1968 1969 1988 C3' A D 65 OK 1986 1989 1990 2009 C3' G D 66 OK 2007 2010 2011 2031 C3' A D 67 OK 2029 2032 2033 2052 C3' C D 68 OK 2050 2053 2054 2071 C3' G D 69 OK 2069 2072 2073 2093 C3' A D 70 OK 2091 2094 2095 2114 C3' A D 71 OK 2112 2115 2116 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1294 C4' T C 2 OK 1296 1293 1295 1314 C4' T C 3 OK 1316 1313 1315 1334 C4' C C 4 OK 1336 1333 1335 1353 C4' G C 5 OK 1355 1352 1354 1375 C4' T C 6 OK 1377 1374 1376 1395 C4' C C 7 OK 1397 1394 1396 1414 C4' T C 8 OK 1416 1413 1415 1434 C4' T C 9 OK 1436 1433 1435 1454 C4' G C 10 OK 1456 1453 1455 1476 C4' G C 11 OK 1478 1475 1477 1498 C4' G C 12 OK 1500 1497 1499 1520 C4' T C 13 OK 1522 1519 1521 1540 C4' G C 14 OK 1542 1539 1541 1562 C4' G C 15 OK 1564 1561 1563 1584 C4' T C 16 OK 1586 1583 1585 1604 C4' C C 17 OK 1606 1603 1605 1623 C4' C C 18 OK 1625 1622 1624 1642 C4' A C 19 OK 1644 1641 1643 1663 C4' C C 20 OK 1665 1662 1664 1682 C4' G C 21 OK 1684 1681 1683 1723 C4' C D 52 OK 1725 1722 1724 1742 C4' G D 53 OK 1744 1741 1743 1764 C4' T D 54 OK 1766 1763 1765 1784 C4' G D 55 OK 1786 1783 1785 1806 C4' G D 56 OK 1808 1805 1807 1828 C4' A D 57 OK 1830 1827 1829 1849 C4' C D 58 OK 1851 1848 1850 1868 C4' C D 59 OK 1870 1867 1869 1887 C4' A D 60 OK 1889 1886 1888 1908 C4' C D 61 OK 1910 1907 1909 1927 C4' C D 62 OK 1929 1926 1928 1946 C4' C D 63 OK 1948 1945 1947 1965 C4' A D 64 OK 1967 1964 1966 1986 C4' A D 65 OK 1988 1985 1987 2007 C4' G D 66 OK 2009 2006 2008 2029 C4' A D 67 OK 2031 2028 2030 2050 C4' C D 68 OK 2052 2049 2051 2069 C4' G D 69 OK 2071 2068 2070 2091 C4' A D 70 OK 2093 2090 2092 2112 C4' A D 71 OK 2114 2111 2113 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1293 C5' T C 2 1292 1294 1313 C5' T C 3 1312 1314 1333 C5' C C 4 1332 1334 1352 C5' G C 5 1351 1353 1374 C5' T C 6 1373 1375 1394 C5' C C 7 1393 1395 1413 C5' T C 8 1412 1414 1433 C5' T C 9 1432 1434 1453 C5' G C 10 1452 1454 1475 C5' G C 11 1474 1476 1497 C5' G C 12 1496 1498 1519 C5' T C 13 1518 1520 1539 C5' G C 14 1538 1540 1561 C5' G C 15 1560 1562 1583 C5' T C 16 1582 1584 1603 C5' C C 17 1602 1604 1622 C5' C C 18 1621 1623 1641 C5' A C 19 1640 1642 1662 C5' C C 20 1661 1663 1681 C5' G C 21 1680 1682 1722 C5' C D 52 1721 1723 1741 C5' G D 53 1740 1742 1763 C5' T D 54 1762 1764 1783 C5' G D 55 1782 1784 1805 C5' G D 56 1804 1806 1827 C5' A D 57 1826 1828 1848 C5' C D 58 1847 1849 1867 C5' C D 59 1866 1868 1886 C5' A D 60 1885 1887 1907 C5' C D 61 1906 1908 1926 C5' C D 62 1925 1927 1945 C5' C D 63 1944 1946 1964 C5' A D 64 1963 1965 1985 C5' A D 65 1984 1986 2006 C5' G D 66 2005 2007 2028 C5' A D 67 2027 2029 2049 C5' C D 68 2048 2050 2068 C5' G D 69 2067 2069 2090 C5' A D 70 2089 2091 2111 C5' A D 71 2110 2112 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1309 P T C 3 distorted distorted 1297 1310 1311 1312 1329 P C C 4 distorted distorted 1317 1330 1331 1332 1348 P G C 5 distorted distorted 1337 1349 1350 1351 1370 P T C 6 distorted distorted 1356 1371 1372 1373 1390 P C C 7 distorted distorted 1378 1391 1392 1393 1409 P T C 8 distorted distorted 1398 1410 1411 1412 1429 P T C 9 distorted distorted 1417 1430 1431 1432 1449 P G C 10 distorted distorted 1437 1450 1451 1452 1471 P G C 11 distorted distorted 1457 1472 1473 1474 1493 P G C 12 distorted distorted 1479 1494 1495 1496 1515 P T C 13 distorted distorted 1501 1516 1517 1518 1535 P G C 14 distorted distorted 1523 1536 1537 1538 1557 P G C 15 distorted distorted 1543 1558 1559 1560 1579 P T C 16 distorted distorted 1565 1580 1581 1582 1599 P C C 17 distorted distorted 1587 1600 1601 1602 1618 P C C 18 distorted distorted 1607 1619 1620 1621 1637 P A C 19 distorted distorted 1626 1638 1639 1640 1658 P C C 20 distorted distorted 1645 1659 1660 1661 1677 P G C 21 distorted distorted 1666 1678 1679 1680 1737 P G D 53 distorted distorted 1726 1738 1739 1740 1759 P T D 54 distorted distorted 1745 1760 1761 1762 1779 P G D 55 distorted distorted 1767 1780 1781 1782 1801 P G D 56 distorted distorted 1787 1802 1803 1804 1823 P A D 57 distorted distorted 1809 1824 1825 1826 1844 P C D 58 distorted distorted 1831 1845 1846 1847 1863 P C D 59 distorted distorted 1852 1864 1865 1866 1882 P A D 60 distorted distorted 1871 1883 1884 1885 1903 P C D 61 distorted distorted 1890 1904 1905 1906 1922 P C D 62 distorted distorted 1911 1923 1924 1925 1941 P C D 63 distorted distorted 1930 1942 1943 1944 1960 P A D 64 distorted distorted 1949 1961 1962 1963 1981 P A D 65 distorted distorted 1968 1982 1983 1984 2002 P G D 66 distorted distorted 1989 2003 2004 2005 2024 P A D 67 distorted distorted 2010 2025 2026 2027 2045 P C D 68 distorted distorted 2032 2046 2047 2048 2064 P G D 69 distorted distorted 2053 2065 2066 2067 2086 P A D 70 distorted distorted 2072 2087 2088 2089 2107 P A D 71 distorted distorted 2094 2108 2109 2110 ---------------------------------------------------------------------------------