ID code: '3FTE' 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' --------------------------------------------------------------------------------- 1888 C1' A C1507 beta 1883 1889 1886 1910 C1' A C1508 beta 1905 1911 1908 1932 C1' C C1509 beta 1927 1933 1930 1952 C1' C C1510 beta 1947 1953 1950 1972 C1' G C1511 beta 1967 1973 1970 1995 C1' U C1512 beta 1990 1996 1993 2015 C1' A C1513 beta 2010 2016 2013 2037 C1' G C1514 beta 2032 2038 2035 2060 C1' G C1515 beta 2055 2061 2058 2083 C1' G C1516 beta 2078 2084 2081 2106 C1' G C1517 beta 2101 2107 2104 2129 C1' A C1518 beta 2124 2130 2127 2151 C1' A C1519 beta 2146 2152 2149 2173 C1' C C1520 beta 2168 2174 2171 2193 C1' C C1521 beta 2188 2194 2191 2213 C1' U C1522 beta 2208 2214 2211 2233 C1' G C1523 beta 2228 2234 2231 2256 C1' C C1524 beta 2251 2257 2254 2276 C1' G C1525 beta 2271 2277 2274 2299 C1' G C1526 beta 2294 2300 2297 2322 C1' U C1527 beta 2317 2323 2320 2342 C1' U C1528 beta 2337 2343 2340 2363 C1' A D1507 beta 2358 2364 2361 2385 C1' A D1508 beta 2380 2386 2383 2407 C1' C D1509 beta 2402 2408 2405 2427 C1' C D1510 beta 2422 2428 2425 2447 C1' G D1511 beta 2442 2448 2445 2470 C1' U D1512 beta 2465 2471 2468 2490 C1' A D1513 beta 2485 2491 2488 2512 C1' G D1514 beta 2507 2513 2510 2535 C1' G D1515 beta 2530 2536 2533 2558 C1' G D1516 beta 2553 2559 2556 2581 C1' G D1517 beta 2576 2582 2579 2604 C1' A D1518 beta 2599 2605 2602 2626 C1' A D1519 beta 2621 2627 2624 2648 C1' C D1520 beta 2643 2649 2646 2668 C1' C D1521 beta 2663 2669 2666 2688 C1' U D1522 beta 2683 2689 2686 2708 C1' G D1523 beta 2703 2709 2706 2731 C1' C D1524 beta 2726 2732 2729 2751 C1' G D1525 beta 2746 2752 2749 2774 C1' G D1526 beta 2769 2775 2772 2797 C1' U D1527 beta 2792 2798 2795 2817 C1' U D1528 beta 2812 2818 2815 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1886 C2' A C1507 OK 1888 1884 1887 1908 C2' A C1508 OK 1910 1906 1909 1930 C2' C C1509 OK 1932 1928 1931 1950 C2' C C1510 OK 1952 1948 1951 1970 C2' G C1511 OK 1972 1968 1971 1993 C2' U C1512 OK 1995 1991 1994 2013 C2' A C1513 OK 2015 2011 2014 2035 C2' G C1514 OK 2037 2033 2036 2058 C2' G C1515 OK 2060 2056 2059 2081 C2' G C1516 OK 2083 2079 2082 2104 C2' G C1517 OK 2106 2102 2105 2127 C2' A C1518 OK 2129 2125 2128 2149 C2' A C1519 OK 2151 2147 2150 2171 C2' C C1520 OK 2173 2169 2172 2191 C2' C C1521 OK 2193 2189 2192 2211 C2' U C1522 OK 2213 2209 2212 2231 C2' G C1523 OK 2233 2229 2232 2254 C2' C C1524 OK 2256 2252 2255 2274 C2' G C1525 OK 2276 2272 2275 2297 C2' G C1526 OK 2299 2295 2298 2320 C2' U C1527 OK 2322 2318 2321 2340 C2' U C1528 OK 2342 2338 2341 2361 C2' A D1507 OK 2363 2359 2362 2383 C2' A D1508 OK 2385 2381 2384 2405 C2' C D1509 OK 2407 2403 2406 2425 C2' C D1510 OK 2427 2423 2426 2445 C2' G D1511 OK 2447 2443 2446 2468 C2' U D1512 OK 2470 2466 2469 2488 C2' A D1513 OK 2490 2486 2489 2510 C2' G D1514 OK 2512 2508 2511 2533 C2' G D1515 OK 2535 2531 2534 2556 C2' G D1516 OK 2558 2554 2557 2579 C2' G D1517 OK 2581 2577 2580 2602 C2' A D1518 OK 2604 2600 2603 2624 C2' A D1519 OK 2626 2622 2625 2646 C2' C D1520 OK 2648 2644 2647 2666 C2' C D1521 OK 2668 2664 2667 2686 C2' U D1522 OK 2688 2684 2687 2706 C2' G D1523 OK 2708 2704 2707 2729 C2' C D1524 OK 2731 2727 2730 2749 C2' G D1525 OK 2751 2747 2750 2772 C2' G D1526 OK 2774 2770 2773 2795 C2' U D1527 OK 2797 2793 2796 2815 C2' U D1528 OK 2817 2813 2816 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1884 