ID code: '1B3T' 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' --------------------------------------------------------------------------------- 2260 C1' G C 101 beta 2256 2261 2259 2282 C1' G C 102 beta 2278 2283 2281 2304 C1' G C 103 beta 2300 2305 2303 2326 C1' A C 104 beta 2322 2327 2325 2347 C1' A C 105 beta 2343 2348 2346 2368 C1' G C 106 beta 2364 2369 2367 2390 C1' C C 107 beta 2386 2391 2389 2409 C1' A C 108 beta 2405 2410 2408 2430 C1' T C 109 beta 2426 2431 2429 2450 C1' A C 110 beta 2446 2451 2449 2471 C1' T C 111 beta 2467 2472 2470 2491 C1' G C 112 beta 2487 2492 2490 2513 C1' C C 113 beta 2509 2514 2512 2532 C1' T C 114 beta 2528 2533 2531 2552 C1' T C 115 beta 2548 2553 2551 2572 C1' C C 116 beta 2568 2573 2571 2591 C1' C C 117 beta 2587 2592 2590 2610 C1' C C 118 beta 2606 2611 2609 2627 C1' G D 201 beta 2623 2628 2626 2649 C1' G D 202 beta 2645 2650 2648 2671 C1' G D 203 beta 2667 2672 2670 2693 C1' A D 204 beta 2689 2694 2692 2714 C1' A D 205 beta 2710 2715 2713 2735 C1' G D 206 beta 2731 2736 2734 2757 C1' C D 207 beta 2753 2758 2756 2776 C1' A D 208 beta 2772 2777 2775 2797 C1' T D 209 beta 2793 2798 2796 2817 C1' A D 210 beta 2813 2818 2816 2838 C1' T D 211 beta 2834 2839 2837 2858 C1' G D 212 beta 2854 2859 2857 2880 C1' C D 213 beta 2876 2881 2879 2899 C1' T D 214 beta 2895 2900 2898 2919 C1' T D 215 beta 2915 2920 2918 2939 C1' C D 216 beta 2935 2940 2938 2958 C1' C D 217 beta 2954 2959 2957 2977 C1' C D 218 beta 2973 2978 2976 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2259 C2' G C 101 2260 2257 2281 C2' G C 102 2282 2279 2303 C2' G C 103 2304 2301 2325 C2' A C 104 2326 2323 2346 C2' A C 105 2347 2344 2367 C2' G C 106 2368 2365 2389 C2' C C 107 2390 2387 2408 C2' A C 108 2409 2406 2429 C2' T C 109 2430 2427 2449 C2' A C 110 2450 2447 2470 C2' T C 111 2471 2468 2490 C2' G C 112 2491 2488 2512 C2' C C 113 2513 2510 2531 C2' T C 114 2532 2529 2551 C2' T C 115 2552 2549 2571 C2' C C 116 2572 2569 2590 C2' C C 117 2591 2588 2609 C2' C C 118 2610 2607 2626 C2' G D 201 2627 2624 2648 C2' G D 202 2649 2646 2670 C2' G D 203 2671 2668 2692 C2' A D 204 2693 2690 2713 C2' A D 205 2714 2711 2734 C2' G D 206 2735 2732 2756 C2' C D 207 2757 2754 2775 C2' A D 208 2776 2773 2796 C2' T D 209 2797 2794 2816 C2' A D 210 2817 2814 2837 C2' T D 211 2838 2835 2857 C2' G D 212 2858 2855 2879 C2' C D 213 2880 2877 2898 C2' T D 214 2899 2896 2918 C2' T D 215 2919 2916 2938 C2' C D 216 2939 2936 2957 C2' C D 217 2958 2955 2976 C2' C D 218 2977 2974 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2257 