ID code: '3K49' 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' --------------------------------------------------------------------------------- 2857 C1' C B 1 beta 2852 2858 2855 2877 C1' C B 2 beta 2872 2878 2875 2897 C1' U B 3 beta 2892 2898 2895 2917 C1' G B 4 beta 2912 2918 2915 2940 C1' U B 5 beta 2935 2941 2938 2960 C1' A B 6 beta 2955 2961 2958 2982 C1' A B 7 beta 2977 2983 2980 3004 C1' A B 8 beta 2999 3005 3002 3026 C1' U B 9 beta 3021 3027 3024 3046 C1' A B 10 beta 3041 3047 3044 5914 C1' C D 1 beta 5909 5915 5912 5934 C1' C D 2 beta 5929 5935 5932 5954 C1' U D 3 beta 5949 5955 5952 5974 C1' G D 4 beta 5969 5975 5972 5997 C1' U D 5 beta 5992 5998 5995 6017 C1' A D 6 beta 6012 6018 6015 6039 C1' A D 7 beta 6034 6040 6037 6061 C1' A D 8 beta 6056 6062 6059 6083 C1' U D 9 beta 6078 6084 6081 6103 C1' A D 10 beta 6098 6104 6101 8971 C1' C F 1 beta 8966 8972 8969 8991 C1' C F 2 beta 8986 8992 8989 9011 C1' U F 3 beta 9006 9012 9009 9031 C1' G F 4 beta 9026 9032 9029 9054 C1' U F 5 beta 9049 9055 9052 9074 C1' A F 6 beta 9069 9075 9072 9096 C1' A F 7 beta 9091 9097 9094 9118 C1' A F 8 beta 9113 9119 9116 9140 C1' U F 9 beta 9135 9141 9138 9160 C1' A F 10 beta 9155 9161 9158 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2855 C2' C B 1 OK 2857 2853 2856 2875 C2' C B 2 OK 2877 2873 2876 2895 C2' U B 3 OK 2897 2893 2896 2915 C2' G B 4 OK 2917 2913 2916 2938 C2' U B 5 OK 2940 2936 2939 2958 C2' A B 6 OK 2960 2956 2959 2980 C2' A B 7 OK 2982 2978 2981 3002 C2' A B 8 OK 3004 3000 3003 3024 C2' U B 9 OK 3026 3022 3025 3044 C2' A B 10 OK 3046 3042 3045 5912 C2' C D 1 OK 5914 5910 5913 5932 C2' C D 2 OK 5934 5930 5933 5952 C2' U D 3 OK 5954 5950 5953 5972 C2' G D 4 OK 5974 5970 5973 5995 C2' U D 5 OK 5997 5993 5996 6015 C2' A D 6 OK 6017 6013 6016 6037 C2' A D 7 OK 6039 6035 6038 6059 C2' A D 8 OK 6061 6057 6060 6081 C2' U D 9 OK 6083 6079 6082 6101 C2' A D 10 OK 6103 6099 6102 8969 C2' C F 1 OK 8971 8967 8970 8989 C2' C F 2 OK 8991 8987 8990 9009 C2' U F 3 OK 9011 9007 9010 9029 C2' G F 4 OK 9031 9027 9030 9052 C2' U F 5 OK 9054 9050 9053 9072 C2' A F 6 OK 9074 9070 9073 9094 C2' A F 7 OK 9096 9092 9095 9116 C2' A F 8 OK 9118 9114 9117 9138 C2' U F 9 OK 9140 9136 9139 9158 C2' A F 10 OK 9160 9156 9159 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2853 C3' C B 1 OK 2851 2854 2855 2873 C3' C B 2 OK 2871 2874 2875 2893 C3' U B 3 OK 2891 2894 2895 2913 C3' G B 4 OK 2911 2914 2915 2936 C3' U B 5 OK 2934 2937 2938 2956 C3' A B 6 OK 2954 2957 2958 2978 C3' A B 7 OK 2976 2979 2980 3000 C3' A B 8 OK 2998 3001 3002 3022 C3' U B 9 OK 3020 3023 3024 3042 C3' A B 10 OK 3040 3043 3044 5910 C3' C D 1 OK 5908 5911 5912 5930 C3' C D 2 OK 5928 5931 5932 5950 C3' U D 3 OK 5948 5951 5952 5970 C3' G D 4 OK 5968 5971 5972 5993 C3' U D 5 OK 5991 5994 5995 6013 C3' A D 6 OK 6011 6014 6015 6035 C3' A D 7 OK 6033 6036 6037 6057 C3' A D 8 OK 6055 6058 6059 6079 C3' U D 9 OK 6077 6080 6081 6099 C3' A D 10 OK 6097 6100 6101 8967 C3' C F 1 OK 8965 8968 8969 8987 C3' C F 2 OK 8985 8988 8989 9007 C3' U F 3 OK 9005 9008 9009 9027 C3' G F 4 OK 9025 9028 9029 9050 C3' U F 5 OK 9048 9051 9052 9070 C3' A F 6 OK 9068 9071 9072 9092 C3' A F 7 OK 9090 9093 9094 9114 C3' A F 8 OK 9112 9115 9116 9136 C3' U F 9 OK 9134 9137 9138 9156 C3' A F 10 OK 9154 9157 9158 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2851 