ID code: '3K4E' 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' --------------------------------------------------------------------------------- 2785 C1' C B 1 beta 2780 2786 2783 2805 C1' U B 2 beta 2800 2806 2803 2825 C1' U B 3 beta 2820 2826 2823 2845 C1' G B 4 beta 2840 2846 2843 2868 C1' U B 5 beta 2863 2869 2866 2888 C1' A B 6 beta 2883 2889 2886 2910 C1' U B 7 beta 2905 2911 2908 2930 C1' A B 8 beta 2925 2931 2928 2952 C1' U B 9 beta 2947 2953 2950 2972 C1' A B 10 beta 2967 2973 2970 5768 C1' C D 1 beta 5763 5769 5766 5788 C1' U D 2 beta 5783 5789 5786 5808 C1' U D 3 beta 5803 5809 5806 5828 C1' G D 4 beta 5823 5829 5826 5851 C1' U D 5 beta 5846 5852 5849 5871 C1' A D 6 beta 5866 5872 5869 5893 C1' U D 7 beta 5888 5894 5891 5913 C1' A D 8 beta 5908 5914 5911 5935 C1' U D 9 beta 5930 5936 5933 5955 C1' A D 10 beta 5950 5956 5953 8751 C1' C F 1 beta 8746 8752 8749 8771 C1' U F 2 beta 8766 8772 8769 8791 C1' U F 3 beta 8786 8792 8789 8811 C1' G F 4 beta 8806 8812 8809 8834 C1' U F 5 beta 8829 8835 8832 8854 C1' A F 6 beta 8849 8855 8852 8876 C1' U F 7 beta 8871 8877 8874 8896 C1' A F 8 beta 8891 8897 8894 8918 C1' U F 9 beta 8913 8919 8916 8938 C1' A F 10 beta 8933 8939 8936 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2783 C2' C B 1 OK 2785 2781 2784 2803 C2' U B 2 OK 2805 2801 2804 2823 C2' U B 3 OK 2825 2821 2824 2843 C2' G B 4 OK 2845 2841 2844 2866 C2' U B 5 OK 2868 2864 2867 2886 C2' A B 6 OK 2888 2884 2887 2908 C2' U B 7 OK 2910 2906 2909 2928 C2' A B 8 OK 2930 2926 2929 2950 C2' U B 9 OK 2952 2948 2951 2970 C2' A B 10 OK 2972 2968 2971 5766 C2' C D 1 OK 5768 5764 5767 5786 C2' U D 2 OK 5788 5784 5787 5806 C2' U D 3 OK 5808 5804 5807 5826 C2' G D 4 OK 5828 5824 5827 5849 C2' U D 5 OK 5851 5847 5850 5869 C2' A D 6 OK 5871 5867 5870 5891 C2' U D 7 OK 5893 5889 5892 5911 C2' A D 8 OK 5913 5909 5912 5933 C2' U D 9 OK 5935 5931 5934 5953 C2' A D 10 OK 5955 5951 5954 8749 C2' C F 1 OK 8751 8747 8750 8769 C2' U F 2 OK 8771 8767 8770 8789 C2' U F 3 OK 8791 8787 8790 8809 C2' G F 4 OK 8811 8807 8810 8832 C2' U F 5 OK 8834 8830 8833 8852 C2' A F 6 OK 8854 8850 8853 8874 C2' U F 7 OK 8876 8872 8875 8894 C2' A F 8 OK 8896 8892 8895 8916 C2' U F 9 OK 8918 8914 8917 8936 C2' A F 10 OK 8938 8934 8937 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2781 C3' C B 1 OK 2779 2782 2783 2801 C3' U B 2 OK 2799 2802 2803 2821 C3' U B 3 OK 2819 2822 2823 2841 C3' G B 4 OK 2839 2842 2843 2864 C3' U B 5 OK 2862 2865 2866 2884 C3' A B 6 OK 2882 2885 2886 2906 C3' U B 7 OK 2904 2907 2908 2926 C3' A B 8 OK 2924 2927 2928 2948 C3' U B 9 OK 2946 2949 2950 2968 C3' A B 10 OK 2966 2969 2970 5764 C3' C D 1 OK 5762 5765 5766 5784 C3' U D 2 OK 5782 5785 5786 5804 C3' U D 3 OK 5802 5805 5806 5824 C3' G D 4 OK 5822 5825 5826 5847 C3' U D 5 OK 5845 5848 5849 5867 C3' A D 6 OK 5865 5868 5869 5889 C3' U D 7 OK 5887 5890 5891 5909 C3' A D 8 OK 5907 5910 5911 5931 C3' U D 9 OK 5929 5932 5933 5951 C3' A D 10 OK 5949 5952 5953 8747 C3' C F 1 OK 8745 8748 8749 8767 C3' U F 2 OK 8765 8768 8769 8787 C3' U F 3 OK 8785 8788 8789 8807 C3' G F 4 OK 8805 8808 8809 8830 C3' U F 5 OK 8828 8831 8832 8850 C3' A F 6 OK 8848 8851 8852 8872 C3' U F 7 OK 8870 8873 8874 8892 C3' A F 8 OK 8890 8893 8894 8914 C3' U F 9 OK 8912 8915 8916 8934 C3' A F 10 OK 8932 8935 8936 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2779 C4' C B 1 OK 2781 2778 2780 2799 C4' U B 2 OK 2801 2798 2800 2819 C4' U B 