ID code: '2HGH' 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' --------------------------------------------------------------------------------- 1418 C1' G B 1 alpha beta 1413 1436 1419 1416 1452 C1' G B 2 alpha beta 1447 1470 1453 1450 1486 C1' G B 3 alpha beta 1481 1504 1487 1484 1520 C1' C B 4 alpha beta 1515 1535 1521 1518 1551 C1' C B 5 alpha beta 1546 1566 1552 1549 1582 C1' A B 6 alpha beta 1577 1599 1583 1580 1615 C1' U B 7 alpha beta 1610 1630 1616 1613 1645 C1' A B 8 alpha beta 1640 1662 1646 1643 1678 C1' C B 9 alpha beta 1673 1693 1679 1676 1709 C1' C B 10 alpha beta 1704 1724 1710 1707 1740 C1' U B 11 alpha beta 1735 1755 1741 1738 1770 C1' C B 12 alpha beta 1765 1785 1771 1768 1801 C1' U B 13 alpha beta 1796 1816 1802 1799 1831 C1' U B 14 alpha beta 1826 1846 1832 1829 1861 C1' G B 15 alpha beta 1856 1879 1862 1859 1895 C1' G B 16 alpha beta 1890 1913 1896 1893 1929 C1' G B 17 alpha beta 1924 1947 1930 1927 1963 C1' C B 18 alpha beta 1958 1978 1964 1961 1994 C1' C B 19 alpha beta 1989 2009 1995 1992 2025 C1' U B 20 alpha beta 2020 2040 2026 2023 2055 C1' G B 21 alpha beta 2050 2073 2056 2053 2089 C1' G B 22 alpha beta 2084 2107 2090 2087 2123 C1' U B 23 alpha beta 2118 2138 2124 2121 2153 C1' U B 24 alpha beta 2148 2168 2154 2151 2183 C1' A B 25 alpha beta 2178 2200 2184 2181 2216 C1' G B 26 alpha beta 2211 2234 2217 2214 2250 C1' U B 27 alpha beta 2245 2265 2251 2248 2280 C1' A B 28 alpha beta 2275 2297 2281 2278 2313 C1' C B 29 alpha beta 2308 2328 2314 2311 2344 C1' C B 30 alpha beta 2339 2359 2345 2342 2375 C1' U B 31 alpha beta 2370 2390 2376 2373 2405 C1' C B 32 alpha beta 2400 2420 2406 2403 2436 C1' U B 33 alpha beta 2431 2451 2437 2434 2466 C1' U B 34 alpha beta 2461 2481 2467 2464 2496 C1' C B 35 alpha beta 2491 2511 2497 2494 2527 C1' G B 36 alpha beta 2522 2545 2528 2525 2561 C1' G B 37 alpha beta 2556 2579 2562 2559 2595 C1' U B 38 alpha beta 2590 2610 2596 2593 2625 C1' G B 39 alpha beta 2620 2643 2626 2623 2659 C1' G B 40 alpha beta 2654 2677 2660 2657 2693 C1' G B 41 alpha beta 2688 2711 2694 2691 2727 C1' A B 42 alpha beta 2722 2744 2728 2725 2760 C1' A B 43 alpha beta 2755 2777 2761 2758 2793 C1' U B 44 alpha beta 2788 2808 2794 2791 2823 C1' A B 45 alpha beta 2818 2840 2824 2821 2856 C1' C B 46 alpha beta 2851 2871 2857 2854 2887 C1' C B 47 alpha beta 2882 2902 2888 2885 2918 C1' A B 48 alpha beta 2913 2935 2919 2916 2951 C1' G B 49 alpha beta 2946 2969 2952 2949 2985 C1' G B 50 alpha beta 2980 3003 2986 2983 3019 C1' U B 51 alpha beta 3014 3034 3020 