ID code: '1ECR' 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' --------------------------------------------------------------------------------- 2524 C1' A B 312 beta 2520 2525 2523 2545 C1' G B 313 beta 2541 2546 2544 2567 C1' T B 314 beta 2563 2568 2566 2587 C1' T B 315 beta 2583 2588 2586 2607 C1' A B 316 beta 2603 2608 2606 2628 C1' C B 317 beta 2624 2629 2627 2647 C1' A B 318 beta 2643 2648 2646 2668 C1' A B 319 beta 2664 2669 2667 2689 C1' C B 320 beta 2685 2690 2688 2708 C1' A B 321 beta 2704 2709 2707 2729 C1' T B 322 beta 2725 2730 2728 2749 C1' A B 323 beta 2745 2750 2748 2770 C1' C B 324 beta 2766 2771 2769 2789 C1' T B 325 beta 2785 2790 2788 2827 C1' A C 328 beta 2823 2828 2826 2848 C1' G C 329 beta 2844 2849 2847 2870 C1' T C 330 beta 2866 2871 2869 2890 C1' A C 331 beta 2886 2891 2889 2911 C1' T C 332 beta 2907 2912 2910 2931 C1' G C 333 beta 2927 2932 2930 2953 C1' T C 334 beta 2949 2954 2952 2973 C1' T C 335 beta 2969 2974 2972 2993 C1' G C 336 beta 2989 2994 2992 3015 C1' T C 337 beta 3011 3016 3014 3035 C1' A C 338 beta 3031 3036 3034 3056 C1' A C 339 beta 3052 3057 3055 3077 C1' C C 340 beta 3073 3078 3076 3096 C1' T C 341 beta 3092 3097 3095 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2523 C2' A B 312 2524 2521 2544 C2' G B 313 2545 2542 2566 C2' T B 314 2567 2564 2586 C2' T B 315 2587 2584 2606 C2' A B 316 2607 2604 2627 C2' C B 317 2628 2625 2646 C2' A B 318 2647 2644 2667 C2' A B 319 2668 2665 2688 C2' C B 320 2689 2686 2707 C2' A B 321 2708 2705 2728 C2' T B 322 2729 2726 2748 C2' A B 323 2749 2746 2769 C2' C B 324 2770 2767 2788 C2' T B 325 2789 2786 2826 C2' A C 328 2827 2824 2847 C2' G C 329 2848 2845 2869 C2' T C 330 2870 2867 2889 C2' A C 331 2890 2887 2910 C2' T C 332 2911 2908 2930 C2' G C 333 2931 2928 2952 C2' T C 334 2953 2950 2972 C2' T C 335 2973 2970 2992 C2' G C 336 2993 2990 3014 C2' T C 337 3015 3012 3034 C2' A C 338 3035 3032 3055 C2' A C 339 3056 3053 3076 C2' C C 340 3077 3074 3095 C2' T C 341 3096 3093 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2521 C3' A B 312 OK 2519 2522 2523 2542 C3' G B 313 OK 2540 2543 2544 2564 C3' T B 314 OK 2562 2565 2566 2584 C3' T B 315 OK 2582 2585 2586 2604 C3' A B 316 OK 2602 2605 2606 2625 C3' C B 317 OK 2623 2626 2627 2644 C3' A B 318 OK 2642 2645 2646 2665 C3' A B 319 OK 2663 2666 2667 2686 C3' C B 320 OK 2684 2687 2688 2705 C3' A B 321 OK 2703 2706 2707 2726 C3' T B 322 OK 2724 2727 2728 2746 C3' A B 323 OK 2744 2747 2748 2767 C3' C B 324 OK 2765 2768 2769 2786 C3' T B 325 OK 2784 2787 2788 2824 C3' A C 328 OK 2822 2825 2826 2845 C3' G C 329 OK 2843 2846 2847 2867 C3' T C 330 OK 2865 2868 2869 2887 C3' A C 331 OK 2885 2888 2889 2908 C3' T C 332 OK 2906 2909 2910 2928 C3' G C 333 OK 2926 2929 2930 2950 C3' T C 334 OK 2948 2951 2952 2970 C3' T C 335 OK 2968 2971 2972 2990 C3' G C 336 OK 2988 2991 2992 3012 C3' T C 337 OK 3010 3013 3014 3032 C3' A C 338 OK 3030 3033 3034 3053 C3' A C 339 OK 3051 3054 3055 3074 C3' C C 340 OK 3072 3075 3076 3093 C3' T C 341 OK 3091 3094 3095 