ID code: '4ERD' 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' --------------------------------------------------------------------------------- 1840 C1' G C 117 beta 1835 1841 1838 1863 C1' G C 118 beta 1858 1864 1861 1886 C1' U C 119 beta 1881 1887 1884 1906 C1' C C 120 beta 1901 1907 1904 1926 C1' G C 121 beta 1921 1927 1924 1949 C1' A C 122 beta 1944 1950 1947 1971 C1' C C 123 beta 1966 1972 1969 1991 C1' A C 124 beta 1986 1992 1989 2013 C1' U C 125 beta 2008 2014 2011 2033 C1' C C 126 beta 2028 2034 2031 2053 C1' U C 127 beta 2048 2054 2051 2073 C1' U C 128 beta 2068 2074 2071 2093 C1' C C 141 beta 2088 2094 2091 2113 C1' G C 142 beta 2108 2114 2111 2136 C1' G C 143 beta 2131 2137 2134 2159 C1' A C 144 beta 2154 2160 2157 2181 C1' U C 145 beta 2176 2182 2179 2201 C1' G C 146 beta 2196 2202 2199 2224 C1' G C 147 beta 2219 2225 2222 2247 C1' A C 148 beta 2242 2248 2245 2269 C1' C C 149 beta 2264 2270 2267 2289 C1' C C 150 beta 2284 2290 2287 2310 C1' G D 117 beta 2305 2311 2308 2333 C1' G D 118 beta 2328 2334 2331 2356 C1' U D 119 beta 2351 2357 2354 2376 C1' C D 120 beta 2371 2377 2374 2396 C1' G D 121 beta 2391 2397 2394 2419 C1' A D 122 beta 2414 2420 2417 2441 C1' C D 123 beta 2436 2442 2439 2461 C1' A D 124 beta 2456 2462 2459 2483 C1' U D 125 beta 2478 2484 2481 2503 C1' C D 126 beta 2498 2504 2501 2523 C1' U D 127 beta 2518 2524 2521 2543 C1' U D 128 beta 2538 2544 2541 2563 C1' C D 141 beta 2558 2564 2561 2583 C1' G D 142 beta 2578 2584 2581 2606 C1' G D 143 beta 2601 2607 2604 2629 C1' A D 144 beta 2624 2630 2627 2651 C1' U D 145 beta 2646 2652 2649 2671 C1' G D 146 beta 2666 2672 2669 2694 C1' G D 147 beta 2689 2695 2692 2717 C1' A D 148 beta 2712 2718 2715 2739 C1' C D 149 beta 2734 2740 2737 2759 C1' C D 150 beta 2754 2760 2757 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1838 C2' G C 117 OK 1840 1836 1839 1861 C2' G C 118 OK 1863 1859 1862 1884 C2' U C 119 OK 1886 1882 1885 1904 C2' C C 120 OK 1906 1902 1905 1924 C2' G C 121 OK 1926 1922 1925 1947 C2' A C 122 OK 1949 1945 1948 1969 C2' C C 123 OK 1971 1967 1970 1989 C2' A C 124 OK 1991 1987 1990 2011 C2' U C 125 OK 2013 2009 2012 2031 C2' C C 126 OK 2033 2029 2032 2051 C2' U C 127 OK 2053 2049 2052 2071 C2' U C 128 OK 2073 2069 2072 2091 C2' C C 141 OK 2093 2089 2092 2111 C2' G C 142 OK 2113 2109 2112 2134 C2' G C 143 OK 2136 2132 2135 2157 C2' A C 144 OK 2159 2155 2158 2179 C2' U C 145 OK 2181 2177 2180 2199 C2' G C 146 OK 2201 2197 2200 2222 C2' G C 147 OK 2224 2220 2223 2245 C2' A C 148 OK 2247 2243 2246 2267 C2' C C 149 OK 2269 2265 2268 2287 C2' C C 150 OK 2289 2285 2288 2308 C2' G D 117 OK 2310 2306 2309 2331 C2' G D 118 OK 2333 2329 2332 2354 C2' U D 119 OK 2356 2352 2355 2374 C2' C D 120 OK 2376 2372 2375 2394 C2' G D 121 OK 2396 2392 2395 2417 C2' A D 122 OK 2419 2415 2418 2439 C2' C D 123 OK 2441 2437 2440 2459 C2' A D 124 OK 2461 2457 2460 2481 C2' U D 125 OK 2483 2479 2482 2501 C2' C D 126 OK 2503 2499 2502 2521 C2' U D 127 OK 2523 2519 2522 2541 C2' U D 128 OK 2543 2539 2542 2561 C2' C D 141 OK 2563 2559 2562 2581 C2' G D 142 OK 2583 2579 2582 2604 C2' G D 143 OK 2606 2602 2605 2627 C2' A D 144 OK 2629 2625 2628 2649 C2' U D 145 OK 2651 2647 2650 2669 C2' G D 146 OK 2671 2667 2670 2692 C2' G D 147 OK 2694 2690 2693 2715 C2' A D 148 OK 2717 2713 2716 2737 C2' C D 149 OK 2739 2735 2738 2757 C2' C D 150 OK 2759 2755 2758 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1836 C3' G