3017 3049 C1' G B 52 alpha beta 3044 3067 3050 3047 3083 C1' C B 53 alpha beta 3078 3098 3084 3081 3114 C1' C B 54 alpha beta 3109 3129 3115 3112 3145 C1' C B 55 alpha beta 3140 3160 3146 3143 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1416 C2' G B 1 OK OK 1418 1414 1434 1417 1450 C2' G B 2 OK OK 1452 1448 1468 1451 1484 C2' G B 3 OK OK 1486 1482 1502 1485 1518 C2' C B 4 OK OK 1520 1516 1533 1519 1549 C2' C B 5 OK OK 1551 1547 1564 1550 1580 C2' A B 6 OK OK 1582 1578 1597 1581 1613 C2' U B 7 OK OK 1615 1611 1628 1614 1643 C2' A B 8 OK OK 1645 1641 1660 1644 1676 C2' C B 9 OK OK 1678 1674 1691 1677 1707 C2' C B 10 OK OK 1709 1705 1722 1708 1738 C2' U B 11 OK OK 1740 1736 1753 1739 1768 C2' C B 12 OK OK 1770 1766 1783 1769 1799 C2' U B 13 OK OK 1801 1797 1814 1800 1829 C2' U B 14 OK OK 1831 1827 1844 1830 1859 C2' G B 15 OK OK 1861 1857 1877 1860 1893 C2' G B 16 OK OK 1895 1891 1911 1894 1927 C2' G B 17 OK OK 1929 1925 1945 1928 1961 C2' C B 18 OK OK 1963 1959 1976 1962 1992 C2' C B 19 OK OK 1994 1990 2007 1993 2023 C2' U B 20 OK OK 2025 2021 2038 2024 2053 C2' G B 21 OK OK 2055 2051 2071 2054 2087 C2' G B 22 OK OK 2089 2085 2105 2088 2121 C2' U B 23 OK OK 2123 2119 2136 2122 2151 C2' U B 24 OK OK 2153 2149 2166 2152 2181 C2' A B 25 OK OK 2183 2179 2198 2182 2214 C2' G B 26 OK OK 2216 2212 2232 2215 2248 C2' U B 27 OK OK 2250 2246 2263 2249 2278 C2' A B 28 OK OK 2280 2276 2295 2279 2311 C2' C B 29 OK OK 2313 2309 2326 2312 2342 C2' C B 30 OK OK 2344 2340 2357 2343 2373 C2' U B 31 OK OK 2375 2371 2388 2374 2403 C2' C B 32 OK OK 2405 2401 2418 2404 2434 C2' U B 33 OK OK 2436 2432 2449 2435 2464 C2' U B 34 OK OK 2466 2462 2479 2465 2494 C2' C B 35 OK OK 2496 2492 2509 2495 2525 C2' G B 36 OK OK 2527 2523 2543 2526 2559 C2' G B 37 OK OK 2561 2557 2577 2560 2593 C2' U B 38 OK OK 2595 2591 2608 2594 2623 C2' G B 39 OK OK 2625 2621 2641 2624 2657 C2' G B 40 OK OK 2659 2655 2675 2658 2691 C2' G B 41 OK OK 2693 2689 2709 2692 2725 C2' A B 42 OK OK 2727 2723 2742 2726 2758 C2' A B 43 OK OK 2760 2756 2775 2759 2791 C2' U B 44 OK OK 2793 2789 2806 2792 2821 C2' A B 45 OK OK 2823 2819 2838 2822 2854 C2' C B 46 OK OK 2856 2852 2869 2855 2885 C2' C B 47 OK OK 2887 2883 2900 2886 2916 C2' A B 48 OK OK 2918 2914 2933 2917 2949 C2' G B 49 OK OK 2951 2947 2967 2950 2983 C2' G B 50 OK OK 2985 2981 3001 2984 3017 C2' U B 51 OK OK 3019 3015 3032 3018 3047 C2' G B 52 OK OK 3049 3045 3065 3048 3081 C2' C B 53 OK OK 3083 3079 3096 3082 3112 C2' C B 54 OK OK 3114 3110 3127 3113 3143 C2' C B 55 OK OK 3145 3141 