ID code: '1D7G' 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' --------------------------------------------------------------------------------- 2008 C1' G A 5 alpha beta 2004 2024 2009 2007 2042 C1' C A 6 alpha beta 2038 2055 2043 2041 2072 C1' C A 7 alpha beta 2068 2085 2073 2071 2102 C1' C A 8 alpha beta 2098 2115 2103 2101 2132 C1' T A 9 alpha beta 2128 2148 2133 2131 2164 C1' A A 10 alpha beta 2160 2179 2165 2163 2196 C1' C A 11 alpha beta 2192 2209 2197 2195 2226 C1' G A 12 alpha beta 2222 2242 2227 2225 2259 C1' T A 13 alpha beta 2255 2275 2260 2258 2291 C1' G A 14 alpha beta 2287 2307 2292 2290 2324 C1' C A 15 alpha beta 2320 2337 2325 2323 2354 C1' T A 16 alpha beta 2350 2370 2355 2353 2386 C1' G A 17 alpha beta 2382 2402 2387 2385 2419 C1' C A 18 alpha beta 2415 2433 2420 2418 2448 C1' G B 5 alpha beta 2444 2464 2449 2447 2482 C1' C B 6 alpha beta 2478 2495 2483 2481 2512 C1' A B 7 alpha beta 2508 2527 2513 2511 2544 C1' G B 8 alpha beta 2540 2560 2545 2543 2577 C1' C B 9 alpha beta 2573 2590 2578 2576 2607 C1' A B 10 alpha beta 2603 2622 2608 2606 2639 C1' C B 11 alpha beta 2635 2652 2640 2638 2669 C1' G B 12 alpha beta 2665 2685 2670 2668 2702 C1' T B 13 alpha beta 2698 2718 2703 2701 2734 C1' A B 14 alpha beta 2730 2749 2735 2733 2766 C1' G B 15 alpha beta 2762 2782 2767 2765 2799 C1' G B 16 alpha beta 2795 2815 2800 2798 2832 C1' G B 17 alpha beta 2828 2848 2833 2831 2865 C1' C B 18 alpha beta 2861 2879 2866 2864 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2007 C2' G A 5 OK OK 2008 2005 2031 2030 2041 C2' C A 6 OK OK 2042 2039 2061 2060 2071 C2' C A 7 OK OK 2072 2069 2091 2090 2101 C2' C A 8 OK OK 2102 2099 2121 2120 2131 C2' T A 9 OK OK 2132 2129 2146 2147 2163 C2' A A 10 OK OK 2164 2161 2185 2184 2195 C2' C A 11 OK OK 2196 2193 2215 2214 2225 C2' G A 12 OK OK 2226 2223 2248 2247 2258 C2' T A 13 OK OK 2259 2256 2273 2274 2290 C2' G A 14 OK OK 2291 2288 2313 2312 2323 C2' C A 15 OK OK 2324 2321 2343 2342 2353 C2' T A 16 OK OK 2354 2351 2368 2369 2385 C2' G A 17 OK OK 2386 2383 2408 2407 2418 C2' C A 18 OK OK 2419 2416 2439 2438 2447 C2' G B 5 OK OK 2448 2445 2471 2470 2481 C2' C B 6 OK OK 2482 2479 2501 2500 2511 C2' A B 7 OK OK 2512 2509 2533 2532 2543 C2' G B 8 OK OK 2544 2541 2566 2565 2576 C2' C B 9 OK OK 2577 2574 2596 2595 2606 C2' A B 10 OK OK 2607 2604 2628 2627 2638 C2' C B 11 OK OK 2639 2636 2658 2657 2668 C2' G B 12 OK OK 2669 2666 2691 2690 2701 C2' T B 13 OK OK 2702 2699 2716 2717 2733 C2' A B 14 OK OK 2734 2731 2755 2754 2765 C2' G B 15 OK OK 2766 2763 2788 2787 2798 C2' G B 16 OK OK 2799 2796 2821 2820 2831 C2' G B 17 OK OK 2832 