C 117 OK 1834 1837 1838 1859 C3' G C 118 OK 1857 1860 1861 1882 C3' U C 119 OK 1880 1883 1884 1902 C3' C C 120 OK 1900 1903 1904 1922 C3' G C 121 OK 1920 1923 1924 1945 C3' A C 122 OK 1943 1946 1947 1967 C3' C C 123 OK 1965 1968 1969 1987 C3' A C 124 OK 1985 1988 1989 2009 C3' U C 125 OK 2007 2010 2011 2029 C3' C C 126 OK 2027 2030 2031 2049 C3' U C 127 OK 2047 2050 2051 2069 C3' U C 128 OK 2067 2070 2071 2089 C3' C C 141 OK 2087 2090 2091 2109 C3' G C 142 OK 2107 2110 2111 2132 C3' G C 143 OK 2130 2133 2134 2155 C3' A C 144 OK 2153 2156 2157 2177 C3' U C 145 OK 2175 2178 2179 2197 C3' G C 146 OK 2195 2198 2199 2220 C3' G C 147 OK 2218 2221 2222 2243 C3' A C 148 OK 2241 2244 2245 2265 C3' C C 149 OK 2263 2266 2267 2285 C3' C C 150 OK 2283 2286 2287 2306 C3' G D 117 OK 2304 2307 2308 2329 C3' G D 118 OK 2327 2330 2331 2352 C3' U D 119 OK 2350 2353 2354 2372 C3' C D 120 OK 2370 2373 2374 2392 C3' G D 121 OK 2390 2393 2394 2415 C3' A D 122 OK 2413 2416 2417 2437 C3' C D 123 OK 2435 2438 2439 2457 C3' A D 124 OK 2455 2458 2459 2479 C3' U D 125 OK 2477 2480 2481 2499 C3' C D 126 OK 2497 2500 2501 2519 C3' U D 127 OK 2517 2520 2521 2539 C3' U D 128 OK 2537 2540 2541 2559 C3' C D 141 OK 2557 2560 2561 2579 C3' G D 142 OK 2577 2580 2581 2602 C3' G D 143 OK 2600 2603 2604 2625 C3' A D 144 OK 2623 2626 2627 2647 C3' U D 145 OK 2645 2648 2649 2667 C3' G D 146 OK 2665 2668 2669 2690 C3' G D 147 OK 2688 2691 2692 2713 C3' A D 148 OK 2711 2714 2715 2735 C3' C D 149 OK 2733 2736 2737 2755 C3' C D 150 OK 2753 2756 2757 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1834 C4' G C 117 OK 1836 1833 1835 1857 C4' G C 118 OK 1859 1856 1858 1880 C4' U C 119 OK 1882 1879 1881 1900 C4' C C 120 OK 1902 1899 1901 1920 C4' G C 121 OK 1922 1919 1921 1943 C4' A C 122 OK 1945 1942 1944 1965 C4' C C 123 OK 1967 1964 1966 1985 C4' A C 124 OK 1987 1984 1986 2007 C4' U C 125 OK 2009 2006 2008 2027 C4' C C 126 OK 2029 2026 2028 2047 C4' U C 127 OK 2049 2046 2048 2067 C4' U C 128 OK 2069 2066 2068 2087 C4' C C 141 OK 2089 2086 2088 2107 C4' G C 142 OK 2109 2106 2108 2130 C4' G C 143 OK 2132 2129 2131 2153 C4' A C 144 OK 2155 2152 2154 2175 C4' U C 145 OK 2177 2174 2176 2195 C4' G C 146 OK 2197 2194 2196 2218 C4' G C 147 OK 2220 2217 2219 2241 C4' A C 148 OK 2243 2240 2242 2263 C4' C C 149 OK 2265 2262 2264 2283 C4' C C 150 OK 2285 2282 2284 2304 C4' G D 117 OK 2306 2303 2305 2327 C4' G D 118 OK 2329 2326 2328 2350 C4' U D 119 OK 2352 2349 2351 2370 C4' C D 120 OK 2372 2369 2371 2390 C4' G D 121 OK 2392 2389 2391 2413 C4' A D 122 OK 2415 2412 2414 2435 C4' C D 123 OK 2437 2434 2436 2455 C4' A D 124 OK 2457 2454 2456 2477 C4' U D 125 OK 2479 2476 2478 2497 C4' C D 126 OK 2499 2496 2498 2517 C4' U D 127 OK 2519 2516 2518 2537 C4' U D 128 OK 2539 2536 2538 2557 C4' C D 141 OK 2559 2556 2558 2577 C4' G D 142 OK 2579 2576 2578 2600 C4' G D 143 OK 2602 2599 2601 2623 C4' A D 144 OK 2625 2622 2624 2645 C4' U D 145 OK 2647 2644 2646 2665 C4' G D 146 OK 2667 2664 2666 2688 C4' G D 147 OK 2690 2687 2689 2711 C4' A D 148 OK 2713 2710 2712 2733 C4' C D 149 OK 2735 2732 2734 2753 C4' C D 150 OK 2755 2752 2754 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1833 C5' G C 117 1832 1834 1856 C5' G C 118 1855 1857 1879 C5' U C 119 1878 1880 1899 C5' C C 120 1898 1900 1919 C5' G C 121 1918 1920 1942 C5' A C 122 1941 1943 1964 C5' C C 123 1963 1965 1984 C5' A C 124 1983 1985 2006 C5' U C 125 2005 2007 2026 C5' C C 126 2025 