3158 3144 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1414 C3' G B 1 OK OK 1412 1433 1415 1416 1448 C3' G B 2 OK OK 1446 1467 1449 1450 1482 C3' G B 3 OK OK 1480 1501 1483 1484 1516 C3' C B 4 OK OK 1514 1532 1517 1518 1547 C3' C B 5 OK OK 1545 1563 1548 1549 1578 C3' A B 6 OK OK 1576 1596 1579 1580 1611 C3' U B 7 OK OK 1609 1627 1612 1613 1641 C3' A B 8 OK OK 1639 1659 1642 1643 1674 C3' C B 9 OK OK 1672 1690 1675 1676 1705 C3' C B 10 OK OK 1703 1721 1706 1707 1736 C3' U B 11 OK OK 1734 1752 1737 1738 1766 C3' C B 12 OK OK 1764 1782 1767 1768 1797 C3' U B 13 OK OK 1795 1813 1798 1799 1827 C3' U B 14 OK OK 1825 1843 1828 1829 1857 C3' G B 15 OK OK 1855 1876 1858 1859 1891 C3' G B 16 OK OK 1889 1910 1892 1893 1925 C3' G B 17 OK OK 1923 1944 1926 1927 1959 C3' C B 18 OK OK 1957 1975 1960 1961 1990 C3' C B 19 OK OK 1988 2006 1991 1992 2021 C3' U B 20 OK OK 2019 2037 2022 2023 2051 C3' G B 21 OK OK 2049 2070 2052 2053 2085 C3' G B 22 OK OK 2083 2104 2086 2087 2119 C3' U B 23 OK OK 2117 2135 2120 2121 2149 C3' U B 24 OK OK 2147 2165 2150 2151 2179 C3' A B 25 OK OK 2177 2197 2180 2181 2212 C3' G B 26 OK OK 2210 2231 2213 2214 2246 C3' U B 27 OK OK 2244 2262 2247 2248 2276 C3' A B 28 OK OK 2274 2294 2277 2278 2309 C3' C B 29 OK OK 2307 2325 2310 2311 2340 C3' C B 30 OK OK 2338 2356 2341 2342 2371 C3' U B 31 OK OK 2369 2387 2372 2373 2401 C3' C B 32 OK OK 2399 2417 2402 2403 2432 C3' U B 33 OK OK 2430 2448 2433 2434 2462 C3' U B 34 OK OK 2460 2478 2463 2464 2492 C3' C B 35 OK OK 2490 2508 2493 2494 2523 C3' G B 36 OK OK 2521 2542 2524 2525 2557 C3' G B 37 OK OK 2555 2576 2558 2559 2591 C3' U B 38 OK OK 2589 2607 2592 2593 2621 C3' G B 39 OK OK 2619 2640 2622 2623 2655 C3' G B 40 OK OK 2653 2674 2656 2657 2689 C3' G B 41 OK OK 2687 2708 2690 2691 2723 C3' A B 42 OK OK 2721 2741 2724 2725 2756 C3' A B 43 OK OK 2754 2774 2757 2758 2789 C3' U B 44 OK OK 2787 2805 2790 2791 2819 C3' A B 45 OK OK 2817 2837 2820 2821 2852 C3' C B 46 OK OK 2850 2868 2853 2854 2883 C3' C B 47 OK OK 2881 2899 2884 2885 2914 C3' A B 48 OK OK 2912 2932 2915 2916 2947 C3' G B 49 OK OK 2945 2966 2948 2949 2981 C3' G B 50 OK OK 2979 3000 2982 2983 3015 C3' U B 51 OK OK 3013 3031 3016 3017 3045 C3' G B 52 OK OK 3043 3064 3046 3047 3079 C3' C B 53 OK OK 3077 3095 3080 3081 3110 C3' C B 54 OK OK 3108 3126 3111 3112 3141 C3' C B 55 OK OK 3139 3157 3142 3143 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1412 C4' G B 1 OK OK 1414 1432 1411 1413 1446 C4' G B 2 OK OK 1448 1466 1445 1447 1480 C4' G B 3 OK OK 1482 1500 1479 