ID code: '5F5H' 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' --------------------------------------------------------------------------------- 2418 C1' C C 2 beta 2413 2419 2416 2438 C1' C C 3 beta 2433 2439 2436 2458 C1' A C 4 beta 2453 2459 2456 2480 C1' C C 5 beta 2475 2481 2478 2500 C1' A C 6 beta 2495 2501 2498 2522 C1' C C 7 beta 2517 2523 2520 2542 C1' C C 8 beta 2537 2543 2540 2562 C1' G C 9 beta 2557 2563 2560 2585 C1' U C 10 beta 2580 2586 2583 2605 C1' U C 11 beta 2600 2606 2603 2625 C1' C C 12 beta 2620 2626 2623 2645 C1' U C 13 beta 2640 2646 2643 2665 C1' A C 14 beta 2660 2666 2663 2687 C1' G C 15 beta 2682 2688 2685 2710 C1' G C 16 beta 2705 2711 2708 2733 C1' U C 17 beta 2728 2734 2731 2753 C1' G C 18 beta 2748 2754 2751 2776 C1' C C 19 beta 2771 2777 2774 2796 C1' U C 20 beta 2791 2797 2794 2816 C1' G C 21 beta 2811 2817 2814 2839 C1' G C 22 beta 2834 2840 2837 2863 C1' C D 2 beta 2858 2864 2861 2883 C1' C D 3 beta 2878 2884 2881 2903 C1' A D 4 beta 2898 2904 2901 2925 C1' C D 5 beta 2920 2926 2923 2945 C1' A D 6 beta 2940 2946 2943 2967 C1' C D 7 beta 2962 2968 2965 2987 C1' C D 8 beta 2982 2988 2985 3007 C1' G D 9 beta 3002 3008 3005 3030 C1' U D 10 beta 3025 3031 3028 3050 C1' U D 11 beta 3045 3051 3048 3070 C1' C D 12 beta 3065 3071 3068 3090 C1' U D 13 beta 3085 3091 3088 3110 C1' A D 14 beta 3105 3111 3108 3132 C1' G D 15 beta 3127 3133 3130 3155 C1' G D 16 beta 3150 3156 3153 3178 C1' U D 17 beta 3173 3179 3176 3198 C1' G D 18 beta 3193 3199 3196 3221 C1' C D 19 beta 3216 3222 3219 3241 C1' U D 20 beta 3236 3242 3239 3261 C1' G D 21 beta 3256 3262 3259 3284 C1' G D 22 beta 3279 3285 3282 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2416 C2' C C 2 OK 2418 2414 2417 2436 C2' C C 3 OK 2438 2434 2437 2456 C2' A C 4 OK 2458 2454 2457 2478 C2' C C 5 OK 2480 2476 2479 2498 C2' A C 6 OK 2500 2496 2499 2520 C2' C C 7 OK 2522 2518 2521 2540 C2' C C 8 OK 2542 2538 2541 2560 C2' G C 9 OK 2562 2558 2561 2583 C2' U C 10 OK 2585 2581 2584 2603 C2' U C 11 OK 2605 2601 2604 2623 C2' C C 12 OK 2625 2621 2624 2643 C2' U C 13 OK 2645 2641 2644 2663 C2' A C 14 OK 2665 2661 2664 2685 C2' G C 15 OK 2687 2683 2686 2708 C2' G C 16 OK 2710 2706 2709 2731 C2' U C 17 OK 2733 2729 2732 2751 C2' G C 18 OK 2753 2749 2752 2774 C2' C C 19 OK 2776 2772 2775 2794 C2' U C 20 OK 2796 2792 2795 2814 C2' G C 21 OK 2816 2812 2815 2837 C2' G C 22 OK 2839 2835 2838 2861 C2' C D 2 OK 2863 2859 2862 2881 C2' C D 3 OK 2883 2879 2882 2901 C2' A D 4 OK 2903 2899 2902 2923 C2' C D 5 OK 2925 2921 2924 2943 C2' A D 6 OK 2945 2941 2944 2965 C2' C D 7 OK 2967 2963 2966 2985 C2' C D 8 OK 2987 2983 2986 3005 C2' G D 9 OK 3007 3003 3006 3028 C2' U D 10 OK 3030 3026 3029 3048 C2' U D 11 OK 3050 3046 3049 3068 C2' C D 12 OK 3070 3066 3069 3088 C2' U D 13 OK 3090 3086 3089 3108 C2' A D 14 OK 3110 3106 3109 3130 C2' G D 15 OK 3132 3128 3131 3153 C2' G D 16 OK 3155 3151 3154 3176 C2' U D 17 OK 3178 3174 3177 3196 C2' G D 18 OK 3198 3194 3197 3219 C2' C D 19 OK 3221 3217 3220 3239 C2' U D 20 OK 3241 3237 3240 3259 C2' G D 21 OK 3261 3257 3260 3282 C2' G D 22 OK 3284 3280 3283 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2414 C3' C C 2 