ID code: '1B69' 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' --------------------------------------------------------------------------------- 1174 C1' G B 101 beta 1170 1175 1173 1208 C1' A B 102 beta 1204 1209 1207 1240 C1' G B 103 beta 1236 1241 1239 1273 C1' T B 104 beta 1269 1274 1272 1305 C1' A B 105 beta 1301 1306 1304 1337 C1' G B 106 beta 1333 1338 1336 1370 C1' T B 107 beta 1366 1371 1369 1402 C1' A B 108 beta 1398 1403 1401 1434 C1' A B 109 beta 1430 1435 1433 1466 C1' A B 110 beta 1462 1467 1465 1498 C1' T B 111 beta 1494 1499 1497 1530 C1' T B 112 beta 1526 1531 1529 1562 C1' C B 113 beta 1558 1563 1561 1591 C1' G C 114 beta 1587 1592 1590 1625 C1' A C 115 beta 1621 1626 1624 1657 C1' A C 116 beta 1653 1658 1656 1689 C1' T C 117 beta 1685 1690 1688 1721 C1' T C 118 beta 1717 1722 1720 1753 C1' T C 119 beta 1749 1754 1752 1785 C1' A C 120 beta 1781 1786 1784 1817 C1' C C 121 beta 1813 1818 1816 1847 C1' T C 122 beta 1843 1848 1846 1879 C1' A C 123 beta 1875 1880 1878 1911 C1' C C 124 beta 1907 1912 1910 1941 C1' T C 125 beta 1937 1942 1940 1973 C1' C C 126 beta 1969 1974 1972 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1173 C2' G B 101 1174 1171 1207 C2' A B 102 1208 1205 1239 C2' G B 103 1240 1237 1272 C2' T B 104 1273 1270 1304 C2' A B 105 1305 1302 1336 C2' G B 106 1337 1334 1369 C2' T B 107 1370 1367 1401 C2' A B 108 1402 1399 1433 C2' A B 109 1434 1431 1465 C2' A B 110 1466 1463 1497 C2' T B 111 1498 1495 1529 C2' T B 112 1530 1527 1561 C2' C B 113 1562 1559 1590 C2' G C 114 1591 1588 1624 C2' A C 115 1625 1622 1656 C2' A C 116 1657 1654 1688 C2' T C 117 1689 1686 1720 C2' T C 118 1721 1718 1752 C2' T C 119 1753 1750 1784 C2' A C 120 1785 1782 1816 C2' C C 121 1817 1814 1846 C2' T C 122 1847 1844 1878 C2' A C 123 1879 1876 1910 C2' C C 124 1911 1908 1940 C2' T C 125 1941 1938 1972 C2' C C 126 1973 1970 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1171 C3' G B 101 OK 1169 1172 1173 1205 C3' A B 102 OK 1203 1206 1207 1237 C3' G B 103 OK 1235 1238 1239 1270 C3' T B 104 OK 1268 1271 1272 1302 C3' A B 105 OK 1300 1303 1304 1334 C3' G B 106 OK 1332 1335 1336 1367 C3' T B 107 OK 1365 1368 1369 1399 C3' A B 108 OK 1397 1400 1401 1431 C3' A B 109 OK 1429 1432 1433 1463 C3' A B 110 OK 1461 1464 1465 1495 C3' T B 111 OK 1493 1496 1497 1527 C3' T B 112 OK 1525 1528 1529 1559 C3' C B 113 OK 1557 1560 1561 1588 C3' G C 114 OK 1586 1589 1590 1622 C3' A C 115 OK 1620 1623 1624 1654 C3' A C 116 OK 1652 1655 1656 1686 C3' T C 117 OK 1684 1687 1688 1718 C3' T C 118 OK 1716 1719 1720 1750 C3' T C 119 OK 1748 1751 1752 1782 C3' A C 120 OK 1780 1783 1784 1814 C3' C C 121 OK 1812 1815 1816 1844 C3' T C 122 OK 1842 1845 1846 1876 C3' A C 123 OK 1874 1877 1878 1908 C3' C C 124 OK 1906 1909 1910 1938 C3' T C 125 OK 1936 1939 1940 1970 C3' C C 126 OK 1968 1971 1972 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1169 C4' G B 101 OK 1171 1168 1170 1203 C4' A B 102 OK 1205 1202 1204 1235 C4' G B 103 OK 1237 1234 1236 1268 C4' T