1481 1514 C4' C B 4 OK OK 1516 1531 1513 1515 1545 C4' C B 5 OK OK 1547 1562 1544 1546 1576 C4' A B 6 OK OK 1578 1595 1575 1577 1609 C4' U B 7 OK OK 1611 1626 1608 1610 1639 C4' A B 8 OK OK 1641 1658 1638 1640 1672 C4' C B 9 OK OK 1674 1689 1671 1673 1703 C4' C B 10 OK OK 1705 1720 1702 1704 1734 C4' U B 11 OK OK 1736 1751 1733 1735 1764 C4' C B 12 OK OK 1766 1781 1763 1765 1795 C4' U B 13 OK OK 1797 1812 1794 1796 1825 C4' U B 14 OK OK 1827 1842 1824 1826 1855 C4' G B 15 OK OK 1857 1875 1854 1856 1889 C4' G B 16 OK OK 1891 1909 1888 1890 1923 C4' G B 17 OK OK 1925 1943 1922 1924 1957 C4' C B 18 OK OK 1959 1974 1956 1958 1988 C4' C B 19 OK OK 1990 2005 1987 1989 2019 C4' U B 20 OK OK 2021 2036 2018 2020 2049 C4' G B 21 OK OK 2051 2069 2048 2050 2083 C4' G B 22 OK OK 2085 2103 2082 2084 2117 C4' U B 23 OK OK 2119 2134 2116 2118 2147 C4' U B 24 OK OK 2149 2164 2146 2148 2177 C4' A B 25 OK OK 2179 2196 2176 2178 2210 C4' G B 26 OK OK 2212 2230 2209 2211 2244 C4' U B 27 OK OK 2246 2261 2243 2245 2274 C4' A B 28 OK OK 2276 2293 2273 2275 2307 C4' C B 29 OK OK 2309 2324 2306 2308 2338 C4' C B 30 OK OK 2340 2355 2337 2339 2369 C4' U B 31 OK OK 2371 2386 2368 2370 2399 C4' C B 32 OK OK 2401 2416 2398 2400 2430 C4' U B 33 OK OK 2432 2447 2429 2431 2460 C4' U B 34 OK OK 2462 2477 2459 2461 2490 C4' C B 35 OK OK 2492 2507 2489 2491 2521 C4' G B 36 OK OK 2523 2541 2520 2522 2555 C4' G B 37 OK OK 2557 2575 2554 2556 2589 C4' U B 38 OK OK 2591 2606 2588 2590 2619 C4' G B 39 OK OK 2621 2639 2618 2620 2653 C4' G B 40 OK OK 2655 2673 2652 2654 2687 C4' G B 41 OK OK 2689 2707 2686 2688 2721 C4' A B 42 OK OK 2723 2740 2720 2722 2754 C4' A B 43 OK OK 2756 2773 2753 2755 2787 C4' U B 44 OK OK 2789 2804 2786 2788 2817 C4' A B 45 OK OK 2819 2836 2816 2818 2850 C4' C B 46 OK OK 2852 2867 2849 2851 2881 C4' C B 47 OK OK 2883 2898 2880 2882 2912 C4' A B 48 OK OK 2914 2931 2911 2913 2945 C4' G B 49 OK OK 2947 2965 2944 2946 2979 C4' G B 50 OK OK 2981 2999 2978 2980 3013 C4' U B 51 OK OK 3015 3030 3012 3014 3043 C4' G B 52 OK OK 3045 3063 3042 3044 3077 C4' C B 53 OK OK 3079 3094 3076 3078 3108 C4' C B 54 OK OK 3110 3125 3107 3109 3139 C4' C B 55 OK OK 3141 3156 3138 3140 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1411 C5' G B 1 OK OK 1410 1430 1431 1412 1445 C5' G B 2 OK OK 1444 1464 1465 1446 1479 C5' G B 3 OK OK 1478 1498 1499 1480 1513 C5' C B 4 OK OK 1512 1529 1530 1514 1544 C5' C B 5 OK OK 1543 1560 1561 1545 1575 C5' A B 6 OK OK 1574 1593 1594 1576 1608 C5' U B 7 OK OK 1607 1624 1625 1609 1638 C5' A B 8 