ID code: '5EV4' 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 1 alpha beta 2987 3007 2993 2990 3022 C1' U B 2 alpha beta 3017 3037 3023 3020 3052 C1' U B 3 alpha beta 3047 3067 3053 3050 3081 C1' DU B 4 beta 3077 3082 3080 3101 C1' U B 5 alpha beta 3096 3116 3102 3099 3131 C1' U B 6 alpha beta 3126 3146 3132 3129 3159 C1' BRU B 7 beta 3164 3150 3160 3180 C1' DU B 8 beta 3176 3181 3179 3200 C1' C B 9 alpha beta 3195 3216 3201 3198 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2990 C2' U B 1 OK OK 2992 2988 3005 2991 3020 C2' U B 2 OK OK 3022 3018 3035 3021 3050 C2' U B 3 OK OK 3052 3048 3065 3051 3080 C2' DU B 4 3081 3078 3099 C2' U B 5 OK OK 3101 3097 3114 3100 3129 C2' U B 6 OK OK 3131 3127 3144 3130 3160 C2' BRU B 7 3159 3161 3179 C2' DU B 8 3180 3177 3198 C2' C B 9 OK OK 3200 3196 3214 3199 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2988 C3' U B 1 OK OK 2986 3004 2989 2990 3018 C3' U B 2 OK OK 3016 3034 3019 3020 3048 C3' U B 3 OK OK 3046 3064 3049 3050 3078 C3' DU B 4 OK 3076 3079 3080 3097 C3' U B 5 OK OK 3095 3113 3098 3099 3127 C3' U B 6 OK OK 3125 3143 3128 3129 3161 C3' BRU B 7 OK 3162 3163 3160 3177 C3' DU B 8 OK 3175 3178 3179 3196 C3' C B 9 OK OK 3194 3212 3197 3198 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2986 C4' U B 1 OK OK 2988 3003 2985 2987 3016 C4' U B 2 OK OK 3018 3033 3015 3017 3046 C4' U B 3 OK OK 3048 3063 3045 3047 3076 C4' DU B 4 OK 3078 3075 3077 3095 C4' U B 5 OK OK 3097 3112 3094 3096 3125 C4' U B 6 OK OK 3127 3142 3124 3126 3162 C4' BRU B 7 OK 3161 3165 3164 3175 C4' DU B 8 OK 3177 3174 3176 3194 C4' C B 9 OK OK 3196 3211 3193 3195 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2985 C5' U B 1 OK OK 2984 3001 3002 2986 3015 C5' U B 2 OK OK 3014 3031 3032 3016 3045 C5' U B 3 OK OK 3044 3061 3062 3046 3075 C5' DU B 4 3074 3076 3094 C5' U B 5 OK OK 3093 3110 3111 3095 3124 C5' U B 6 OK OK 3123 3140 3141 3125 3165 C5' BRU B 7 3166 3162 3174 C5' DU B 8 3173 3175 3193 C5' C B 9 OK OK 3192 3209 3210 3194 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2981 P U B 1 OK OK 2982 2983 2984 3011 P U B 2 distorted distorted 2989 3012 3013 3014 3041 P U B 3 distorted distorted 3019 3042 3043 3044 3071 P DU B 4 distorted distorted 3049 3072 3073 3074 3090 P U B 5 distorted distorted 3079 3091 3092 3093 3120 P U B 6 distorted distorted 3098 3121 3122 3123 3167 P BRU B 7 distorted distorted 3128 3168 3169 3166 3170 P DU B 8 distorted distorted 3163 3171 3172 3173 3189 P C B 9 distorted distorted 3178 3190 3191 3192 ---------------------------------------------------------------------------------