ID code: '1AWC' 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' --------------------------------------------------------------------------------- 2094 C1' A D 2 beta 2090 2095 2093 2115 C1' +U D 3 beta 2111 2116 2114 2134 C1' G D 4 beta 2130 2135 2133 2156 C1' A D 5 beta 2152 2157 2155 2177 C1' C D 6 beta 2173 2178 2176 2196 C1' C D 7 beta 2192 2197 2195 2215 C1' G D 8 beta 2211 2216 2214 2237 C1' G D 9 beta 2233 2238 2236 2259 C1' A D 10 beta 2255 2260 2258 2280 C1' A D 11 beta 2276 2281 2279 2301 C1' G D 12 beta 2297 2302 2300 2323 C1' T D 13 beta 2319 2324 2322 2343 C1' A D 14 beta 2339 2344 2342 2364 C1' +C D 15 beta 2360 2365 2363 2383 C1' A D 16 beta 2379 2384 2382 2404 C1' C D 17 beta 2400 2405 2403 2423 C1' +C D 18 beta 2419 2424 2422 2442 C1' G D 19 beta 2438 2443 2441 2464 C1' G D 20 beta 2460 2465 2463 2486 C1' A D 21 beta 2482 2487 2485 2528 C1' T E 23 beta 2524 2529 2527 2548 C1' C E 24 beta 2544 2549 2547 2567 C1' C E 25 beta 2563 2568 2566 2586 C1' G E 26 beta 2582 2587 2585 2608 C1' G E 27 beta 2604 2609 2607 2630 C1' +U E 28 beta 2626 2631 2629 2649 C1' G E 29 beta 2645 2650 2648 2671 C1' +U E 30 beta 2667 2672 2670 2690 C1' A E 31 beta 2686 2691 2689 2711 C1' C E 32 beta 2707 2712 2710 2730 C1' T E 33 beta 2726 2731 2729 2750 C1' T E 34 beta 2746 2751 2749 2770 C1' C E 35 beta 2766 2771 2769 2789 C1' C E 36 beta 2785 2790 2788 2808 C1' G E 37 beta 2804 2809 2807 2830 C1' G E 38 beta 2826 2831 2829 2852 C1' T E 39 beta 2848 2853 2851 2872 C1' C E 40 beta 2868 2873 2871 2891 C1' A E 41 beta 2887 2892 2890 2912 C1' T E 42 beta 2908 2913 2911 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2093 C2' A D 2 2094 2091 2114 C2' +U D 3 2115 2112 2133 C2' G D 4 2134 2131 2155 C2' A D 5 2156 2153 2176 C2' C D 6 2177 2174 2195 C2' C D 7 2196 2193 2214 C2' G D 8 2215 2212 2236 C2' G D 9 2237 2234 2258 C2' A D 10 2259 2256 2279 C2' A D 11 2280 2277 2300 C2' G D 12 2301 2298 2322 C2' T D 13 2323 2320 2342 C2' A D 14 2343 2340 2363 C2' +C D 15 2364 2361 2382 C2' A D 16 2383 2380 2403 C2' C D 17 2404 2401 2422 C2' +C D 18 2423 2420 2441 C2' G D 19 2442 2439 2463 C2' G D 20 2464 2461 2485 C2' A D 21 2486 2483 2527 C2' T E 23 2528 2525 2547 C2' C E 24 2548 2545 2566 C2' C E 25 2567 2564 2585 C2' G E 26 2586 2583 2607 C2' G E 27 2608 2605 2629 C2' +U E 28 2630 2627 2648 C2' G E 29 2649 2646 2670 C2' +U E 30 2671 2668 2689 C2' A E 31 2690 2687 2710 C2' C E 32 2711 2708 2729 C2' T E 33 2730 2727 2749 C2' T E 34 2750 2747 2769 C2' C E 35 2770 2767 2788 C2' C E 36 2789 2786 2807 C2' G E 37 2808 2805 2829 C2' G E 38 2830 2827 2851 C2' T E 39 2852 2849 2871 C2' C E 40 2872 2869 2890 C2' A E 41 2891 2888 2911 C2' T E 42 2912 2909 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2091 C3' A D 2 