OK OK 1637 1656 1657 1639 1671 C5' C B 9 OK OK 1670 1687 1688 1672 1702 C5' C B 10 OK OK 1701 1718 1719 1703 1733 C5' U B 11 OK OK 1732 1749 1750 1734 1763 C5' C B 12 OK OK 1762 1779 1780 1764 1794 C5' U B 13 OK OK 1793 1810 1811 1795 1824 C5' U B 14 OK OK 1823 1840 1841 1825 1854 C5' G B 15 OK OK 1853 1873 1874 1855 1888 C5' G B 16 OK OK 1887 1907 1908 1889 1922 C5' G B 17 OK OK 1921 1941 1942 1923 1956 C5' C B 18 OK OK 1955 1972 1973 1957 1987 C5' C B 19 OK OK 1986 2003 2004 1988 2018 C5' U B 20 OK OK 2017 2034 2035 2019 2048 C5' G B 21 OK OK 2047 2067 2068 2049 2082 C5' G B 22 OK OK 2081 2101 2102 2083 2116 C5' U B 23 OK OK 2115 2132 2133 2117 2146 C5' U B 24 OK OK 2145 2162 2163 2147 2176 C5' A B 25 OK OK 2175 2194 2195 2177 2209 C5' G B 26 OK OK 2208 2228 2229 2210 2243 C5' U B 27 OK OK 2242 2259 2260 2244 2273 C5' A B 28 OK OK 2272 2291 2292 2274 2306 C5' C B 29 OK OK 2305 2322 2323 2307 2337 C5' C B 30 OK OK 2336 2353 2354 2338 2368 C5' U B 31 OK OK 2367 2384 2385 2369 2398 C5' C B 32 OK OK 2397 2414 2415 2399 2429 C5' U B 33 OK OK 2428 2445 2446 2430 2459 C5' U B 34 OK OK 2458 2475 2476 2460 2489 C5' C B 35 OK OK 2488 2505 2506 2490 2520 C5' G B 36 OK OK 2519 2539 2540 2521 2554 C5' G B 37 OK OK 2553 2573 2574 2555 2588 C5' U B 38 OK OK 2587 2604 2605 2589 2618 C5' G B 39 OK OK 2617 2637 2638 2619 2652 C5' G B 40 OK OK 2651 2671 2672 2653 2686 C5' G B 41 OK OK 2685 2705 2706 2687 2720 C5' A B 42 OK OK 2719 2738 2739 2721 2753 C5' A B 43 OK OK 2752 2771 2772 2754 2786 C5' U B 44 OK OK 2785 2802 2803 2787 2816 C5' A B 45 OK OK 2815 2834 2835 2817 2849 C5' C B 46 OK OK 2848 2865 2866 2850 2880 C5' C B 47 OK OK 2879 2896 2897 2881 2911 C5' A B 48 OK OK 2910 2929 2930 2912 2944 C5' G B 49 OK OK 2943 2963 2964 2945 2978 C5' G B 50 OK OK 2977 2997 2998 2979 3012 C5' U B 51 OK OK 3011 3028 3029 3013 3042 C5' G B 52 OK OK 3041 3061 3062 3043 3076 C5' C B 53 OK OK 3075 3092 3093 3077 3107 C5' C B 54 OK OK 3106 3123 3124 3108 3138 C5' C B 55 OK OK 3137 3154 3155 3139 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1407 P G B 1 OK OK 1408 1409 1410 1441 P G B 2 distorted distorted 1415 1442 1443 1444 1475 P G B 3 distorted distorted 1449 1476 1477 1478 1509 P C B 4 distorted distorted 1483 1510 1511 1512 1540 P C B 5 distorted distorted 1517 1541 1542 1543 1571 P A B 6 distorted distorted 1548 1572 1573 1574 1604 P U B 7 distorted distorted 1579 1605 1606 1607 1634 P A B 8 distorted distorted 1612 1635 1636 1637 1667 P C B 9 distorted distorted 1642 1668 1669 1670 1698 P C B 10 distorted