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2519 C4' A B 312 OK 2521 2518 2520 2540 C4' G B 313 OK 2542 2539 2541 2562 C4' T B 314 OK 2564 2561 2563 2582 C4' T B 315 OK 2584 2581 2583 2602 C4' A B 316 OK 2604 2601 2603 2623 C4' C B 317 OK 2625 2622 2624 2642 C4' A B 318 OK 2644 2641 2643 2663 C4' A B 319 OK 2665 2662 2664 2684 C4' C B 320 OK 2686 2683 2685 2703 C4' A B 321 OK 2705 2702 2704 2724 C4' T B 322 OK 2726 2723 2725 2744 C4' A B 323 OK 2746 2743 2745 2765 C4' C B 324 OK 2767 2764 2766 2784 C4' T B 325 OK 2786 2783 2785 2822 C4' A C 328 OK 2824 2821 2823 2843 C4' G C 329 OK 2845 2842 2844 2865 C4' T C 330 OK 2867 2864 2866 2885 C4' A C 331 OK 2887 2884 2886 2906 C4' T C 332 OK 2908 2905 2907 2926 C4' G C 333 OK 2928 2925 2927 2948 C4' T C 334 OK 2950 2947 2949 2968 C4' T C 335 OK 2970 2967 2969 2988 C4' G C 336 OK 2990 2987 2989 3010 C4' T C 337 OK 3012 3009 3011 3030 C4' A C 338 OK 3032 3029 3031 3051 C4' A C 339 OK 3053 3050 3052 3072 C4' C C 340 OK 3074 3071 3073 3091 C4' T C 341 OK 3093 3090 3092 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2518 C5' A B 312 2517 2519 2539 C5' G B 313 2538 2540 2561 C5' T B 314 2560 2562 2581 C5' T B 315 2580 2582 2601 C5' A B 316 2600 2602 2622 C5' C B 317 2621 2623 2641 C5' A B 318 2640 2642 2662 C5' A B 319 2661 2663 2683 C5' C B 320 2682 2684 2702 C5' A B 321 2701 2703 2723 C5' T B 322 2722 2724 2743 C5' A B 323 2742 2744 2764 C5' C B 324 2763 2765 2783 C5' T B 325 2782 2784 2821 C5' A C 328 2820 2822 2842 C5' G C 329 2841 2843 2864 C5' T C 330 2863 2865 2884 C5' A C 331 2883 2885 2905 C5' T C 332 2904 2906 2925 C5' G C 333 2924 2926 2947 C5' T C 334 2946 2948 2967 C5' T C 335 2966 2968 2987 C5' G C 336 2986 2988 3009 C5' T C 337 3008 3010 3029 C5' A C 338 3028 3030 3050 C5' A C 339 3049 3051 3071 C5' C C 340 3070 3072 3090 C5' T C 341 3089 3091 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2535 P G B 313 OK OK 2522 2536 2537 2538 2557 P T B 314 OK OK 2543 2558 2559 2560 2577 P T B 315 OK OK 2565 2578 2579 2580 2597 P A B 316 OK OK 2585 2598 2599 2600 2618 P C B 317 OK OK 2605 2619 2620 2621 2637 P A B 318 OK OK 2626 2638 2639 2640 2658 P A B 319 OK OK 2645 2659 2660 2661 2679 P C B 320 OK OK 2666 2680 2681 2682 2698 P A B 321 OK OK 2687 2699 2700 2701 2719 P T B 322 OK OK 2706 2720 2721 2722 2739 P A B 323 OK OK 2727 2740 2741 2742 2760 P C B 324 OK OK 2747 2761 2762 2763 2779 P T B 325 OK OK 2768 2780 2781 2782 2838 P G C 329 OK OK 2825 2839 2840 2841 2860 P T C 330 OK OK 2846 2861 2862 2863 2880 P A C 331 OK OK 2868 2881 2882 2883 2901 P T C 332 OK OK 2888 2902 2903 2904 2921 P G C 333 OK OK 2909 2922 2923 2924 2943 P T C 334 OK OK 2929 2944 2945 2946 2963 P T C 335 OK OK 2951 2964 2965 2966 2983 P G C 336 OK OK 2971 2984 2985 2986 3005 P T C 337 OK OK 2991 3006 3007 3008 3025 P A C 338 OK OK 3013 3026 3027 3028 3046 P A C 339 OK OK 3033 3047 3048 3049 3067 P C C 340 OK OK 3054 3068 3069 3070 3086 P T C 341 OK OK 3075 3087 3088 3089 ---------------------------------------------------------------------------------