C3' A C1507 OK 1882 1885 1886 1906 C3' A C1508 OK 1904 1907 1908 1928 C3' C C1509 OK 1926 1929 1930 1948 C3' C C1510 OK 1946 1949 1950 1968 C3' G C1511 OK 1966 1969 1970 1991 C3' U C1512 OK 1989 1992 1993 2011 C3' A C1513 OK 2009 2012 2013 2033 C3' G C1514 OK 2031 2034 2035 2056 C3' G C1515 OK 2054 2057 2058 2079 C3' G C1516 OK 2077 2080 2081 2102 C3' G C1517 OK 2100 2103 2104 2125 C3' A C1518 OK 2123 2126 2127 2147 C3' A C1519 OK 2145 2148 2149 2169 C3' C C1520 OK 2167 2170 2171 2189 C3' C C1521 OK 2187 2190 2191 2209 C3' U C1522 OK 2207 2210 2211 2229 C3' G C1523 OK 2227 2230 2231 2252 C3' C C1524 OK 2250 2253 2254 2272 C3' G C1525 OK 2270 2273 2274 2295 C3' G C1526 OK 2293 2296 2297 2318 C3' U C1527 OK 2316 2319 2320 2338 C3' U C1528 OK 2336 2339 2340 2359 C3' A D1507 OK 2357 2360 2361 2381 C3' A D1508 OK 2379 2382 2383 2403 C3' C D1509 OK 2401 2404 2405 2423 C3' C D1510 OK 2421 2424 2425 2443 C3' G D1511 OK 2441 2444 2445 2466 C3' U D1512 OK 2464 2467 2468 2486 C3' A D1513 OK 2484 2487 2488 2508 C3' G D1514 OK 2506 2509 2510 2531 C3' G D1515 OK 2529 2532 2533 2554 C3' G D1516 OK 2552 2555 2556 2577 C3' G D1517 OK 2575 2578 2579 2600 C3' A D1518 OK 2598 2601 2602 2622 C3' A D1519 OK 2620 2623 2624 2644 C3' C D1520 OK 2642 2645 2646 2664 C3' C D1521 OK 2662 2665 2666 2684 C3' U D1522 OK 2682 2685 2686 2704 C3' G D1523 OK 2702 2705 2706 2727 C3' C D1524 OK 2725 2728 2729 2747 C3' G D1525 OK 2745 2748 2749 2770 C3' G D1526 OK 2768 2771 2772 2793 C3' U D1527 OK 2791 2794 2795 2813 C3' U D1528 OK 2811 2814 2815 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1882 C4' A C1507 OK 1884 1881 1883 1904 C4' A C1508 OK 1906 1903 1905 1926 C4' C C1509 OK 1928 1925 1927 1946 C4' C C1510 OK 1948 1945 1947 1966 C4' G C1511 OK 1968 1965 1967 1989 C4' U C1512 OK 1991 1988 1990 2009 C4' A C1513 OK 2011 2008 2010 2031 C4' G C1514 OK 2033 2030 2032 2054 C4' G C1515 OK 2056 2053 2055 2077 C4' G C1516 OK 2079 2076 2078 2100 C4' G C1517 OK 2102 2099 2101 2123 C4' A C1518 OK 2125 2122 2124 2145 C4' A C1519 OK 2147 2144 2146 2167 C4' C C1520 OK 2169 2166 2168 2187 C4' C C1521 OK 2189 2186 2188 2207 C4' U C1522 OK 2209 2206 2208 2227 C4' G C1523 OK 2229 2226 2228 2250 C4' C C1524 OK 2252 2249 2251 2270 C4' G C1525 OK 2272 2269 2271 2293 C4' G C1526 OK 2295 2292 2294 2316 C4' U C1527 OK 2318 2315 2317 2336 C4' U C1528 OK 2338 2335 2337 2357 C4' A D1507 OK 2359 2356 2358 2379 C4' A D1508 OK 2381 2378 2380 2401 C4' C D1509 OK 2403 2400 2402 2421 C4' C D1510 OK 2423 2420 2422 2441 C4' G D1511 OK 2443 2440 2442 2464 C4' U D1512 OK 2466 2463 2465 2484 C4' A D1513 OK 2486 2483 2485 2506 C4' G D1514 OK 2508 2505 2507 2529 C4' G D1515 OK 2531 2528 2530 2552 C4' G D1516 OK 2554 2551 2553 2575 C4' G D1517 OK 2577 2574 2576 2598 C4' A D1518 OK 2600 2597 2599 2620 C4' A D1519 OK 2622 2619 2621 2642 C4' C D1520 OK 2644 2641 2643 2662 C4' C D1521 OK 2664 2661 2663 2682 C4' U D1522 OK 2684 2681 2683 2702 C4' G D1523 OK 2704 2701 2703 2725 C4' C D1524 OK 2727 2724 2726 2745 C4' G D1525 OK 2747 2744 2746 2768 C4' G D1526 OK 2770 2767 2769 2791 C4' U D1527 OK 2793 2790 2792 2811 C4' U D1528 OK 2813 2810 2812 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1881 C5' A C1507 1880 1882 1903 C5' A C1508 1902 1904 1925 C5' C C1509 1924 1926 1945 C5' C C1510 1944 1946 1965 C5' G C1511 1964 1966 1988 C5' U C1512 1987 1989 2008 C5' A C1513 2007 2009 2030 C5' G C1514 2029 2031 2053 C5' G C1515 2052 2054 2076 C5' G