C3' G C 101 OK 2255 2258 2259 2279 C3' G C 102 OK 2277 2280 2281 2301 C3' G C 103 OK 2299 2302 2303 2323 C3' A C 104 OK 2321 2324 2325 2344 C3' A C 105 OK 2342 2345 2346 2365 C3' G C 106 OK 2363 2366 2367 2387 C3' C C 107 OK 2385 2388 2389 2406 C3' A C 108 OK 2404 2407 2408 2427 C3' T C 109 OK 2425 2428 2429 2447 C3' A C 110 OK 2445 2448 2449 2468 C3' T C 111 OK 2466 2469 2470 2488 C3' G C 112 OK 2486 2489 2490 2510 C3' C C 113 OK 2508 2511 2512 2529 C3' T C 114 OK 2527 2530 2531 2549 C3' T C 115 OK 2547 2550 2551 2569 C3' C C 116 OK 2567 2570 2571 2588 C3' C C 117 OK 2586 2589 2590 2607 C3' C C 118 OK 2605 2608 2609 2624 C3' G D 201 OK 2622 2625 2626 2646 C3' G D 202 OK 2644 2647 2648 2668 C3' G D 203 OK 2666 2669 2670 2690 C3' A D 204 OK 2688 2691 2692 2711 C3' A D 205 OK 2709 2712 2713 2732 C3' G D 206 OK 2730 2733 2734 2754 C3' C D 207 OK 2752 2755 2756 2773 C3' A D 208 OK 2771 2774 2775 2794 C3' T D 209 OK 2792 2795 2796 2814 C3' A D 210 OK 2812 2815 2816 2835 C3' T D 211 OK 2833 2836 2837 2855 C3' G D 212 OK 2853 2856 2857 2877 C3' C D 213 OK 2875 2878 2879 2896 C3' T D 214 OK 2894 2897 2898 2916 C3' T D 215 OK 2914 2917 2918 2936 C3' C D 216 OK 2934 2937 2938 2955 C3' C D 217 OK 2953 2956 2957 2974 C3' C D 218 OK 2972 2975 2976 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2255 C4' G C 101 OK 2257 2254 2256 2277 C4' G C 102 OK 2279 2276 2278 2299 C4' G C 103 OK 2301 2298 2300 2321 C4' A C 104 OK 2323 2320 2322 2342 C4' A C 105 OK 2344 2341 2343 2363 C4' G C 106 OK 2365 2362 2364 2385 C4' C C 107 OK 2387 2384 2386 2404 C4' A C 108 OK 2406 2403 2405 2425 C4' T C 109 OK 2427 2424 2426 2445 C4' A C 110 OK 2447 2444 2446 2466 C4' T C 111 OK 2468 2465 2467 2486 C4' G C 112 OK 2488 2485 2487 2508 C4' C C 113 OK 2510 2507 2509 2527 C4' T C 114 OK 2529 2526 2528 2547 C4' T C 115 OK 2549 2546 2548 2567 C4' C C 116 OK 2569 2566 2568 2586 C4' C C 117 OK 2588 2585 2587 2605 C4' C C 118 OK 2607 2604 2606 2622 C4' G D 201 OK 2624 2621 2623 2644 C4' G D 202 OK 2646 2643 2645 2666 C4' G D 203 OK 2668 2665 2667 2688 C4' A D 204 OK 2690 2687 2689 2709 C4' A D 205 OK 2711 2708 2710 2730 C4' G D 206 OK 2732 2729 2731 2752 C4' C D 207 OK 2754 2751 2753 2771 C4' A D 208 OK 2773 2770 2772 2792 C4' T D 209 OK 2794 2791 2793 2812 C4' A D 210 OK 2814 2811 2813 2833 C4' T D 211 OK 2835 2832 2834 2853 C4' G D 212 OK 2855 2852 2854 2875 C4' C D 213 OK 2877 2874 2876 2894 C4' T D 214 OK 2896 2893 2895 2914 C4' T D 215 OK 2916 2913 2915 2934 C4' C D 216 OK 2936 2933 2935 2953 C4' C D 217 OK 2955 2952 2954 2972 C4' C D 218 OK 2974 