ID code: '1PVI' 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' --------------------------------------------------------------------------------- 2700 C1' G C 3 beta 2696 2701 2699 2722 C1' A C 4 beta 2718 2723 2721 2743 C1' C C 5 beta 2739 2744 2742 2762 C1' C C 6 beta 2758 2763 2761 2781 C1' A C 7 beta 2777 2782 2780 2802 C1' G C 8 beta 2798 2803 2801 2824 C1' C C 9 beta 2820 2825 2823 2840 C1' T C 10 beta 2839 2841 2852 2863 C1' G C 11 beta 2859 2864 2862 2885 C1' G C 12 beta 2881 2886 2884 2904 C1' T C 13 beta 2903 2905 2916 2927 C1' C C 14 beta 2923 2928 2926 2964 C1' G D 3 beta 2960 2965 2963 2986 C1' A D 4 beta 2982 2987 2985 3007 C1' C D 5 beta 3003 3008 3006 3026 C1' C D 6 beta 3022 3027 3025 3045 C1' A D 7 beta 3041 3046 3044 3066 C1' G D 8 beta 3062 3067 3065 3088 C1' C D 9 beta 3084 3089 3087 3104 C1' T D 10 beta 3103 3105 3116 3127 C1' G D 11 beta 3123 3128 3126 3149 C1' G D 12 beta 3145 3150 3148 3168 C1' T D 13 beta 3167 3169 3180 3191 C1' C D 14 beta 3187 3192 3190 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2699 C2' G C 3 2700 2697 2721 C2' A C 4 2722 2719 2742 C2' C C 5 2743 2740 2761 C2' C C 6 2762 2759 2780 C2' A C 7 2781 2778 2801 C2' G C 8 2802 2799 2823 C2' C C 9 2824 2821 2852 C2' T C 10 2840 2850 2862 C2' G C 11 2863 2860 2884 C2' G C 12 2885 2882 2916 C2' T C 13 2904 2914 2926 C2' C C 14 2927 2924 2963 C2' G D 3 2964 2961 2985 C2' A D 4 2986 2983 3006 C2' C D 5 3007 3004 3025 C2' C D 6 3026 3023 3044 C2' A D 7 3045 3042 3065 C2' G D 8 3066 3063 3087 C2' C D 9 3088 3085 3116 C2' T D 10 3104 3114 3126 C2' G D 11 3127 3124 3148 C2' G D 12 3149 3146 3180 C2' T D 13 3168 3178 3190 C2' C D 14 3191 3188 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2697 C3' G C 3 OK 2695 2698 2699 2719 C3' A C 4 OK 2717 2720 2721 2740 C3' C C 5 OK 2738 2741 2742 2759 C3' C C 6 OK 2757 2760 2761 2778 C3' A C 7 OK 2776 2779 2780 2799 C3' G C 8 OK 2797 2800 2801 2821 C3' C C 9 OK 2819 2822 2823 2850 C3' T C 10 OK 2838 2851 2852 2860 C3' G C 11 OK 2858 2861 2862 2882 C3' G C 12 OK 2880 2883 2884 2914 C3' T C 13 OK 2902 2915 2916 2924 C3' C C 14 OK 2922 2925 2926 2961 C3' G D 3 OK 2959 2962 2963 2983 C3' A D 4 OK 2981 2984 2985 3004 C3' C D 5 OK 3002 3005 3006 3023 C3' C D 6 OK 3021 3024 3025 3042 C3' A D 7 OK 3040 3043 3044 3063 C3' G D 8 OK 3061 3064 3065 3085 C3' C D 9 OK 3083 3086 3087 3114 C3' T D 10 OK 3102 3115 3116 3124 C3' G D 11 OK 3122 3125 3126 3146 C3' G D 12 OK 3144 3147 3148 3178 C3' T D 13 OK 3166 3179 3180 3188 C3' C D 14 OK 3186 3189 3190 