ID code: '1A73' 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' --------------------------------------------------------------------------------- 2520 C1' T C 2 beta 2516 2521 2519 2540 C1' G C 3 beta 2536 2541 2539 2562 C1' A C 4 beta 2558 2563 2561 2583 C1' C C 5 beta 2579 2584 2582 2602 C1' T C 6 beta 2598 2603 2601 2622 C1' C C 7 beta 2618 2623 2621 2641 C1' T C 8 beta 2637 2642 2640 2661 C1' C C 9 beta 2657 2662 2660 2680 C1' T C 10 beta 2676 2681 2679 2700 C1' T C 11 beta 2696 2701 2699 2720 C1' A C 12 beta 2716 2721 2719 2741 C1' A C 13 beta 2737 2742 2740 2762 C1' G C 14 beta 2758 2763 2761 2785 C1' A C 15 beta 2781 2786 2784 2806 C1' G C 16 beta 2802 2807 2805 2828 C1' A C 17 beta 2824 2829 2827 2849 C1' G C 18 beta 2845 2850 2848 2871 C1' T C 19 beta 2867 2872 2870 2891 C1' C C 20 beta 2887 2892 2890 2910 C1' A C 21 beta 2906 2911 2909 2949 C1' T D 2 beta 2945 2950 2948 2969 C1' G D 3 beta 2965 2970 2968 2991 C1' A D 4 beta 2987 2992 2990 3012 C1' C D 5 beta 3008 3013 3011 3031 C1' T D 6 beta 3027 3032 3030 3051 C1' C D 7 beta 3047 3052 3050 3070 C1' T D 8 beta 3066 3071 3069 3090 C1' C D 9 beta 3086 3091 3089 3109 C1' T D 10 beta 3105 3110 3108 3129 C1' T D 11 beta 3125 3130 3128 3149 C1' A D 12 beta 3145 3150 3148 3170 C1' A D 13 beta 3166 3171 3169 3191 C1' G D 14 beta 3187 3192 3190 3214 C1' A D 15 beta 3210 3215 3213 3235 C1' G D 16 beta 3231 3236 3234 3257 C1' A D 17 beta 3253 3258 3256 3278 C1' G D 18 beta 3274 3279 3277 3300 C1' T D 19 beta 3296 3301 3299 3320 C1' C D 20 beta 3316 3321 3319 3339 C1' A D 21 beta 3335 3340 3338 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2519 C2' T C 2 2520 2517 2539 C2' G C 3 2540 2537 2561 C2' A C 4 2562 2559 2582 C2' C C 5 2583 2580 2601 C2' T C 6 2602 2599 2621 C2' C C 7 2622 2619 2640 C2' T C 8 2641 2638 2660 C2' C C 9 2661 2658 2679 C2' T C 10 2680 2677 2699 C2' T C 11 2700 2697 2719 C2' A C 12 2720 2717 2740 C2' A C 13 2741 2738 2761 C2' G C 14 2762 2759 2784 C2' A C 15 2785 2782 2805 C2' G C 16 2806 2803 2827 C2' A C 17 2828 2825 2848 C2' G C 18 2849 2846 2870 C2' T C 19 2871 2868 2890 C2' C C 20 2891 2888 2909 C2' A C 21 2910 2907 2948 C2' T D 2 2949 2946 2968 C2' G D 3 2969 2966 2990 C2' A D 4 2991 2988 3011 C2' C D 5 3012 3009 3030 C2' T D 6 3031 3028 3050 C2' C D 7 3051 3048 3069 C2' T D 8 3070 3067 3089 C2' C D 9 3090 3087 3108 C2' T D 10 3109 3106 3128 C2' T D 11 3129 3126 3148 C2' A D 12 3149 3146 3169 C2' A D 13 3170 3167 3190 C2' G D 14 3191 3188 3213 C2' A D 15 3214 3211 3234 C2' G D 16 3235 3232 3256 C2' A D 17 3257 3254 3277 C2' G D 18 3278 3275 3299 C2' T D 19 3300 3297 3319 C2' C D 20 3320 3317 3338 C2' A D 21 3339 3336 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2517 C3' T