C1516 2075 2077 2099 C5' G C1517 2098 2100 2122 C5' A C1518 2121 2123 2144 C5' A C1519 2143 2145 2166 C5' C C1520 2165 2167 2186 C5' C C1521 2185 2187 2206 C5' U C1522 2205 2207 2226 C5' G C1523 2225 2227 2249 C5' C C1524 2248 2250 2269 C5' G C1525 2268 2270 2292 C5' G C1526 2291 2293 2315 C5' U C1527 2314 2316 2335 C5' U C1528 2334 2336 2356 C5' A D1507 2355 2357 2378 C5' A D1508 2377 2379 2400 C5' C D1509 2399 2401 2420 C5' C D1510 2419 2421 2440 C5' G D1511 2439 2441 2463 C5' U D1512 2462 2464 2483 C5' A D1513 2482 2484 2505 C5' G D1514 2504 2506 2528 C5' G D1515 2527 2529 2551 C5' G D1516 2550 2552 2574 C5' G D1517 2573 2575 2597 C5' A D1518 2596 2598 2619 C5' A D1519 2618 2620 2641 C5' C D1520 2640 2642 2661 C5' C D1521 2660 2662 2681 C5' U D1522 2680 2682 2701 C5' G D1523 2700 2702 2724 C5' C D1524 2723 2725 2744 C5' G D1525 2743 2745 2767 C5' G D1526 2766 2768 2790 C5' U D1527 2789 2791 2810 C5' U D1528 2809 2811 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1877 P A C1507 OK OK 1878 1879 1880 1899 P A C1508 distorted distorted 1885 1900 1901 1902 1921 P C C1509 distorted distorted 1907 1922 1923 1924 1941 P C C1510 distorted distorted 1929 1942 1943 1944 1961 P G C1511 distorted distorted 1949 1962 1963 1964 1984 P U C1512 distorted distorted 1969 1985 1986 1987 2004 P A C1513 distorted distorted 1992 2005 2006 2007 2026 P G C1514 distorted distorted 2012 2027 2028 2029 2049 P G C1515 distorted distorted 2034 2050 2051 2052 2072 P G C1516 distorted distorted 2057 2073 2074 2075 2095 P G C1517 distorted distorted 2080 2096 2097 2098 2118 P A C1518 distorted distorted 2103 2119 2120 2121 2140 P A C1519 distorted distorted 2126 2141 2142 2143 2162 P C C1520 distorted distorted 2148 2163 2164 2165 2182 P C C1521 distorted distorted 2170 2183 2184 2185 2202 P U C1522 distorted distorted 2190 2203 2204 2205 2222 P G C1523 distorted distorted 2210 2223 2224 2225 2245 P C C1524 distorted distorted 2230 2246 2247 2248 2265 P G C1525 distorted distorted 2253 2266 2267 2268 2288 P G C1526 distorted distorted 2273 2289 2290 2291 2311 P U C1527 distorted distorted 2296 2312 2313 2314 2331 P U C1528 distorted distorted 2319 2332 2333 2334 2352 P A D1507 distorted distorted 2353 2354 2355 2374 P A D1508 distorted distorted 2360 2375 2376 2377 2396 P C D1509 distorted distorted 2382 2397 2398 2399 2416 P C D1510 distorted distorted 2404 2417 2418 2419 2436 P G D1511 distorted distorted 2424 2437 2438 2439 2459 P U D1512 distorted distorted 2444 2460 2461 2462 2479 P A D1513 distorted distorted 2467 2480 2481 2482 2501 P G D1514 distorted distorted 2487 2502 2503 2504 2524 P G D1515 distorted distorted 2509 2525 2526 2527 2547 P G D1516 distorted distorted 2532 2548 2549 2550 2570 P G D1517 distorted distorted 2555 2571 2572 2573 2593 P A D1518 distorted distorted 2578 2594 2595 2596 2615 P A D1519 distorted distorted 2601 2616 2617 2618 2637 P C D1520 distorted distorted 2623 2638 2639 2640 2657 P C D1521 distorted distorted 2645 2658 2659 2660 2677 P U D1522 distorted distorted 2665 2678 2679 2680 2697 P G D1523 distorted distorted 2685 2698 2699 2700 2720 P C D1524 distorted distorted 2705 2721 2722 2723 2740 P G D1525 distorted distorted 2728 2741 2742 2743 2763 P G D1526 distorted distorted 2748 2764 2765 2766 2786 P U D1527 distorted distorted 2771 2787 2788 2789 2806 P U D1528 distorted distorted 2794 2807 2808 2809 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