3 OK 2821 2818 2820 2839 C4' G B 4 OK 2841 2838 2840 2862 C4' U B 5 OK 2864 2861 2863 2882 C4' A B 6 OK 2884 2881 2883 2904 C4' U B 7 OK 2906 2903 2905 2924 C4' A B 8 OK 2926 2923 2925 2946 C4' U B 9 OK 2948 2945 2947 2966 C4' A B 10 OK 2968 2965 2967 5762 C4' C D 1 OK 5764 5761 5763 5782 C4' U D 2 OK 5784 5781 5783 5802 C4' U D 3 OK 5804 5801 5803 5822 C4' G D 4 OK 5824 5821 5823 5845 C4' U D 5 OK 5847 5844 5846 5865 C4' A D 6 OK 5867 5864 5866 5887 C4' U D 7 OK 5889 5886 5888 5907 C4' A D 8 OK 5909 5906 5908 5929 C4' U D 9 OK 5931 5928 5930 5949 C4' A D 10 OK 5951 5948 5950 8745 C4' C F 1 OK 8747 8744 8746 8765 C4' U F 2 OK 8767 8764 8766 8785 C4' U F 3 OK 8787 8784 8786 8805 C4' G F 4 OK 8807 8804 8806 8828 C4' U F 5 OK 8830 8827 8829 8848 C4' A F 6 OK 8850 8847 8849 8870 C4' U F 7 OK 8872 8869 8871 8890 C4' A F 8 OK 8892 8889 8891 8912 C4' U F 9 OK 8914 8911 8913 8932 C4' A F 10 OK 8934 8931 8933 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2778 C5' C B 1 2777 2779 2798 C5' U B 2 2797 2799 2818 C5' U B 3 2817 2819 2838 C5' G B 4 2837 2839 2861 C5' U B 5 2860 2862 2881 C5' A B 6 2880 2882 2903 C5' U B 7 2902 2904 2923 C5' A B 8 2922 2924 2945 C5' U B 9 2944 2946 2965 C5' A B 10 2964 2966 5761 C5' C D 1 5760 5762 5781 C5' U D 2 5780 5782 5801 C5' U D 3 5800 5802 5821 C5' G D 4 5820 5822 5844 C5' U D 5 5843 5845 5864 C5' A D 6 5863 5865 5886 C5' U D 7 5885 5887 5906 C5' A D 8 5905 5907 5928 C5' U D 9 5927 5929 5948 C5' A D 10 5947 5949 8744 C5' C F 1 8743 8745 8764 C5' U F 2 8763 8765 8784 C5' U F 3 8783 8785 8804 C5' G F 4 8803 8805 8827 C5' U F 5 8826 8828 8847 C5' A F 6 8846 8848 8869 C5' U F 7 8868 8870 8889 C5' A F 8 8888 8890 8911 C5' U F 9 8910 8912 8931 C5' A F 10 8930 8932 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2774 P C B 1 distorted distorted 2775 2776 2777 2794 P U B 2 distorted distorted 2782 2795 2796 2797 2814 P U B 3 distorted distorted 2802 2815 2816 2817 2834 P G B 4 distorted distorted 2822 2835 2836 2837 2857 P U B 5 distorted distorted 2842 2858 2859 2860 2877 P A B 6 distorted distorted 2865 2878 2879 2880 2899 P U B 7 distorted distorted 2885 2900 2901 2902 2919 P A B 8 distorted distorted 2907 2920 2921 2922 2941 P U B 9 distorted distorted 2927 2942 2943 2944 2961 P A B 10 distorted distorted 2949 2962 2963 2964 5757 P C D 1 distorted distorted 5758 5759 5760 5777 P U D 2 distorted distorted 5765 5778 5779 5780 5797 P U D 3 distorted distorted 5785 5798 5799 5800 5817 P G D 4 distorted distorted 5805 5818 5819 5820 5840 P U D 5 distorted distorted 5825 5841 5842 5843 5860 P A D 6 distorted distorted 5848 5861 5862 5863 5882 P U D 7 distorted distorted 5868 5883 5884 5885 5902 P A D 8 distorted distorted 5890 5903 5904 5905 5924 P U D 9 distorted distorted 5910 5925 5926 5927 5944 P A D 10 distorted distorted 5932 5945 5946 5947 8740 P C F 1 distorted distorted 8741 8742 8743 8760 P U F 2 distorted distorted 8748 8761 8762 8763 8780 P U F 3 distorted distorted 8768 8781 8782 8783 8800 P G F 4 distorted distorted 8788 8801 8802 8803 8823 P U F 5 distorted distorted 8808 8824 8825 8826 8843 P A F 6 distorted distorted 8831 8844 8845 8846 8865 P U F 7 distorted distorted 8851 8866 8867 8868 8885 P A F 8 distorted distorted 8873 8886 8887 8888 8907 P U F 9 distorted distorted 8893 8908 8909 8910 8927 P A F 10 distorted distorted 8915 8928 8929 8930 ---------------------------------------------------------------------------------