ID code: '2LEF' 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' --------------------------------------------------------------------------------- 1457 C1' C B 1 beta 1453 1458 1456 1488 C1' A B 2 beta 1484 1489 1487 1520 C1' C B 3 beta 1516 1521 1519 1550 C1' C B 4 beta 1546 1551 1549 1580 C1' C B 5 beta 1576 1581 1579 1610 C1' T B 6 beta 1606 1611 1609 1642 C1' T B 7 beta 1638 1643 1641 1674 C1' T B 8 beta 1670 1675 1673 1706 C1' G B 9 beta 1702 1707 1705 1739 C1' A B 10 beta 1735 1740 1738 1771 C1' A B 11 beta 1767 1772 1770 1803 C1' G B 12 beta 1799 1804 1802 1836 C1' C B 13 beta 1832 1837 1835 1866 C1' T B 14 beta 1862 1867 1865 1898 C1' C B 15 beta 1894 1899 1897 1927 C1' G C 1 beta 1923 1928 1926 1961 C1' A C 2 beta 1957 1962 1960 1993 C1' G C 3 beta 1989 1994 1992 2026 C1' C C 4 beta 2022 2027 2025 2056 C1' T C 5 beta 2052 2057 2055 2088 C1' T C 6 beta 2084 2089 2087 2120 C1' C C 7 beta 2116 2121 2119 2150 C1' A C 8 beta 2146 2151 2149 2182 C1' A C 9 beta 2178 2183 2181 2214 C1' A C 10 beta 2210 2215 2213 2246 C1' G C 11 beta 2242 2247 2245 2279 C1' G C 12 beta 2275 2280 2278 2312 C1' G C 13 beta 2308 2313 2311 2345 C1' T C 14 beta 2341 2346 2344 2377 C1' G C 15 beta 2373 2378 2376 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1456 C2' C B 1 1457 1454 1487 C2' A B 2 1488 1485 1519 C2' C B 3 1520 1517 1549 C2' C B 4 1550 1547 1579 C2' C B 5 1580 1577 1609 C2' T B 6 1610 1607 1641 C2' T B 7 1642 1639 1673 C2' T B 8 1674 1671 1705 C2' G B 9 1706 1703 1738 C2' A B 10 1739 1736 1770 C2' A B 11 1771 1768 1802 C2' G B 12 1803 1800 1835 C2' C B 13 1836 1833 1865 C2' T B 14 1866 1863 1897 C2' C B 15 1898 1895 1926 C2' G C 1 1927 1924 1960 C2' A C 2 1961 1958 1992 C2' G C 3 1993 1990 2025 C2' C C 4 2026 2023 2055 C2' T C 5 2056 2053 2087 C2' T C 6 2088 2085 2119 C2' C C 7 2120 2117 2149 C2' A C 8 2150 2147 2181 C2' A C 9 2182 2179 2213 C2' A C 10 2214 2211 2245 C2' G C 11 2246 2243 2278 C2' G C 12 2279 2276 2311 C2' G C 13 2312 2309 2344 C2' T C 14 2345 2342 2376 C2' G C 15 2377 2374 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1454 C3' C B 1 OK 1452 1455 1456 1485 C3' A B 2 OK 1483 1486 1487 1517 C3' C B 3 OK 1515 1518 1519 1547 C3' C B 4 OK 1545 1548 1549 1577 C3' C B 5 OK 1575 1578 1579 1607 C3' T B 6 OK 1605 1608 1609 1639 C3' T B 7 OK 1637 1640 1641 1671 C3' T B 8 OK 1669 1672 1673 1703 C3' G B 9 OK 1701 1704 1705 1736 C3' A B 10 OK 1734 1737 1738 1768 C3' A B 11 OK 1766 1769 1770 1800 C3' G B 12 OK 1798 1801 1802 1833 C3' C B 13 OK 1831 1834 1835 1863 C3' T B 14 OK 1861 1864 1865 1895 C3' C B 15 OK 1893 1896 1897 1924 C3' G C 1 OK 1922 1925 1926 1958 C3' A C 2 OK 1956 1959 1960 1990 C3' G C 3 OK 1988 1991 1992 2023 C3' C C 4 OK 2021 2024 2025 2053 C3' T C 5 OK 2051 2054 2055 2085 C3' T C 6 OK 2083 2086 2087 2117 C3' C C 7 OK 2115 2118 2119 2147 C3' A C 8 OK 2145 2148 2149 2179 C3' A C 9 OK 2177 2180 2181 2211 C3' A C 10 OK 2209 2212 2213 2243 C3' G C 11 OK 2241 2244 2245 2276 C3' G C 12 OK 2274 2277 2278 2309 C3' G C 13 OK 2307 2310 2311 2342 C3' T C 14 OK 2340 2343 2344 2374 C3' G C 15 OK 2372 2375 2376 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1452 C4' C B 1 OK 1454 1451 1453 1483 C4' A B 2 OK 1485 1482 1484 1515 C4' C B 3 OK 1517 1514 1516 1545 C4' C B 4 OK 1547 1544 1546 1575 C4' C B 5 OK 1577 