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2695 C4' G C 3 OK 2697 2694 2696 2717 C4' A C 4 OK 2719 2716 2718 2738 C4' C C 5 OK 2740 2737 2739 2757 C4' C C 6 OK 2759 2756 2758 2776 C4' A C 7 OK 2778 2775 2777 2797 C4' G C 8 OK 2799 2796 2798 2819 C4' C C 9 OK 2821 2818 2820 2838 C4' T C 10 OK 2850 2837 2839 2858 C4' G C 11 OK 2860 2857 2859 2880 C4' G C 12 OK 2882 2879 2881 2902 C4' T C 13 OK 2914 2901 2903 2922 C4' C C 14 OK 2924 2921 2923 2959 C4' G D 3 OK 2961 2958 2960 2981 C4' A D 4 OK 2983 2980 2982 3002 C4' C D 5 OK 3004 3001 3003 3021 C4' C D 6 OK 3023 3020 3022 3040 C4' A D 7 OK 3042 3039 3041 3061 C4' G D 8 OK 3063 3060 3062 3083 C4' C D 9 OK 3085 3082 3084 3102 C4' T D 10 OK 3114 3101 3103 3122 C4' G D 11 OK 3124 3121 3123 3144 C4' G D 12 OK 3146 3143 3145 3166 C4' T D 13 OK 3178 3165 3167 3186 C4' C D 14 OK 3188 3185 3187 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2694 C5' G C 3 2693 2695 2716 C5' A C 4 2715 2717 2737 C5' C C 5 2736 2738 2756 C5' C C 6 2755 2757 2775 C5' A C 7 2774 2776 2796 C5' G C 8 2795 2797 2818 C5' C C 9 2817 2819 2837 C5' T C 10 2836 2838 2857 C5' G C 11 2856 2858 2879 C5' G C 12 2878 2880 2901 C5' T C 13 2900 2902 2921 C5' C C 14 2920 2922 2958 C5' G D 3 2957 2959 2980 C5' A D 4 2979 2981 3001 C5' C D 5 3000 3002 3020 C5' C D 6 3019 3021 3039 C5' A D 7 3038 3040 3060 C5' G D 8 3059 3061 3082 C5' C D 9 3081 3083 3101 C5' T D 10 3100 3102 3121 C5' G D 11 3120 3122 3143 C5' G D 12 3142 3144 3165 C5' T D 13 3164 3166 3185 C5' C D 14 3184 3186 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2712 P A C 4 OK OK 2698 2713 2714 2715 2733 P C C 5 OK OK 2720 2734 2735 2736 2752 P C C 6 OK OK 2741 2753 2754 2755 2771 P A C 7 OK OK 2760 2772 2773 2774 2792 P G C 8 OK OK 2779 2793 2794 2795 2814 P C C 9 OK OK 2800 2815 2816 2817 2833 P T C 10 OK OK 2822 2834 2835 2836 2853 P G C 11 OK OK 2851 2854 2855 2856 2875 P G C 12 OK OK 2861 2876 2877 2878 2897 P T C 13 OK OK 2883 2898 2899 2900 2917 P C C 14 OK OK 2915 2918 2919 2920 2976 P A D 4 OK OK 2962 2977 2978 2979 2997 P C D 5 OK OK 2984 2998 2999 3000 3016 P C D 6 OK OK 3005 3017 3018 3019 3035 P A D 7 OK OK 3024 3036 3037 3038 3056 P G D 8 OK OK 3043 3057 3058 3059 3078 P C D 9 OK OK 3064 3079 3080 3081 3097 P T D 10 OK OK 3086 3098 3099 3100 3117 P G D 11 OK OK 3115 3118 3119 3120 3139 P G D 12 OK OK 3125 3140 3141 3142 3161 P T D 13 OK OK 3147 3162 3163 3164 3181 P C D 14 OK OK 3179 3182 3183 3184 ---------------------------------------------------------------------------------