2971 2973 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2254 C5' G C 101 2253 2255 2276 C5' G C 102 2275 2277 2298 C5' G C 103 2297 2299 2320 C5' A C 104 2319 2321 2341 C5' A C 105 2340 2342 2362 C5' G C 106 2361 2363 2384 C5' C C 107 2383 2385 2403 C5' A C 108 2402 2404 2424 C5' T C 109 2423 2425 2444 C5' A C 110 2443 2445 2465 C5' T C 111 2464 2466 2485 C5' G C 112 2484 2486 2507 C5' C C 113 2506 2508 2526 C5' T C 114 2525 2527 2546 C5' T C 115 2545 2547 2566 C5' C C 116 2565 2567 2585 C5' C C 117 2584 2586 2604 C5' C C 118 2603 2605 2621 C5' G D 201 2620 2622 2643 C5' G D 202 2642 2644 2665 C5' G D 203 2664 2666 2687 C5' A D 204 2686 2688 2708 C5' A D 205 2707 2709 2729 C5' G D 206 2728 2730 2751 C5' C D 207 2750 2752 2770 C5' A D 208 2769 2771 2791 C5' T D 209 2790 2792 2811 C5' A D 210 2810 2812 2832 C5' T D 211 2831 2833 2852 C5' G D 212 2851 2853 2874 C5' C D 213 2873 2875 2893 C5' T D 214 2892 2894 2913 C5' T D 215 2912 2914 2933 C5' C D 216 2932 2934 2952 C5' C D 217 2951 2953 2971 C5' C D 218 2970 2972 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2272 P G C 102 OK OK 2258 2273 2274 2275 2294 P G C 103 OK OK 2280 2295 2296 2297 2316 P A C 104 OK OK 2302 2317 2318 2319 2337 P A C 105 OK OK 2324 2338 2339 2340 2358 P G C 106 OK OK 2345 2359 2360 2361 2380 P C C 107 OK OK 2366 2381 2382 2383 2399 P A C 108 OK OK 2388 2400 2401 2402 2420 P T C 109 OK OK 2407 2421 2422 2423 2440 P A C 110 OK OK 2428 2441 2442 2443 2461 P T C 111 OK OK 2448 2462 2463 2464 2481 P G C 112 OK OK 2469 2482 2483 2484 2503 P C C 113 OK OK 2489 2504 2505 2506 2522 P T C 114 OK OK 2511 2523 2524 2525 2542 P T C 115 OK OK 2530 2543 2544 2545 2562 P C C 116 OK OK 2550 2563 2564 2565 2581 P C C 117 OK OK 2570 2582 2583 2584 2600 P C C 118 OK OK 2589 2601 2602 2603 2639 P G D 202 OK OK 2625 2640 2641 2642 2661 P G D 203 OK OK 2647 2662 2663 2664 2683 P A D 204 OK OK 2669 2684 2685 2686 2704 P A D 205 OK OK 2691 2705 2706 2707 2725 P G D 206 OK OK 2712 2726 2727 2728 2747 P C D 207 OK OK 2733 2748 2749 2750 2766 P A D 208 OK OK 2755 2767 2768 2769 2787 P T D 209 OK OK 2774 2788 2789 2790 2807 P A D 210 OK OK 2795 2808 2809 2810 2828 P T D 211 OK OK 2815 2829 2830 2831 2848 P G D 212 OK OK 2836 2849 2850 2851 2870 P C D 213 OK OK 2856 2871 2872 2873 2889 P T D 214 OK OK 2878 2890 2891 2892 2909 P T D 215 OK OK 2897 2910 2911 2912 2929 P C D 216 OK OK 2917 2930 2931 2932 2948 P C D 217 OK OK 2937 2949 2950 2951 2967 P C D 218 OK OK 2956 2968 2969 2970 ---------------------------------------------------------------------------------