1574 1576 1605 C4' T B 6 OK 1607 1604 1606 1637 C4' T B 7 OK 1639 1636 1638 1669 C4' T B 8 OK 1671 1668 1670 1701 C4' G B 9 OK 1703 1700 1702 1734 C4' A B 10 OK 1736 1733 1735 1766 C4' A B 11 OK 1768 1765 1767 1798 C4' G B 12 OK 1800 1797 1799 1831 C4' C B 13 OK 1833 1830 1832 1861 C4' T B 14 OK 1863 1860 1862 1893 C4' C B 15 OK 1895 1892 1894 1922 C4' G C 1 OK 1924 1921 1923 1956 C4' A C 2 OK 1958 1955 1957 1988 C4' G C 3 OK 1990 1987 1989 2021 C4' C C 4 OK 2023 2020 2022 2051 C4' T C 5 OK 2053 2050 2052 2083 C4' T C 6 OK 2085 2082 2084 2115 C4' C C 7 OK 2117 2114 2116 2145 C4' A C 8 OK 2147 2144 2146 2177 C4' A C 9 OK 2179 2176 2178 2209 C4' A C 10 OK 2211 2208 2210 2241 C4' G C 11 OK 2243 2240 2242 2274 C4' G C 12 OK 2276 2273 2275 2307 C4' G C 13 OK 2309 2306 2308 2340 C4' T C 14 OK 2342 2339 2341 2372 C4' G C 15 OK 2374 2371 2373 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1451 C5' C B 1 1450 1452 1482 C5' A B 2 1481 1483 1514 C5' C B 3 1513 1515 1544 C5' C B 4 1543 1545 1574 C5' C B 5 1573 1575 1604 C5' T B 6 1603 1605 1636 C5' T B 7 1635 1637 1668 C5' T B 8 1667 1669 1700 C5' G B 9 1699 1701 1733 C5' A B 10 1732 1734 1765 C5' A B 11 1764 1766 1797 C5' G B 12 1796 1798 1830 C5' C B 13 1829 1831 1860 C5' T B 14 1859 1861 1892 C5' C B 15 1891 1893 1921 C5' G C 1 1920 1922 1955 C5' A C 2 1954 1956 1987 C5' G C 3 1986 1988 2020 C5' C C 4 2019 2021 2050 C5' T C 5 2049 2051 2082 C5' T C 6 2081 2083 2114 C5' C C 7 2113 2115 2144 C5' A C 8 2143 2145 2176 C5' A C 9 2175 2177 2208 C5' A C 10 2207 2209 2240 C5' G C 11 2239 2241 2273 C5' G C 12 2272 2274 2306 C5' G C 13 2305 2307 2339 C5' T C 14 2338 2340 2371 C5' G C 15 2370 2372 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1478 P A B 2 distorted distorted 1455 1479 1480 1481 1510 P C B 3 distorted distorted 1486 1511 1512 1513 1540 P C B 4 distorted distorted 1518 1541 1542 1543 1570 P C B 5 distorted distorted 1548 1571 1572 1573 1600 P T B 6 distorted distorted 1578 1601 1602 1603 1632 P T B 7 distorted distorted 1608 1633 1634 1635 1664 P T B 8 distorted distorted 1640 1665 1666 1667 1696 P G B 9 distorted distorted 1672 1697 1698 1699 1729 P A B 10 distorted distorted 1704 1730 1731 1732 1761 P A B 11 distorted distorted 1737 1762 1763 1764 1793 P G B 12 distorted distorted 1769 1794 1795 1796 1826 P C B 13 distorted distorted 1801 1827 1828 1829 1856 P T B 14 distorted distorted 1834 1857 1858 1859 1888 P C B 15 distorted distorted 1864 1889 1890 1891 1951 P A C 2 distorted distorted 1925 1952 1953 1954 1983 P G C 3 distorted distorted 1959 1984 1985 1986 2016 P C C 4 distorted distorted 1991 2017 2018 2019 2046 P T C 5 distorted distorted 2024 2047 2048 2049 2078 P T C 6 distorted distorted 2054 2079 2080 2081 2110 P C C 7 distorted distorted 2086 2111 2112 2113 2140 P A C 8 distorted distorted 2118 2141 2142 2143 2172 P A C 9 distorted distorted 2148 2173 2174 2175 2204 P A C 10 distorted distorted 2180 2205 2206 2207 2236 P G C 11 distorted distorted 2212 2237 2238 2239 2269 P G C 12 distorted distorted 2244 2270 2271 2272 2302 P G C 13 distorted distorted 2277 2303 2304 2305 2335 P T C 14 distorted distorted 2310 2336 2337 2338 2367 P G C 15 distorted distorted 2343 2368 2369 2370 ---------------------------------------------------------------------------------