ID code: '406D' 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' --------------------------------------------------------------------------------- 9 C1' C A 1 beta 4 10 7 33 C1' A A 2 beta 28 34 31 58 C1' C A 3 beta 53 59 56 81 C1' C A 4 beta 76 82 79 104 C1' G A 5 beta 99 105 102 131 C1' G A 6 beta 126 132 129 158 C1' A A 7 beta 153 159 156 183 C1' U A 8 beta 178 184 181 205 C1' G A 9 beta 200 206 203 232 C1' G A 10 beta 227 233 230 259 C1' U A 11 beta 254 260 257 281 C1' +U A 12 beta 276 282 279 303 C1' C A 13 beta 298 304 301 326 C1' G A 14 beta 321 327 324 353 C1' G A 15 beta 348 354 351 380 C1' U A 16 beta 375 381 378 402 C1' G A 17 beta 397 403 400 1689 C1' C E 18 beta 1684 1690 1687 1713 C1' A E 19 beta 1708 1714 1711 1738 C1' C E 20 beta 1733 1739 1736 1761 C1' C E 21 beta 1756 1762 1759 1784 C1' G E 22 beta 1779 1785 1782 1811 C1' G E 23 beta 1806 1812 1809 1838 C1' A E 24 beta 1833 1839 1836 1863 C1' U E 25 beta 1858 1864 1861 1885 C1' G E 26 beta 1880 1886 1883 1912 C1' G E 27 beta 1907 1913 1910 1939 C1' U E 28 beta 1934 1940 1937 1961 C1' +U E 29 beta 1956 1962 1959 1983 C1' C E 30 beta 1978 1984 1981 2006 C1' G E 31 beta 2001 2007 2004 2033 C1' G E 32 beta 2028 2034 2031 2060 C1' U E 33 beta 2055 2061 2058 2082 C1' G E 34 beta 2077 2083 2080 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 31 C2' A A 2 OK 33 29 32 56 C2' C A 3 OK 58 54 57 79 C2' C A 4 OK 81 77 80 102 C2' G A 5 OK 104 100 103 129 C2' G A 6 OK 131 127 130 156 C2' A A 7 OK 158 154 157 181 C2' U A 8 OK 183 179 182 203 C2' G A 9 OK 205 201 204 230 C2' G A 10 OK 232 228 231 257 C2' U A 11 OK 259 255 258 279 C2' +U A 12 OK 281 277 280 301 C2' C A 13 OK 303 299 302 324 C2' G A 14 OK 326 322 325 351 C2' G A 15 OK 353 349 352 378 C2' U A 16 OK 380 376 379 400 C2' G A 17 OK 402 398 401 1687 C2' C E 18 OK 1689 1685 1688 1711 C2' A E 19 OK 1713 1709 1712 1736 C2' C E 20 OK 1738 1734 1737 1759 C2' C E 21 OK 1761 1757 1760 1782 C2' G E 22 OK 1784 1780 1783 1809 C2' G E 23 OK 1811 1807 1810 1836 C2' A E 24 OK 1838 1834 1837 1861 C2' U E 25 OK 1863 1859 1862 1883 C2' G E 26 OK 1885 1881 1884 1910 C2' G E 27 OK 1912 1908 1911 1937 C2' U E 28 OK 1939 1935 1938 1959 C2' +U E 29 OK 1961 1957 1960 1981 C2' C E 30 OK 1983 1979 1982 2004 C2' G E 31 OK 2006 2002 2005 2031 C2' G E 32 OK 2033 2029 2032 2058 C2' U E 33 OK 2060 2056 2059 2080 C2' G E 34 OK 2082 2078 2081 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 29 C3' A A 2 OK 27 30 31 54 C3' C A 3 OK 52 55 56 77 C3' C A 4 OK 75 78 79 100 C3' G A 5 OK 98 101 102 127 C3' G A 6 OK 125 128 129 154 C3' A A 7 OK 152 155 156 179 C3' U A 8 OK 177 180 181 201 C3' G A 9 OK 199 202 203 228 C3' G A 10 OK 226 229 230 255 C3' U A 11 OK 253 256 257 277 C3' +U A 12 OK 275 278 279 299 C3' C A 13 OK 297 300 301 322 C3' G A 14 OK 320 323 324 349 C3' G A 15 OK 347 350 351 376 C3' U A 16 OK 374 377 378 398 C3' G A 17 OK 396 399 400 1685 C3' C E 18 OK 1683 1686 1687 1709 C3' A E 19 OK 1707 1710 1711 1734 C3' C E 20 OK 1732 1735 1736 1757 C3' C E 21 OK 1755 1758 1759 1780 C3' G E 22 OK 1778 1781 1782 1807 C3' G E 23 OK 1805 1808 1809 1834 C3' A E 24 OK 1832 1835 1836 1859 C3' U E 25 OK 1857 1860 1861 1881 C3' G E 26 OK 1879 1882 1883 1908 C3' G E 27 OK 1906 1909 1910 1935 C3' U E 28 OK 1933 1936 1937 1957 C3' +U E 29 OK 1955 1958 1959 1979 C3' C E 30 OK 1977 1980 1981 2002 C3' G E 31 OK 2000 2003 2004 2029 C3' G E 32 OK 2027 2030 2031 2056 C3' U E 33 OK 2054 2057 2058 2078 C3' G E 34 OK 2076 2079 2080 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 27 C4' A A 2 OK 29 26 28 52 C4' C A 3 OK 54 51 53 75 C4' C