distorted 1675 1699 1700 1701 1729 P U B 11 distorted distorted 1706 1730 1731 1732 1759 P C B 12 distorted distorted 1737 1760 1761 1762 1790 P U B 13 distorted distorted 1767 1791 1792 1793 1820 P U B 14 distorted distorted 1798 1821 1822 1823 1850 P G B 15 distorted distorted 1828 1851 1852 1853 1884 P G B 16 distorted distorted 1858 1885 1886 1887 1918 P G B 17 distorted distorted 1892 1919 1920 1921 1952 P C B 18 distorted distorted 1926 1953 1954 1955 1983 P C B 19 distorted distorted 1960 1984 1985 1986 2014 P U B 20 distorted distorted 1991 2015 2016 2017 2044 P G B 21 distorted distorted 2022 2045 2046 2047 2078 P G B 22 distorted distorted 2052 2079 2080 2081 2112 P U B 23 distorted distorted 2086 2113 2114 2115 2142 P U B 24 distorted distorted 2120 2143 2144 2145 2172 P A B 25 distorted distorted 2150 2173 2174 2175 2205 P G B 26 distorted distorted 2180 2206 2207 2208 2239 P U B 27 distorted distorted 2213 2240 2241 2242 2269 P A B 28 distorted distorted 2247 2270 2271 2272 2302 P C B 29 distorted distorted 2277 2303 2304 2305 2333 P C B 30 distorted distorted 2310 2334 2335 2336 2364 P U B 31 distorted distorted 2341 2365 2366 2367 2394 P C B 32 distorted distorted 2372 2395 2396 2397 2425 P U B 33 distorted distorted 2402 2426 2427 2428 2455 P U B 34 distorted distorted 2433 2456 2457 2458 2485 P C B 35 distorted distorted 2463 2486 2487 2488 2516 P G B 36 distorted distorted 2493 2517 2518 2519 2550 P G B 37 distorted distorted 2524 2551 2552 2553 2584 P U B 38 distorted distorted 2558 2585 2586 2587 2614 P G B 39 distorted distorted 2592 2615 2616 2617 2648 P G B 40 distorted distorted 2622 2649 2650 2651 2682 P G B 41 distorted distorted 2656 2683 2684 2685 2716 P A B 42 distorted distorted 2690 2717 2718 2719 2749 P A B 43 distorted distorted 2724 2750 2751 2752 2782 P U B 44 distorted distorted 2757 2783 2784 2785 2812 P A B 45 distorted distorted 2790 2813 2814 2815 2845 P C B 46 distorted distorted 2820 2846 2847 2848 2876 P C B 47 distorted distorted 2853 2877 2878 2879 2907 P A B 48 distorted distorted 2884 2908 2909 2910 2940 P G B 49 distorted distorted 2915 2941 2942 2943 2974 P G B 50 distorted distorted 2948 2975 2976 2977 3008 P U B 51 distorted distorted 2982 3009 3010 3011 3038 P G B 52 distorted distorted 3016 3039 3040 3041 3072 P C B 53 distorted distorted 3046 3073 3074 3075 3103 P C B 54 distorted distorted 3080 3104 3105 3106 3134 P C B 55 distorted distorted 3111 3135 3136 3137 ---------------------------------------------------------------------------------