ID code: '5EV1' 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' --------------------------------------------------------------------------------- 2992 C1' U B 2 alpha beta 2987 3007 2993 2990 3023 C1' U B 3 alpha beta 3018 3038 3024 3021 3053 C1' U B 4 alpha beta 3048 3068 3054 3051 3082 C1' DU B 5 beta 3078 3083 3081 3101 C1' DU B 6 beta 3097 3102 3100 3119 C1' BRU B 7 beta 3124 3110 3120 3140 C1' DU B 8 beta 3136 3141 3139 3160 C1' U B 9 alpha beta 3155 3175 3161 3158 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2990 C2' U B 2 OK OK 2992 2988 3005 2991 3021 C2' U B 3 OK OK 3023 3019 3036 3022 3051 C2' U B 4 OK OK 3053 3049 3066 3052 3081 C2' DU B 5 3082 3079 3100 C2' DU B 6 3101 3098 3120 C2' BRU B 7 3119 3121 3139 C2' DU B 8 3140 3137 3158 C2' U B 9 OK OK 3160 3156 3173 3159 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2988 C3' U B 2 OK OK 2986 3004 2989 2990 3019 C3' U B 3 OK OK 3017 3035 3020 3021 3049 C3' U B 4 OK OK 3047 3065 3050 3051 3079 C3' DU B 5 OK 3077 3080 3081 3098 C3' DU B 6 OK 3096 3099 3100 3121 C3' BRU B 7 OK 3122 3123 3120 3137 C3' DU B 8 OK 3135 3138 3139 3156 C3' U B 9 OK OK 3154 3172 3157 3158 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2986 C4' U B 2 OK OK 2988 3003 2985 2987 3017 C4' U B 3 OK OK 3019 3034 3016 3018 3047 C4' U B 4 OK OK 3049 3064 3046 3048 3077 C4' DU B 5 OK 3079 3076 3078 3096 C4' DU B 6 OK 3098 3095 3097 3122 C4' BRU B 7 OK 3121 3125 3124 3135 C4' DU B 8 OK 3137 3134 3136 3154 C4' U B 9 OK OK 3156 3171 3153 3155 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2985 C5' U B 2 OK OK 2984 3001 3002 2986 3016 C5' U B 3 OK OK 3015 3032 3033 3017 3046 C5' U B 4 OK OK 3045 3062 3063 3047 3076 C5' DU B 5 3075 3077 3095 C5' DU B 6 3094 3096 3125 C5' BRU B 7 3126 3122 3134 C5' DU B 8 3133 3135 3153 C5' U B 9 OK OK 3152 3169 3170 3154 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3012 P U B 3 distorted distorted 2989 3013 3014 3015 3042 P U B 4 distorted distorted 3020 3043 3044 3045 3072 P DU B 5 distorted distorted 3050 3073 3074 3075 3091 P DU B 6 distorted distorted 3080 3092 3093 3094 3127 P BRU B 7 distorted distorted 3099 3128 3129 3126 3130 P DU B 8 distorted distorted 3123 3131 3132 3133 3149 P U B 9 distorted distorted 3138 3150 3151 3152 ---------------------------------------------------------------------------------