OK 2412 2415 2416 2434 C3' C C 3 OK 2432 2435 2436 2454 C3' A C 4 OK 2452 2455 2456 2476 C3' C C 5 OK 2474 2477 2478 2496 C3' A C 6 OK 2494 2497 2498 2518 C3' C C 7 OK 2516 2519 2520 2538 C3' C C 8 OK 2536 2539 2540 2558 C3' G C 9 OK 2556 2559 2560 2581 C3' U C 10 OK 2579 2582 2583 2601 C3' U C 11 OK 2599 2602 2603 2621 C3' C C 12 OK 2619 2622 2623 2641 C3' U C 13 OK 2639 2642 2643 2661 C3' A C 14 OK 2659 2662 2663 2683 C3' G C 15 OK 2681 2684 2685 2706 C3' G C 16 OK 2704 2707 2708 2729 C3' U C 17 OK 2727 2730 2731 2749 C3' G C 18 OK 2747 2750 2751 2772 C3' C C 19 OK 2770 2773 2774 2792 C3' U C 20 OK 2790 2793 2794 2812 C3' G C 21 OK 2810 2813 2814 2835 C3' G C 22 OK 2833 2836 2837 2859 C3' C D 2 OK 2857 2860 2861 2879 C3' C D 3 OK 2877 2880 2881 2899 C3' A D 4 OK 2897 2900 2901 2921 C3' C D 5 OK 2919 2922 2923 2941 C3' A D 6 OK 2939 2942 2943 2963 C3' C D 7 OK 2961 2964 2965 2983 C3' C D 8 OK 2981 2984 2985 3003 C3' G D 9 OK 3001 3004 3005 3026 C3' U D 10 OK 3024 3027 3028 3046 C3' U D 11 OK 3044 3047 3048 3066 C3' C D 12 OK 3064 3067 3068 3086 C3' U D 13 OK 3084 3087 3088 3106 C3' A D 14 OK 3104 3107 3108 3128 C3' G D 15 OK 3126 3129 3130 3151 C3' G D 16 OK 3149 3152 3153 3174 C3' U D 17 OK 3172 3175 3176 3194 C3' G D 18 OK 3192 3195 3196 3217 C3' C D 19 OK 3215 3218 3219 3237 C3' U D 20 OK 3235 3238 3239 3257 C3' G D 21 OK 3255 3258 3259 3280 C3' G D 22 OK 3278 3281 3282 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2412 C4' C C 2 OK 2414 2411 2413 2432 C4' C C 3 OK 2434 2431 2433 2452 C4' A C 4 OK 2454 2451 2453 2474 C4' C C 5 OK 2476 2473 2475 2494 C4' A C 6 OK 2496 2493 2495 2516 C4' C C 7 OK 2518 2515 2517 2536 C4' C C 8 OK 2538 2535 2537 2556 C4' G C 9 OK 2558 2555 2557 2579 C4' U C 10 OK 2581 2578 2580 2599 C4' U C 11 OK 2601 2598 2600 2619 C4' C C 12 OK 2621 2618 2620 2639 C4' U C 13 OK 2641 2638 2640 2659 C4' A C 14 OK 2661 2658 2660 2681 C4' G C 15 OK 2683 2680 2682 2704 C4' G C 16 OK 2706 2703 2705 2727 C4' U C 17 OK 2729 2726 2728 2747 C4' G C 18 OK 2749 2746 2748 2770 C4' C C 19 OK 2772 2769 2771 2790 C4' U C 20 OK 2792 2789 2791 2810 C4' G C 21 OK 2812 2809 2811 2833 C4' G C 22 OK 2835 2832 2834 2857 C4' C D 2 OK 2859 2856 2858 2877 C4' C D 3 OK 2879 2876 2878 2897 C4' A D 4 OK 2899 2896 2898 2919 C4' C D 5 OK 2921 2918 2920 2939 C4' A D 6 OK 2941 2938 2940 2961 C4' C D 7 OK 2963 2960 2962 2981 C4' C D 8 OK 2983 2980 2982 3001 C4' G D 9 OK 3003 3000 3002 3024 C4' U D 10 OK 3026 3023 3025 3044 C4' U D 11 OK 3046 3043 3045 3064 C4' C D 12 OK 3066 3063 3065 3084 C4' U D 13 OK 3086 3083 3085 3104 C4' A D 14 OK 3106 3103 3105 3126 C4' G D 15 OK 3128 3125 3127 3149 C4' G D 16 OK 3151 3148 3150 3172 C4' U D 17 OK 3174 3171 3173 3192 C4' G D 18 OK 3194 3191 3193 3215 C4' C D 19 OK 3217 3214 3216 3235 C4' U D 20 OK 3237 3234 3236 3255 C4' G D 21 OK 3257 3254 3256 3278 C4' G D 22 OK 3280 3277 3279 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2411 C5' C C 2 2410 2412 2431 C5' C C 3 2430 2432 2451 C5' A C 4 2450 2452 2473 C5' C C 5 2472 2474 2493 C5' A C 6 2492 2494 2515 C5' C C 7 2514 2516 2535 C5' C C 8 2534 2536 2555 C5' G C 9 2554 2556 2578 C5' U C 10 2577 2579 2598 C5' U C 11 2597 2599 2618 C5' C C 12 