A 4 OK 77 74 76 98 C4' G A 5 OK 100 97 99 125 C4' G A 6 OK 127 124 126 152 C4' A A 7 OK 154 151 153 177 C4' U A 8 OK 179 176 178 199 C4' G A 9 OK 201 198 200 226 C4' G A 10 OK 228 225 227 253 C4' U A 11 OK 255 252 254 275 C4' +U A 12 OK 277 274 276 297 C4' C A 13 OK 299 296 298 320 C4' G A 14 OK 322 319 321 347 C4' G A 15 OK 349 346 348 374 C4' U A 16 OK 376 373 375 396 C4' G A 17 OK 398 395 397 1683 C4' C E 18 OK 1685 1682 1684 1707 C4' A E 19 OK 1709 1706 1708 1732 C4' C E 20 OK 1734 1731 1733 1755 C4' C E 21 OK 1757 1754 1756 1778 C4' G E 22 OK 1780 1777 1779 1805 C4' G E 23 OK 1807 1804 1806 1832 C4' A E 24 OK 1834 1831 1833 1857 C4' U E 25 OK 1859 1856 1858 1879 C4' G E 26 OK 1881 1878 1880 1906 C4' G E 27 OK 1908 1905 1907 1933 C4' U E 28 OK 1935 1932 1934 1955 C4' +U E 29 OK 1957 1954 1956 1977 C4' C E 30 OK 1979 1976 1978 2000 C4' G E 31 OK 2002 1999 2001 2027 C4' G E 32 OK 2029 2026 2028 2054 C4' U E 33 OK 2056 2053 2055 2076 C4' G E 34 OK 2078 2075 2077 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 26 C5' A A 2 25 27 51 C5' C A 3 50 52 74 C5' C A 4 73 75 97 C5' G A 5 96 98 124 C5' G A 6 123 125 151 C5' A A 7 150 152 176 C5' U A 8 175 177 198 C5' G A 9 197 199 225 C5' G A 10 224 226 252 C5' U A 11 251 253 274 C5' +U A 12 273 275 296 C5' C A 13 295 297 319 C5' G A 14 318 320 346 C5' G A 15 345 347 373 C5' U A 16 372 374 395 C5' G A 17 394 396 1682 C5' C E 18 1681 1683 1706 C5' A E 19 1705 1707 1731 C5' C E 20 1730 1732 1754 C5' C E 21 1753 1755 1777 C5' G E 22 1776 1778 1804 C5' G E 23 1803 1805 1831 C5' A E 24 1830 1832 1856 C5' U E 25 1855 1857 1878 C5' G E 26 1877 1879 1905 C5' G E 27 1904 1906 1932 C5' U E 28 1931 1933 1954 C5' +U E 29 1953 1955 1976 C5' C E 30 1975 1977 1999 C5' G E 31 1998 2000 2026 C5' G E 32 2025 2027 2053 C5' U E 33 2052 2054 2075 C5' G E 34 2074 2076 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 22 P A A 2 distorted distorted 6 23 24 25 47 P C A 3 distorted distorted 30 48 49 50 70 P C A 4 distorted distorted 55 71 72 73 93 P G A 5 distorted distorted 78 94 95 96 120 P G A 6 distorted distorted 101 121 122 123 147 P A A 7 distorted distorted 128 148 149 150 172 P U A 8 distorted distorted 155 173 174 175 194 P G A 9 distorted distorted 180 195 196 197 221 P G A 10 distorted distorted 202 222 223 224 248 P U A 11 distorted distorted 229 249 250 251 270 P +U A 12 distorted distorted 256 271 272 273 292 P C A 13 distorted distorted 278 293 294 295 315 P G A 14 distorted distorted 300 316 317 318 342 P G A 15 distorted distorted 323 343 344 345 369 P U A 16 distorted distorted 350 370 371 372 391 P G A 17 distorted distorted 377 392 393 394 1702 P A E 19 distorted distorted 1686 1703 1704 1705 1727 P C E 20 distorted distorted 1710 1728 1729 1730 1750 P C E 21 distorted distorted 1735 1751 1752 1753 1773 P G E 22 distorted distorted 1758 1774 1775 1776 1800 P G E 23 distorted distorted 1781 1801 1802 1803 1827 P A E 24 distorted distorted 1808 1828 1829 1830 1852 P U E 25 distorted distorted 1835 1853 1854 1855 1874 P G E 26 distorted distorted 1860 1875 1876 1877 1901 P G E 27 distorted distorted 1882 1902 1903 1904 1928 P U E 28 distorted distorted 1909 1929 1930 1931 1950 P +U E 29 distorted distorted 1936 1951 1952 1953 1972 P C E 30 distorted distorted 1958 1973 1974 1975 1995 P G E 31 distorted distorted 1980 1996 1997 1998 2022 P G E 32 distorted distorted 2003 2023 2024 2025 2049 P U E 33 distorted distorted 2030 2050 2051 2052 2071 P G E 34 distorted distorted 2057 2072 2073 2074 ---------------------------------------------------------------------------------