2829 2854 2853 2864 C2' C B 18 OK OK 2865 2862 2885 2884 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2005 C3' G A 5 OK OK 2003 2023 2006 2007 2039 C3' C A 6 OK OK 2037 2054 2040 2041 2069 C3' C A 7 OK OK 2067 2084 2070 2071 2099 C3' C A 8 OK OK 2097 2114 2100 2101 2129 C3' T A 9 OK OK 2127 2145 2130 2131 2161 C3' A A 10 OK OK 2159 2178 2162 2163 2193 C3' C A 11 OK OK 2191 2208 2194 2195 2223 C3' G A 12 OK OK 2221 2241 2224 2225 2256 C3' T A 13 OK OK 2254 2272 2257 2258 2288 C3' G A 14 OK OK 2286 2306 2289 2290 2321 C3' C A 15 OK OK 2319 2336 2322 2323 2351 C3' T A 16 OK OK 2349 2367 2352 2353 2383 C3' G A 17 OK OK 2381 2401 2384 2385 2416 C3' C A 18 OK OK 2414 2431 2417 2418 2445 C3' G B 5 OK OK 2443 2463 2446 2447 2479 C3' C B 6 OK OK 2477 2494 2480 2481 2509 C3' A B 7 OK OK 2507 2526 2510 2511 2541 C3' G B 8 OK OK 2539 2559 2542 2543 2574 C3' C B 9 OK OK 2572 2589 2575 2576 2604 C3' A B 10 OK OK 2602 2621 2605 2606 2636 C3' C B 11 OK OK 2634 2651 2637 2638 2666 C3' G B 12 OK OK 2664 2684 2667 2668 2699 C3' T B 13 OK OK 2697 2715 2700 2701 2731 C3' A B 14 OK OK 2729 2748 2732 2733 2763 C3' G B 15 OK OK 2761 2781 2764 2765 2796 C3' G B 16 OK OK 2794 2814 2797 2798 2829 C3' G B 17 OK OK 2827 2847 2830 2831 2862 C3' C B 18 OK OK 2860 2877 2863 2864 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2003 C4' G A 5 OK OK 2005 2022 2002 2004 2037 C4' C A 6 OK OK 2039 2053 2036 2038 2067 C4' C A 7 OK OK 2069 2083 2066 2068 2097 C4' C A 8 OK OK 2099 2113 2096 2098 2127 C4' T A 9 OK OK 2129 2144 2126 2128 2159 C4' A A 10 OK OK 2161 2177 2158 2160 2191 C4' C A 11 OK OK 2193 2207 2190 2192 2221 C4' G A 12 OK OK 2223 2240 2220 2222 2254 C4' T A 13 OK OK 2256 2271 2253 2255 2286 C4' G A 14 OK OK 2288 2305 2285 2287 2319 C4' C A 15 OK OK 2321 2335 2318 2320 2349 C4' T A 16 OK OK 2351 2366 2348 2350 2381 C4' G A 17 OK OK 2383 2400 2380 2382 2414 C4' C A 18 OK OK 2416 2430 2413 2415 2443 C4' G B 5 OK OK 2445 2462 2442 2444 2477 C4' C B 6 OK OK 2479 2493 2476 2478 2507 C4' A B 7 OK OK 2509 2525 2506 2508 2539 C4' G B 8 OK OK 2541 2558 2538 2540 2572 C4' C B 9 OK OK 2574 2588 2571 2573 2602 C4' A B 10 OK OK 2604 2620 2601 2603 2634 C4' C B 11 OK OK 2636 2650 2633 2635 2664 C4' G B 12 OK OK 2666 2683 2663 2665 2697 C4' T B 13 OK OK 2699 2714 2696 2698 2729 C4' A B 14 OK OK 2731 2747 2728 2730 2761 C4' G B 15 OK OK 2763 2780 2760 2762 2794 C4' G B 16 OK OK 2796 2813 2793 2795 2827 C4' G B 17 OK OK 2829 2846 2826 2828 2860 C4' C B 18 OK OK 2862 2876 2859 2861 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2002 C5' G A 5 OK OK 2001 2020 2021 2003 2036 C5' C A 6 OK OK 2035 2051 