OK 2089 2092 2093 2112 C3' +U D 3 OK 2110 2113 2114 2131 C3' G D 4 OK 2129 2132 2133 2153 C3' A D 5 OK 2151 2154 2155 2174 C3' C D 6 OK 2172 2175 2176 2193 C3' C D 7 OK 2191 2194 2195 2212 C3' G D 8 OK 2210 2213 2214 2234 C3' G D 9 OK 2232 2235 2236 2256 C3' A D 10 OK 2254 2257 2258 2277 C3' A D 11 OK 2275 2278 2279 2298 C3' G D 12 OK 2296 2299 2300 2320 C3' T D 13 OK 2318 2321 2322 2340 C3' A D 14 OK 2338 2341 2342 2361 C3' +C D 15 OK 2359 2362 2363 2380 C3' A D 16 OK 2378 2381 2382 2401 C3' C D 17 OK 2399 2402 2403 2420 C3' +C D 18 OK 2418 2421 2422 2439 C3' G D 19 OK 2437 2440 2441 2461 C3' G D 20 OK 2459 2462 2463 2483 C3' A D 21 OK 2481 2484 2485 2525 C3' T E 23 OK 2523 2526 2527 2545 C3' C E 24 OK 2543 2546 2547 2564 C3' C E 25 OK 2562 2565 2566 2583 C3' G E 26 OK 2581 2584 2585 2605 C3' G E 27 OK 2603 2606 2607 2627 C3' +U E 28 OK 2625 2628 2629 2646 C3' G E 29 OK 2644 2647 2648 2668 C3' +U E 30 OK 2666 2669 2670 2687 C3' A E 31 OK 2685 2688 2689 2708 C3' C E 32 OK 2706 2709 2710 2727 C3' T E 33 OK 2725 2728 2729 2747 C3' T E 34 OK 2745 2748 2749 2767 C3' C E 35 OK 2765 2768 2769 2786 C3' C E 36 OK 2784 2787 2788 2805 C3' G E 37 OK 2803 2806 2807 2827 C3' G E 38 OK 2825 2828 2829 2849 C3' T E 39 OK 2847 2850 2851 2869 C3' C E 40 OK 2867 2870 2871 2888 C3' A E 41 OK 2886 2889 2890 2909 C3' T E 42 OK 2907 2910 2911 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2089 C4' A D 2 OK 2091 2088 2090 2110 C4' +U D 3 OK 2112 2109 2111 2129 C4' G D 4 OK 2131 2128 2130 2151 C4' A D 5 OK 2153 2150 2152 2172 C4' C D 6 OK 2174 2171 2173 2191 C4' C D 7 OK 2193 2190 2192 2210 C4' G D 8 OK 2212 2209 2211 2232 C4' G D 9 OK 2234 2231 2233 2254 C4' A D 10 OK 2256 2253 2255 2275 C4' A D 11 OK 2277 2274 2276 2296 C4' G D 12 OK 2298 2295 2297 2318 C4' T D 13 OK 2320 2317 2319 2338 C4' A D 14 OK 2340 2337 2339 2359 C4' +C D 15 OK 2361 2358 2360 2378 C4' A D 16 OK 2380 2377 2379 2399 C4' C D 17 OK 2401 2398 2400 2418 C4' +C D 18 OK 2420 2417 2419 2437 C4' G D 19 OK 2439 2436 2438 2459 C4' G D 20 OK 2461 2458 2460 2481 C4' A D 21 OK 2483 2480 2482 2523 C4' T E 23 OK 2525 2522 2524 2543 C4' C E 24 OK 2545 2542 2544 2562 C4' C E 25 OK 2564 2561 2563 2581 C4' G E 26 OK 2583 2580 2582 2603 C4' G E 27 OK 2605 2602 2604 2625 C4' +U E 28 OK 2627 2624 2626 2644 C4' G E 29 OK 2646 2643 2645 2666 C4' +U E 30 OK 2668 2665 2667 2685 C4' A E 31 OK 2687 2684 2686 2706 C4' C E 32 OK 2708 2705 2707 2725 C4' T E 33 OK 2727 2724 2726 2745 C4' T E 34 OK 2747 2744 2746 2765 C4' C E 35 OK 2767 2764 2766 2784 C4' C E 36 OK 2786 2783 2785 2803 C4' G E 37 OK 2805 2802 2804 2825 C4' G E 38 OK 2827 2824 2826 2847 C4' T E 39 OK 2849 2846 2848 2867 C4' C E 40 OK 2869 2866 2868 2886 C4' A E 41 OK 2888 2885 2887 2907 C4' T E 42 OK 2909 2906 