C4' C B 1 OK 2853 2850 2852 2871 C4' C B 2 OK 2873 2870 2872 2891 C4' U B 3 OK 2893 2890 2892 2911 C4' G B 4 OK 2913 2910 2912 2934 C4' U B 5 OK 2936 2933 2935 2954 C4' A B 6 OK 2956 2953 2955 2976 C4' A B 7 OK 2978 2975 2977 2998 C4' A B 8 OK 3000 2997 2999 3020 C4' U B 9 OK 3022 3019 3021 3040 C4' A B 10 OK 3042 3039 3041 5908 C4' C D 1 OK 5910 5907 5909 5928 C4' C D 2 OK 5930 5927 5929 5948 C4' U D 3 OK 5950 5947 5949 5968 C4' G D 4 OK 5970 5967 5969 5991 C4' U D 5 OK 5993 5990 5992 6011 C4' A D 6 OK 6013 6010 6012 6033 C4' A D 7 OK 6035 6032 6034 6055 C4' A D 8 OK 6057 6054 6056 6077 C4' U D 9 OK 6079 6076 6078 6097 C4' A D 10 OK 6099 6096 6098 8965 C4' C F 1 OK 8967 8964 8966 8985 C4' C F 2 OK 8987 8984 8986 9005 C4' U F 3 OK 9007 9004 9006 9025 C4' G F 4 OK 9027 9024 9026 9048 C4' U F 5 OK 9050 9047 9049 9068 C4' A F 6 OK 9070 9067 9069 9090 C4' A F 7 OK 9092 9089 9091 9112 C4' A F 8 OK 9114 9111 9113 9134 C4' U F 9 OK 9136 9133 9135 9154 C4' A F 10 OK 9156 9153 9155 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2850 C5' C B 1 2849 2851 2870 C5' C B 2 2869 2871 2890 C5' U B 3 2889 2891 2910 C5' G B 4 2909 2911 2933 C5' U B 5 2932 2934 2953 C5' A B 6 2952 2954 2975 C5' A B 7 2974 2976 2997 C5' A B 8 2996 2998 3019 C5' U B 9 3018 3020 3039 C5' A B 10 3038 3040 5907 C5' C D 1 5906 5908 5927 C5' C D 2 5926 5928 5947 C5' U D 3 5946 5948 5967 C5' G D 4 5966 5968 5990 C5' U D 5 5989 5991 6010 C5' A D 6 6009 6011 6032 C5' A D 7 6031 6033 6054 C5' A D 8 6053 6055 6076 C5' U D 9 6075 6077 6096 C5' A D 10 6095 6097 8964 C5' C F 1 8963 8965 8984 C5' C F 2 8983 8985 9004 C5' U F 3 9003 9005 9024 C5' G F 4 9023 9025 9047 C5' U F 5 9046 9048 9067 C5' A F 6 9066 9068 9089 C5' A F 7 9088 9090 9111 C5' A F 8 9110 9112 9133 C5' U F 9 9132 9134 9153 C5' A F 10 9152 9154 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2866 P C B 2 distorted distorted 2854 2867 2868 2869 2886 P U B 3 distorted distorted 2874 2887 2888 2889 2906 P G B 4 distorted distorted 2894 2907 2908 2909 2929 P U B 5 distorted distorted 2914 2930 2931 2932 2949 P A B 6 distorted distorted 2937 2950 2951 2952 2971 P A B 7 distorted distorted 2957 2972 2973 2974 2993 P A B 8 distorted distorted 2979 2994 2995 2996 3015 P U B 9 distorted distorted 3001 3016 3017 3018 3035 P A B 10 distorted distorted 3023 3036 3037 3038 5923 P C D 2 distorted distorted 5911 5924 5925 5926 5943 P U D 3 distorted distorted 5931 5944 5945 5946 5963 P G D 4 distorted distorted 5951 5964 5965 5966 5986 P U D 5 distorted distorted 5971 5987 5988 5989 6006 P A D 6 distorted distorted 5994 6007 6008 6009 6028 P A D 7 distorted distorted 6014 6029 6030 6031 6050 P A D 8 distorted distorted 6036 6051 6052 6053 6072 P U D 9 distorted distorted 6058 6073 6074 6075 6092 P A D 10 distorted distorted 6080 6093 6094 6095 8980 P C F 2 distorted distorted 8968 8981 8982 8983 9000 P U F 3 distorted distorted 8988 9001 9002 9003 9020 P G F 4 distorted distorted 9008 9021 9022 9023 9043 P U F 5 distorted distorted 9028 9044 9045 9046 9063 P A F 6 distorted distorted 9051 9064 9065 9066 9085 P A F 7 distorted distorted 9071 9086 9087 9088 9107 P A F 8 distorted distorted 9093 9108 9109 9110 9129 P U F 9 distorted distorted 9115 9130 9131 9132 9149 P A F 10 distorted distorted 9137 9150 9151 9152 ---------------------------------------------------------------------------------