B 104 OK 1270 1267 1269 1300 C4' A B 105 OK 1302 1299 1301 1332 C4' G B 106 OK 1334 1331 1333 1365 C4' T B 107 OK 1367 1364 1366 1397 C4' A B 108 OK 1399 1396 1398 1429 C4' A B 109 OK 1431 1428 1430 1461 C4' A B 110 OK 1463 1460 1462 1493 C4' T B 111 OK 1495 1492 1494 1525 C4' T B 112 OK 1527 1524 1526 1557 C4' C B 113 OK 1559 1556 1558 1586 C4' G C 114 OK 1588 1585 1587 1620 C4' A C 115 OK 1622 1619 1621 1652 C4' A C 116 OK 1654 1651 1653 1684 C4' T C 117 OK 1686 1683 1685 1716 C4' T C 118 OK 1718 1715 1717 1748 C4' T C 119 OK 1750 1747 1749 1780 C4' A C 120 OK 1782 1779 1781 1812 C4' C C 121 OK 1814 1811 1813 1842 C4' T C 122 OK 1844 1841 1843 1874 C4' A C 123 OK 1876 1873 1875 1906 C4' C C 124 OK 1908 1905 1907 1936 C4' T C 125 OK 1938 1935 1937 1968 C4' C C 126 OK 1970 1967 1969 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1168 C5' G B 101 1167 1169 1202 C5' A B 102 1201 1203 1234 C5' G B 103 1233 1235 1267 C5' T B 104 1266 1268 1299 C5' A B 105 1298 1300 1331 C5' G B 106 1330 1332 1364 C5' T B 107 1363 1365 1396 C5' A B 108 1395 1397 1428 C5' A B 109 1427 1429 1460 C5' A B 110 1459 1461 1492 C5' T B 111 1491 1493 1524 C5' T B 112 1523 1525 1556 C5' C B 113 1555 1557 1585 C5' G C 114 1584 1586 1619 C5' A C 115 1618 1620 1651 C5' A C 116 1650 1652 1683 C5' T C 117 1682 1684 1715 C5' T C 118 1714 1716 1747 C5' T C 119 1746 1748 1779 C5' A C 120 1778 1780 1811 C5' C C 121 1810 1812 1841 C5' T C 122 1840 1842 1873 C5' A C 123 1872 1874 1905 C5' C C 124 1904 1906 1935 C5' T C 125 1934 1936 1967 C5' C C 126 1966 1968 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1198 P A B 102 distorted distorted 1172 1199 1200 1201 1230 P G B 103 distorted distorted 1206 1231 1232 1233 1263 P T B 104 distorted distorted 1238 1264 1265 1266 1295 P A B 105 distorted distorted 1271 1296 1297 1298 1327 P G B 106 distorted distorted 1303 1328 1329 1330 1360 P T B 107 distorted distorted 1335 1361 1362 1363 1392 P A B 108 distorted distorted 1368 1393 1394 1395 1424 P A B 109 distorted distorted 1400 1425 1426 1427 1456 P A B 110 distorted distorted 1432 1457 1458 1459 1488 P T B 111 distorted distorted 1464 1489 1490 1491 1520 P T B 112 distorted distorted 1496 1521 1522 1523 1552 P C B 113 distorted distorted 1528 1553 1554 1555 1615 P A C 115 distorted distorted 1589 1616 1617 1618 1647 P A C 116 distorted distorted 1623 1648 1649 1650 1679 P T C 117 distorted distorted 1655 1680 1681 1682 1711 P T C 118 distorted distorted 1687 1712 1713 1714 1743 P T C 119 distorted distorted 1719 1744 1745 1746 1775 P A C 120 distorted distorted 1751 1776 1777 1778 1807 P C C 121 distorted distorted 1783 1808 1809 1810 1837 P T C 122 distorted distorted 1815 1838 1839 1840 1869 P A C 123 distorted distorted 1845 1870 1871 1872 1901 P C C 124 distorted distorted 1877 1902 1903 1904 1931 P T C 125 distorted distorted 1909 1932 1933 1934 1963 P C C 126 distorted distorted 1939 1964 1965 1966 ---------------------------------------------------------------------------------