2027 2046 C5' U C 127 2045 2047 2066 C5' U C 128 2065 2067 2086 C5' C C 141 2085 2087 2106 C5' G C 142 2105 2107 2129 C5' G C 143 2128 2130 2152 C5' A C 144 2151 2153 2174 C5' U C 145 2173 2175 2194 C5' G C 146 2193 2195 2217 C5' G C 147 2216 2218 2240 C5' A C 148 2239 2241 2262 C5' C C 149 2261 2263 2282 C5' C C 150 2281 2283 2303 C5' G D 117 2302 2304 2326 C5' G D 118 2325 2327 2349 C5' U D 119 2348 2350 2369 C5' C D 120 2368 2370 2389 C5' G D 121 2388 2390 2412 C5' A D 122 2411 2413 2434 C5' C D 123 2433 2435 2454 C5' A D 124 2453 2455 2476 C5' U D 125 2475 2477 2496 C5' C D 126 2495 2497 2516 C5' U D 127 2515 2517 2536 C5' U D 128 2535 2537 2556 C5' C D 141 2555 2557 2576 C5' G D 142 2575 2577 2599 C5' G D 143 2598 2600 2622 C5' A D 144 2621 2623 2644 C5' U D 145 2643 2645 2664 C5' G D 146 2663 2665 2687 C5' G D 147 2686 2688 2710 C5' A D 148 2709 2711 2732 C5' C D 149 2731 2733 2752 C5' C D 150 2751 2753 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1829 P G C 117 distorted distorted 1830 1831 1832 1852 P G C 118 distorted distorted 1837 1853 1854 1855 1875 P U C 119 distorted distorted 1860 1876 1877 1878 1895 P C C 120 distorted distorted 1883 1896 1897 1898 1915 P G C 121 distorted distorted 1903 1916 1917 1918 1938 P A C 122 distorted distorted 1923 1939 1940 1941 1960 P C C 123 distorted distorted 1946 1961 1962 1963 1980 P A C 124 distorted distorted 1968 1981 1982 1983 2002 P U C 125 distorted distorted 1988 2003 2004 2005 2022 P C C 126 distorted distorted 2010 2023 2024 2025 2042 P U C 127 distorted distorted 2030 2043 2044 2045 2062 P U C 128 distorted distorted 2050 2063 2064 2065 2082 P C C 141 distorted distorted 2070 2083 2084 2085 2102 P G C 142 distorted distorted 2090 2103 2104 2105 2125 P G C 143 distorted distorted 2110 2126 2127 2128 2148 P A C 144 distorted distorted 2133 2149 2150 2151 2170 P U C 145 distorted distorted 2156 2171 2172 2173 2190 P G C 146 distorted distorted 2178 2191 2192 2193 2213 P G C 147 distorted distorted 2198 2214 2215 2216 2236 P A C 148 distorted distorted 2221 2237 2238 2239 2258 P C C 149 distorted distorted 2244 2259 2260 2261 2278 P C C 150 distorted distorted 2266 2279 2280 2281 2299 P G D 117 distorted distorted 2300 2301 2302 2322 P G D 118 distorted distorted 2307 2323 2324 2325 2345 P U D 119 distorted distorted 2330 2346 2347 2348 2365 P C D 120 distorted distorted 2353 2366 2367 2368 2385 P G D 121 distorted distorted 2373 2386 2387 2388 2408 P A D 122 distorted distorted 2393 2409 2410 2411 2430 P C D 123 distorted distorted 2416 2431 2432 2433 2450 P A D 124 distorted distorted 2438 2451 2452 2453 2472 P U D 125 distorted distorted 2458 2473 2474 2475 2492 P C D 126 distorted distorted 2480 2493 2494 2495 2512 P U D 127 distorted distorted 2500 2513 2514 2515 2532 P U D 128 distorted distorted 2520 2533 2534 2535 2552 P C D 141 distorted distorted 2540 2553 2554 2555 2572 P G D 142 distorted distorted 2560 2573 2574 2575 2595 P G D 143 distorted distorted 2580 2596 2597 2598 2618 P A D 144 distorted distorted 2603 2619 2620 2621 2640 P U D 145 distorted distorted 2626 2641 2642 2643 2660 P G D 146 distorted distorted 2648 2661 2662 2663 2683 P G D 147 distorted distorted 2668 2684 2685 2686 2706 P A D 148 distorted distorted 2691 2707 2708 2709 2728 P C D 149 distorted distorted 2714 2729 2730 2731 2748 P C D 150 distorted distorted 2736 2749 2750 2751 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