ID code: '2HDC' 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' --------------------------------------------------------------------------------- 1616 C1' G B 249 beta 1612 1617 1615 1647 C1' C B 250 beta 1643 1648 1646 1675 C1' T B 251 beta 1671 1676 1674 1702 C1' T B 252 beta 1698 1703 1701 1729 C1' A B 253 beta 1725 1730 1728 1759 C1' A B 254 beta 1755 1760 1758 1789 C1' A B 255 beta 1785 1790 1788 1819 C1' A B 256 beta 1815 1820 1818 1849 C1' T B 257 beta 1845 1850 1848 1876 C1' A B 258 beta 1872 1877 1875 1906 C1' A B 259 beta 1902 1907 1905 1936 C1' C B 260 beta 1932 1937 1935 1964 C1' A B 261 beta 1960 1965 1963 1994 C1' A B 262 beta 1990 1995 1993 2024 C1' T B 263 beta 2020 2025 2023 2051 C1' A B 264 beta 2047 2052 2050 2081 C1' C B 265 beta 2077 2082 2080 2110 C1' G C 349 beta 2106 2111 2109 2141 C1' T C 350 beta 2137 2142 2140 2168 C1' A C 351 beta 2164 2169 2167 2198 C1' T C 352 beta 2194 2199 2197 2225 C1' T C 353 beta 2221 2226 2224 2252 C1' G C 354 beta 2248 2253 2251 2283 C1' T C 355 beta 2279 2284 2282 2310 C1' T C 356 beta 2306 2311 2309 2337 C1' A C 357 beta 2333 2338 2336 2367 C1' T C 358 beta 2363 2368 2366 2394 C1' T C 359 beta 2390 2395 2393 2421 C1' T C 360 beta 2417 2422 2420 2448 C1' T C 361 beta 2444 2449 2447 2475 C1' A C 362 beta 2471 2476 2474 2505 C1' A C 363 beta 2501 2506 2504 2535 C1' G C 364 beta 2531 2536 2534 2566 C1' C C 365 beta 2562 2567 2565 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1615 C2' G B 249 1616 1613 1646 C2' C B 250 1647 1644 1674 C2' T B 251 1675 1672 1701 C2' T B 252 1702 1699 1728 C2' A B 253 1729 1726 1758 C2' A B 254 1759 1756 1788 C2' A B 255 1789 1786 1818 C2' A B 256 1819 1816 1848 C2' T B 257 1849 1846 1875 C2' A B 258 1876 1873 1905 C2' A B 259 1906 1903 1935 C2' C B 260 1936 1933 1963 C2' A B 261 1964 1961 1993 C2' A B 262 1994 1991 2023 C2' T B 263 2024 2021 2050 C2' A B 264 2051 2048 2080 C2' C B 265 2081 2078 2109 C2' G C 349 2110 2107 2140 C2' T C 350 2141 2138 2167 C2' A C 351 2168 2165 2197 C2' T C 352 2198 2195 2224 C2' T C 353 2225 2222 2251 C2' G C 354 2252 2249 2282 C2' T C 355 2283 2280 2309 C2' T C 356 2310 2307 2336 C2' A C 357 2337 2334 2366 C2' T C 358 2367 2364 2393 C2' T C 359 2394 2391 2420 C2' T C 360 2421 2418 2447 C2' T C 361 2448 2445 2474 C2' A C 362 2475 2472 2504 C2' A C 363 2505 2502 2534 C2' G C 364 2535 2532 2565 C2' C C 365 2566 2563 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1613 C3' G B 249 OK 1611 1614 1615 1644 C3' C B 250 OK 1642 1645 1646 1672 C3' T B 251 OK 1670 1673 1674 1699 C3' T B 252 OK 1697 1700 1701 1726 C3' A B 253 OK 1724 1727 1728 1756 C3' A B 254 OK 1754 1757 1758 1786 C3' A B 255 OK 1784 1787 1788 1816 C3' A B 256 OK 1814 1817 1818 1846 C3' T B 257 OK 1844 1847 1848 1873 C3' A B 258 OK 1871 1874 1875 1903 C3' A B 259 OK 1901 1904 1905 1933 C3' C B 260 OK 1931 1934 1935 1961 C3' A B 261 OK 1959 1962 1963 1991 C3' A B 262 OK 1989 1992 1993 2021 C3' T B 263 OK 2019 2022 2023 2048 C3' A B 264 OK 2046 2049 2050 2078 C3' C B 265 OK 2076 2079 2080 2107 C3' G C 349 OK 2105 2108 2109 2138 C3' T C 350 OK 2136 2139 2140 2165 C3' A C 351 OK 2163 2166 2167 2195 C3' T C 352 OK 2193 2196 2197 2222 C3' T C 353 OK 2220 2223 2224 2249 C3' G C 354 OK 2247 2250 2251 2280 C3' T C 355 OK 2278 2281 2282 2307 C3' T C 356 OK 2305 2308 2309 2334 C3' A C 357 OK 2332 2335 2336 2364 C3' T C 358 OK 2362 2365 2366 2391 C3' T C 359 OK 2389 2392 2393 2418 C3' T C 360 OK 2416 2419 2420 2445 C3' T C 361 OK 2443 2446 2447 2472 C3' A C 362 OK 2470 2473 2474 2502 C3' A C 363 OK 2500 2503 2504 2532 C3' G C 364 OK 2530 2533 2534 2563 C3' C C 365 OK 2561 2564 2565 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1611 C4' G B 249 OK 1613 1610 1612 1642 C4' C B 250 OK 1644 1641 1643 1670 C4' T B 251 OK 1672 1669 1671 1697 C4' T B 252 OK 1699 1696 1698 1724 C4' A B 253 distorted 1726 1723 1725 1754 C4' A B 254 OK 1756 