ID code: '2B2D' 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' --------------------------------------------------------------------------------- 2900 C1' G R 307 beta 2895 2901 2898 2923 C1' U R 308 beta 2918 2924 2921 2943 C1' C R 309 beta 2938 2944 2941 2963 C1' U R 310 beta 2958 2964 2961 2983 C1' A R 311 beta 2978 2984 2981 3005 C1' A R 312 beta 3000 3006 3003 3027 C1' G R 313 beta 3022 3028 3025 3050 C1' A R 314 beta 3045 3051 3048 3072 C1' C R 315 beta 3067 3073 3070 3093 C1' A S 411 beta 3088 3094 3091 3115 C1' A S 412 beta 3110 3116 3113 3137 C1' G S 413 beta 3132 3138 3135 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2898 C2' G R 307 OK 2900 2896 2899 2921 C2' U R 308 OK 2923 2919 2922 2941 C2' C R 309 OK 2943 2939 2942 2961 C2' U R 310 OK 2963 2959 2962 2981 C2' A R 311 OK 2983 2979 2982 3003 C2' A R 312 OK 3005 3001 3004 3025 C2' G R 313 OK 3027 3023 3026 3048 C2' A R 314 OK 3050 3046 3049 3070 C2' C R 315 OK 3072 3068 3071 3091 C2' A S 411 OK 3093 3089 3092 3113 C2' A S 412 OK 3115 3111 3114 3135 C2' G S 413 OK 3137 3133 3136 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2896 C3' G R 307 OK 2894 2897 2898 2919 C3' U R 308 OK 2917 2920 2921 2939 C3' C R 309 OK 2937 2940 2941 2959 C3' U R 310 OK 2957 2960 2961 2979 C3' A R 311 OK 2977 2980 2981 3001 C3' A R 312 OK 2999 3002 3003 3023 C3' G R 313 OK 3021 3024 3025 3046 C3' A R 314 OK 3044 3047 3048 3068 C3' C R 315 OK 3066 3069 3070 3089 C3' A S 411 distorted 3087 3090 3091 3111 C3' A S 412 OK 3109 3112 3113 3133 C3' G S 413 OK 3131 3134 3135 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2894 C4' G R 307 OK 2896 2893 2895 2917 C4' U R 308 OK 2919 2916 2918 2937 C4' C R 309 OK 2939 2936 2938 2957 C4' U R 310 OK 2959 2956 2958 2977 C4' A R 311 OK 2979 2976 2978 2999 C4' A R 312 OK 3001 2998 3000 3021 C4' G R 313 OK 3023 3020 3022 3044 C4' A R 314 OK 3046 3043 3045 3066 C4' C R 315 OK 3068 3065 3067 3087 C4' A S 411 OK 3089 3086 3088 3109 C4' A S 412 OK 3111 3108 3110 3131 C4' G S 413 OK 3133 3130 3132 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2893 C5' G R 307 2894 2916 C5' U R 308 2915 2917 2936 C5' C R 309 2935 2937 2956 C5' U R 310 2955 2957 2976 C5' A R 311 2975 2977 2998 C5' A R 312 2997 2999 3020 C5' G R 313 3019 3021 3043 C5' A R 314 3042 3044 3065 C5' C R 315 3064 3066 3086 C5' A S 411 3085 3087 3108 C5' A S 412 3107 3109 3130 C5' G S 413 3129 3131 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2890 P G R 307 2891 2892 2912 P U R 308 distorted distorted 2897 2913 2914 2915 2932 P C R 309 distorted distorted 2920 2933 2934 2935 2952 P U R 310 distorted distorted 2940 2953 2954 2955 2972 P A R 311 distorted distorted 2960 2973 2974 2975 2994 P A R 312 distorted distorted 2980 2995 2996 2997 3016 P G R 313 distorted distorted 3002 3017 3018 3019 3039 P A R 314 distorted distorted 3024 3040 3041 3042 3061 P C R 315 distorted distorted 3047 3062 3063 3064 3082 P A S 411 distorted distorted 3083 3084 3085 3104 P A S 412 distorted distorted 3090 3105 3106 3107 3126 P G S 413 distorted distorted 3112 3127 3128 3129 ---------------------------------------------------------------------------------