C 2 OK 2515 2518 2519 2537 C3' G C 3 OK 2535 2538 2539 2559 C3' A C 4 OK 2557 2560 2561 2580 C3' C C 5 OK 2578 2581 2582 2599 C3' T C 6 OK 2597 2600 2601 2619 C3' C C 7 OK 2617 2620 2621 2638 C3' T C 8 OK 2636 2639 2640 2658 C3' C C 9 OK 2656 2659 2660 2677 C3' T C 10 OK 2675 2678 2679 2697 C3' T C 11 OK 2695 2698 2699 2717 C3' A C 12 OK 2715 2718 2719 2738 C3' A C 13 OK 2736 2739 2740 2759 C3' G C 14 OK 2757 2760 2761 2782 C3' A C 15 OK 2780 2783 2784 2803 C3' G C 16 OK 2801 2804 2805 2825 C3' A C 17 OK 2823 2826 2827 2846 C3' G C 18 OK 2844 2847 2848 2868 C3' T C 19 OK 2866 2869 2870 2888 C3' C C 20 OK 2886 2889 2890 2907 C3' A C 21 OK 2905 2908 2909 2946 C3' T D 2 OK 2944 2947 2948 2966 C3' G D 3 OK 2964 2967 2968 2988 C3' A D 4 OK 2986 2989 2990 3009 C3' C D 5 OK 3007 3010 3011 3028 C3' T D 6 OK 3026 3029 3030 3048 C3' C D 7 OK 3046 3049 3050 3067 C3' T D 8 OK 3065 3068 3069 3087 C3' C D 9 OK 3085 3088 3089 3106 C3' T D 10 OK 3104 3107 3108 3126 C3' T D 11 OK 3124 3127 3128 3146 C3' A D 12 OK 3144 3147 3148 3167 C3' A D 13 OK 3165 3168 3169 3188 C3' G D 14 OK 3186 3189 3190 3211 C3' A D 15 OK 3209 3212 3213 3232 C3' G D 16 OK 3230 3233 3234 3254 C3' A D 17 OK 3252 3255 3256 3275 C3' G D 18 OK 3273 3276 3277 3297 C3' T D 19 OK 3295 3298 3299 3317 C3' C D 20 OK 3315 3318 3319 3336 C3' A D 21 OK 3334 3337 3338 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2515 C4' T C 2 OK 2517 2514 2516 2535 C4' G C 3 OK 2537 2534 2536 2557 C4' A C 4 OK 2559 2556 2558 2578 C4' C C 5 OK 2580 2577 2579 2597 C4' T C 6 OK 2599 2596 2598 2617 C4' C C 7 OK 2619 2616 2618 2636 C4' T C 8 OK 2638 2635 2637 2656 C4' C C 9 OK 2658 2655 2657 2675 C4' T C 10 OK 2677 2674 2676 2695 C4' T C 11 OK 2697 2694 2696 2715 C4' A C 12 OK 2717 2714 2716 2736 C4' A C 13 OK 2738 2735 2737 2757 C4' G C 14 OK 2759 2756 2758 2780 C4' A C 15 OK 2782 2779 2781 2801 C4' G C 16 OK 2803 2800 2802 2823 C4' A C 17 OK 2825 2822 2824 2844 C4' G C 18 OK 2846 2843 2845 2866 C4' T C 19 OK 2868 2865 2867 2886 C4' C C 20 OK 2888 2885 2887 2905 C4' A C 21 OK 2907 2904 2906 2944 C4' T D 2 OK 2946 2943 2945 2964 C4' G D 3 OK 2966 2963 2965 2986 C4' A D 4 OK 2988 2985 2987 3007 C4' C D 5 OK 3009 3006 3008 3026 C4' T D 6 OK 3028 3025 3027 3046 C4' C D 7 OK 3048 3045 3047 3065 C4' T D 8 OK 3067 3064 3066 3085 C4' C D 9 OK 3087 3084 3086 3104 C4' T D 10 OK 3106 3103 3105 3124 C4' T D 11 OK 3126 3123 3125 3144 C4' A D 12 OK 3146 3143 3145 3165 C4' A D 13 OK 3167 3164 3166 3186 C4' G D 14 OK 3188 3185 3187 3209 C4' A D 15 OK 3211 3208 3210 3230 C4' G D 16 OK 3232 3229 3231 3252 C4' A D 17 OK 3254 3251 3253 3273 C4' G D 18 OK 3275 3272 3274 3295 C4' T D 19 OK 3297 3294 3296 3315 C4' C D 20 OK 3317 3314 3316 3334 C4' A D 21 OK 3336 