1753 1755 1784 C4' A B 255 distorted 1786 1783 1785 1814 C4' A B 256 distorted 1816 1813 1815 1844 C4' T B 257 OK 1846 1843 1845 1871 C4' A B 258 OK 1873 1870 1872 1901 C4' A B 259 OK 1903 1900 1902 1931 C4' C B 260 distorted 1933 1930 1932 1959 C4' A B 261 OK 1961 1958 1960 1989 C4' A B 262 OK 1991 1988 1990 2019 C4' T B 263 distorted 2021 2018 2020 2046 C4' A B 264 OK 2048 2045 2047 2076 C4' C B 265 OK 2078 2075 2077 2105 C4' G C 349 OK 2107 2104 2106 2136 C4' T C 350 OK 2138 2135 2137 2163 C4' A C 351 OK 2165 2162 2164 2193 C4' T C 352 OK 2195 2192 2194 2220 C4' T C 353 OK 2222 2219 2221 2247 C4' G C 354 OK 2249 2246 2248 2278 C4' T C 355 OK 2280 2277 2279 2305 C4' T C 356 OK 2307 2304 2306 2332 C4' A C 357 OK 2334 2331 2333 2362 C4' T C 358 distorted 2364 2361 2363 2389 C4' T C 359 OK 2391 2388 2390 2416 C4' T C 360 OK 2418 2415 2417 2443 C4' T C 361 OK 2445 2442 2444 2470 C4' A C 362 OK 2472 2469 2471 2500 C4' A C 363 OK 2502 2499 2501 2530 C4' G C 364 OK 2532 2529 2531 2561 C4' C C 365 OK 2563 2560 2562 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1610 C5' G B 249 1609 1611 1641 C5' C B 250 1640 1642 1669 C5' T B 251 1668 1670 1696 C5' T B 252 1695 1697 1723 C5' A B 253 1722 1724 1753 C5' A B 254 1752 1754 1783 C5' A B 255 1782 1784 1813 C5' A B 256 1812 1814 1843 C5' T B 257 1842 1844 1870 C5' A B 258 1869 1871 1900 C5' A B 259 1899 1901 1930 C5' C B 260 1929 1931 1958 C5' A B 261 1957 1959 1988 C5' A B 262 1987 1989 2018 C5' T B 263 2017 2019 2045 C5' A B 264 2044 2046 2075 C5' C B 265 2074 2076 2104 C5' G C 349 2103 2105 2135 C5' T C 350 2134 2136 2162 C5' A C 351 2161 2163 2192 C5' T C 352 2191 2193 2219 C5' T C 353 2218 2220 2246 C5' G C 354 2245 2247 2277 C5' T C 355 2276 2278 2304 C5' T C 356 2303 2305 2331 C5' A C 357 2330 2332 2361 C5' T C 358 2360 2362 2388 C5' T C 359 2387 2389 2415 C5' T C 360 2414 2416 2442 C5' T C 361 2441 2443 2469 C5' A C 362 2468 2470 2499 C5' A C 363 2498 2500 2529 C5' G C 364 2528 2530 2560 C5' C C 365 2559 2561 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1637 P C B 250 distorted distorted 1614 1638 1639 1640 1665 P T B 251 distorted distorted 1645 1666 1667 1668 1692 P T B 252 distorted distorted 1673 1693 1694 1695 1719 P A B 253 distorted distorted 1700 1720 1721 1722 1749 P A B 254 distorted distorted 1727 1750 1751 1752 1779 P A B 255 distorted distorted 1757 1780 1781 1782 1809 P A B 256 distorted distorted 1787 1810 1811 1812 1839 P T B 257 distorted distorted 1817 1840 1841 1842 1866 P A B 258 distorted distorted 1847 1867 1868 1869 1896 P A B 259 distorted distorted 1874 1897 1898 1899 1926 P C B 260 distorted distorted 1904 1927 1928 1929 1954 P A B 261 distorted distorted 1934 1955 1956 1957 1984 P A B 262 distorted distorted 1962 1985 1986 1987 2014 P T B 263 distorted distorted 1992 2015 2016 2017 2041 P A B 264 distorted distorted 2022 2042 2043 2044 2071 P C B 265 distorted distorted 2049 2072 2073 2074 2131 P T C 350 distorted distorted 2108 2132 2133 2134 2158 P A C 351 distorted distorted 2139 2159 2160 2161 2188 P T C 352 distorted distorted 2166 2189 2190 2191 2215 P T C 353 distorted distorted 2196 2216 2217 2218 2242 P G C 354 distorted distorted 2223 2243 2244 2245 2273 P T C 355 distorted distorted 2250 2274 2275 2276 2300 P T C 356 distorted distorted 2281 2301 2302 2303 2327 P A C 357 distorted distorted 2308 2328 2329 2330 2357 P T C 358 distorted distorted 2335 2358 2359 2360 2384 P T C 359 distorted distorted 2365 2385 2386 2387 2411 P T C 360 distorted distorted 2392 2412 2413 2414 2438 P T C 361 distorted distorted 2419 2439 2440 2441 2465 P A C 362 distorted distorted 2446 2466 2467 2468 2495 P A C 363 distorted distorted 2473 2496 2497 2498 2525 P G C 364 distorted distorted 2503 2526 2527 2528 2556 P C C 365 distorted distorted 2533 2557 2558 2559 ---------------------------------------------------------------------------------