2617 2619 2638 C5' U C 13 2637 2639 2658 C5' A C 14 2657 2659 2680 C5' G C 15 2679 2681 2703 C5' G C 16 2702 2704 2726 C5' U C 17 2725 2727 2746 C5' G C 18 2745 2747 2769 C5' C C 19 2768 2770 2789 C5' U C 20 2788 2790 2809 C5' G C 21 2808 2810 2832 C5' G C 22 2831 2833 2856 C5' C D 2 2855 2857 2876 C5' C D 3 2875 2877 2896 C5' A D 4 2895 2897 2918 C5' C D 5 2917 2919 2938 C5' A D 6 2937 2939 2960 C5' C D 7 2959 2961 2980 C5' C D 8 2979 2981 3000 C5' G D 9 2999 3001 3023 C5' U D 10 3022 3024 3043 C5' U D 11 3042 3044 3063 C5' C D 12 3062 3064 3083 C5' U D 13 3082 3084 3103 C5' A D 14 3102 3104 3125 C5' G D 15 3124 3126 3148 C5' G D 16 3147 3149 3171 C5' U D 17 3170 3172 3191 C5' G D 18 3190 3192 3214 C5' C D 19 3213 3215 3234 C5' U D 20 3233 3235 3254 C5' G D 21 3253 3255 3277 C5' G D 22 3276 3278 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2407 P C C 2 distorted distorted 2408 2409 2410 2427 P C C 3 distorted distorted 2415 2428 2429 2430 2447 P A C 4 distorted distorted 2435 2448 2449 2450 2469 P C C 5 distorted distorted 2455 2470 2471 2472 2489 P A C 6 distorted distorted 2477 2490 2491 2492 2511 P C C 7 distorted distorted 2497 2512 2513 2514 2531 P C C 8 distorted distorted 2519 2532 2533 2534 2551 P G C 9 distorted distorted 2539 2552 2553 2554 2574 P U C 10 distorted distorted 2559 2575 2576 2577 2594 P U C 11 distorted distorted 2582 2595 2596 2597 2614 P C C 12 distorted distorted 2602 2615 2616 2617 2634 P U C 13 distorted distorted 2622 2635 2636 2637 2654 P A C 14 distorted distorted 2642 2655 2656 2657 2676 P G C 15 distorted distorted 2662 2677 2678 2679 2699 P G C 16 distorted distorted 2684 2700 2701 2702 2722 P U C 17 distorted distorted 2707 2723 2724 2725 2742 P G C 18 distorted distorted 2730 2743 2744 2745 2765 P C C 19 distorted distorted 2750 2766 2767 2768 2785 P U C 20 distorted distorted 2773 2786 2787 2788 2805 P G C 21 distorted distorted 2793 2806 2807 2808 2828 P G C 22 distorted distorted 2813 2829 2830 2831 2852 P C D 2 distorted distorted 2853 2854 2855 2872 P C D 3 distorted distorted 2860 2873 2874 2875 2892 P A D 4 distorted distorted 2880 2893 2894 2895 2914 P C D 5 distorted distorted 2900 2915 2916 2917 2934 P A D 6 distorted distorted 2922 2935 2936 2937 2956 P C D 7 distorted distorted 2942 2957 2958 2959 2976 P C D 8 distorted distorted 2964 2977 2978 2979 2996 P G D 9 distorted distorted 2984 2997 2998 2999 3019 P U D 10 distorted distorted 3004 3020 3021 3022 3039 P U D 11 distorted distorted 3027 3040 3041 3042 3059 P C D 12 distorted distorted 3047 3060 3061 3062 3079 P U D 13 distorted distorted 3067 3080 3081 3082 3099 P A D 14 distorted distorted 3087 3100 3101 3102 3121 P G D 15 distorted distorted 3107 3122 3123 3124 3144 P G D 16 distorted distorted 3129 3145 3146 3147 3167 P U D 17 distorted distorted 3152 3168 3169 3170 3187 P G D 18 distorted distorted 3175 3188 3189 3190 3210 P C D 19 distorted distorted 3195 3211 3212 3213 3230 P U D 20 distorted distorted 3218 3231 3232 3233 3250 P G D 21 distorted distorted 3238 3251 3252 3253 3273 P G D 22 distorted distorted 3258 3274 3275 3276 ---------------------------------------------------------------------------------