2908 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2088 C5' A D 2 2087 2089 2109 C5' +U D 3 2108 2110 2128 C5' G D 4 2127 2129 2150 C5' A D 5 2149 2151 2171 C5' C D 6 2170 2172 2190 C5' C D 7 2189 2191 2209 C5' G D 8 2208 2210 2231 C5' G D 9 2230 2232 2253 C5' A D 10 2252 2254 2274 C5' A D 11 2273 2275 2295 C5' G D 12 2294 2296 2317 C5' T D 13 2316 2318 2337 C5' A D 14 2336 2338 2358 C5' +C D 15 2357 2359 2377 C5' A D 16 2376 2378 2398 C5' C D 17 2397 2399 2417 C5' +C D 18 2416 2418 2436 C5' G D 19 2435 2437 2458 C5' G D 20 2457 2459 2480 C5' A D 21 2479 2481 2522 C5' T E 23 2521 2523 2542 C5' C E 24 2541 2543 2561 C5' C E 25 2560 2562 2580 C5' G E 26 2579 2581 2602 C5' G E 27 2601 2603 2624 C5' +U E 28 2623 2625 2643 C5' G E 29 2642 2644 2665 C5' +U E 30 2664 2666 2684 C5' A E 31 2683 2685 2705 C5' C E 32 2704 2706 2724 C5' T E 33 2723 2725 2744 C5' T E 34 2743 2745 2764 C5' C E 35 2763 2765 2783 C5' C E 36 2782 2784 2802 C5' G E 37 2801 2803 2824 C5' G E 38 2823 2825 2846 C5' T E 39 2845 2847 2866 C5' C E 40 2865 2867 2885 C5' A E 41 2884 2886 2906 C5' T E 42 2905 2907 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2105 P +U D 3 OK OK 2092 2106 2107 2108 2124 P G D 4 OK OK 2113 2125 2126 2127 2146 P A D 5 OK OK 2132 2147 2148 2149 2167 P C D 6 OK OK 2154 2168 2169 2170 2186 P C D 7 OK OK 2175 2187 2188 2189 2205 P G D 8 OK OK 2194 2206 2207 2208 2227 P G D 9 OK OK 2213 2228 2229 2230 2249 P A D 10 OK OK 2235 2250 2251 2252 2270 P A D 11 OK OK 2257 2271 2272 2273 2291 P G D 12 OK OK 2278 2292 2293 2294 2313 P T D 13 OK OK 2299 2314 2315 2316 2333 P A D 14 OK OK 2321 2334 2335 2336 2354 P +C D 15 OK OK 2341 2355 2356 2357 2373 P A D 16 OK OK 2362 2374 2375 2376 2394 P C D 17 OK OK 2381 2395 2396 2397 2413 P +C D 18 OK OK 2402 2414 2415 2416 2432 P G D 19 OK OK 2421 2433 2434 2435 2454 P G D 20 OK OK 2440 2455 2456 2457 2476 P A D 21 OK OK 2462 2477 2478 2479 2538 P C E 24 OK OK 2526 2539 2540 2541 2557 P C E 25 OK OK 2546 2558 2559 2560 2576 P G E 26 OK OK 2565 2577 2578 2579 2598 P G E 27 OK OK 2584 2599 2600 2601 2620 P +U E 28 OK OK 2606 2621 2622 2623 2639 P G E 29 OK OK 2628 2640 2641 2642 2661 P +U E 30 OK OK 2647 2662 2663 2664 2680 P A E 31 OK OK 2669 2681 2682 2683 2701 P C E 32 OK OK 2688 2702 2703 2704 2720 P T E 33 OK OK 2709 2721 2722 2723 2740 P T E 34 OK OK 2728 2741 2742 2743 2760 P C E 35 OK OK 2748 2761 2762 2763 2779 P C E 36 OK OK 2768 2780 2781 2782 2798 P G E 37 OK OK 2787 2799 2800 2801 2820 P G E 38 OK OK 2806 2821 2822 2823 2842 P T E 39 OK OK 2828 2843 2844 2845 2862 P C E 40 OK OK 2850 2863 2864 2865 2881 P A E 41 OK OK 2870 2882 2883 2884 2902 P T E 42 OK OK 2889 2903 2904 2905 ---------------------------------------------------------------------------------