2052 2037 2066 C5' C A 7 OK OK 2065 2081 2082 2067 2096 C5' C A 8 OK OK 2095 2111 2112 2097 2126 C5' T A 9 OK OK 2125 2142 2143 2127 2158 C5' A A 10 OK OK 2157 2175 2176 2159 2190 C5' C A 11 OK OK 2189 2205 2206 2191 2220 C5' G A 12 OK OK 2219 2238 2239 2221 2253 C5' T A 13 OK OK 2252 2269 2270 2254 2285 C5' G A 14 OK OK 2284 2303 2304 2286 2318 C5' C A 15 OK OK 2317 2333 2334 2319 2348 C5' T A 16 OK OK 2347 2364 2365 2349 2380 C5' G A 17 OK OK 2379 2398 2399 2381 2413 C5' C A 18 OK OK 2412 2428 2429 2414 2442 C5' G B 5 OK OK 2441 2460 2461 2443 2476 C5' C B 6 OK OK 2475 2491 2492 2477 2506 C5' A B 7 OK OK 2505 2523 2524 2507 2538 C5' G B 8 OK OK 2537 2556 2557 2539 2571 C5' C B 9 OK OK 2570 2586 2587 2572 2601 C5' A B 10 OK OK 2600 2618 2619 2602 2633 C5' C B 11 OK OK 2632 2648 2649 2634 2663 C5' G B 12 OK OK 2662 2681 2682 2664 2696 C5' T B 13 OK OK 2695 2712 2713 2697 2728 C5' A B 14 OK OK 2727 2745 2746 2729 2760 C5' G B 15 OK OK 2759 2778 2779 2761 2793 C5' G B 16 OK OK 2792 2811 2812 2794 2826 C5' G B 17 OK OK 2825 2844 2845 2827 2859 C5' C B 18 OK OK 2858 2874 2875 2860 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2032 P C A 6 distorted distorted 2006 2033 2034 2035 2062 P C A 7 distorted distorted 2040 2063 2064 2065 2092 P C A 8 distorted distorted 2070 2093 2094 2095 2122 P T A 9 distorted distorted 2100 2123 2124 2125 2154 P A A 10 distorted distorted 2130 2155 2156 2157 2186 P C A 11 distorted distorted 2162 2187 2188 2189 2216 P G A 12 distorted distorted 2194 2217 2218 2219 2249 P T A 13 distorted distorted 2224 2250 2251 2252 2281 P G A 14 distorted distorted 2257 2282 2283 2284 2314 P C A 15 distorted distorted 2289 2315 2316 2317 2344 P T A 16 distorted distorted 2322 2345 2346 2347 2376 P G A 17 distorted distorted 2352 2377 2378 2379 2409 P C A 18 distorted distorted 2384 2410 2411 2412 2472 P C B 6 distorted distorted 2446 2473 2474 2475 2502 P A B 7 distorted distorted 2480 2503 2504 2505 2534 P G B 8 distorted distorted 2510 2535 2536 2537 2567 P C B 9 distorted distorted 2542 2568 2569 2570 2597 P A B 10 distorted distorted 2575 2598 2599 2600 2629 P C B 11 distorted distorted 2605 2630 2631 2632 2659 P G B 12 distorted distorted 2637 2660 2661 2662 2692 P T B 13 distorted distorted 2667 2693 2694 2695 2724 P A B 14 distorted distorted 2700 2725 2726 2727 2756 P G B 15 distorted distorted 2732 2757 2758 2759 2789 P G B 16 distorted distorted 2764 2790 2791 2792 2822 P G B 17 distorted distorted 2797 2823 2824 2825 2855 P C B 18 distorted distorted 2830 2856 2857 2858 ---------------------------------------------------------------------------------