3333 3335 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2514 C5' T C 2 2513 2515 2534 C5' G C 3 2533 2535 2556 C5' A C 4 2555 2557 2577 C5' C C 5 2576 2578 2596 C5' T C 6 2595 2597 2616 C5' C C 7 2615 2617 2635 C5' T C 8 2634 2636 2655 C5' C C 9 2654 2656 2674 C5' T C 10 2673 2675 2694 C5' T C 11 2693 2695 2714 C5' A C 12 2713 2715 2735 C5' A C 13 2734 2736 2756 C5' G C 14 2774 2757 2779 C5' A C 15 2778 2780 2800 C5' G C 16 2799 2801 2822 C5' A C 17 2821 2823 2843 C5' G C 18 2842 2844 2865 C5' T C 19 2864 2866 2885 C5' C C 20 2884 2886 2904 C5' A C 21 2903 2905 2943 C5' T D 2 2942 2944 2963 C5' G D 3 2962 2964 2985 C5' A D 4 2984 2986 3006 C5' C D 5 3005 3007 3025 C5' T D 6 3024 3026 3045 C5' C D 7 3044 3046 3064 C5' T D 8 3063 3065 3084 C5' C D 9 3083 3085 3103 C5' T D 10 3102 3104 3123 C5' T D 11 3122 3124 3143 C5' A D 12 3142 3144 3164 C5' A D 13 3163 3165 3185 C5' G D 14 3203 3186 3208 C5' A D 15 3207 3209 3229 C5' G D 16 3228 3230 3251 C5' A D 17 3250 3252 3272 C5' G D 18 3271 3273 3294 C5' T D 19 3293 3295 3314 C5' C D 20 3313 3315 3333 C5' A D 21 3332 3334 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2530 P G C 3 OK OK 2518 2531 2532 2533 2552 P A C 4 OK OK 2538 2553 2554 2555 2573 P C C 5 OK OK 2560 2574 2575 2576 2592 P T C 6 OK OK 2581 2593 2594 2595 2612 P C C 7 OK OK 2600 2613 2614 2615 2631 P T C 8 OK OK 2620 2632 2633 2634 2651 P C C 9 OK OK 2639 2652 2653 2654 2670 P T C 10 OK OK 2659 2671 2672 2673 2690 P T C 11 OK OK 2678 2691 2692 2693 2710 P A C 12 OK OK 2698 2711 2712 2713 2731 P A C 13 OK OK 2718 2732 2733 2734 2752 P G C 14 OK OK 2753 2754 2774 2775 P A C 15 OK OK 2760 2776 2777 2778 2796 P G C 16 OK OK 2783 2797 2798 2799 2818 P A C 17 OK OK 2804 2819 2820 2821 2839 P G C 18 OK OK 2826 2840 2841 2842 2861 P T C 19 OK OK 2847 2862 2863 2864 2881 P C C 20 OK OK 2869 2882 2883 2884 2900 P A C 21 OK OK 2889 2901 2902 2903 2959 P G D 3 OK OK 2947 2960 2961 2962 2981 P A D 4 OK OK 2967 2982 2983 2984 3002 P C D 5 OK OK 2989 3003 3004 3005 3021 P T D 6 OK OK 3010 3022 3023 3024 3041 P C D 7 OK OK 3029 3042 3043 3044 3060 P T D 8 OK OK 3049 3061 3062 3063 3080 P C D 9 OK OK 3068 3081 3082 3083 3099 P T D 10 OK OK 3088 3100 3101 3102 3119 P T D 11 OK OK 3107 3120 3121 3122 3139 P A D 12 OK OK 3127 3140 3141 3142 3160 P A D 13 OK OK 3147 3161 3162 3163 3181 P G D 14 OK OK 3182 3183 3203 3204 P A D 15 OK OK 3189 3205 3206 3207 3225 P G D 16 OK OK 3212 3226 3227 3228 3247 P A D 17 OK OK 3233 3248 3249 3250 3268 P G D 18 OK OK 3255 3269 3270 3271 3290 P T D 19 OK OK 3276 3291 3292 3293 3310 P C D 20 OK OK 3298 3311 3312 3313 3329 P A D 21 OK OK 3318 3330 3331 3332 ---------------------------------------------------------------------------------