ID code: '5KL8' 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' --------------------------------------------------------------------------------- 3030 C1' U C 1 beta 3025 3031 3028 3050 C1' A C 2 beta 3045 3051 3048 3072 C1' U C 3 beta 3067 3073 3070 3092 C1' U C 4 beta 3087 3093 3090 3112 C1' U C 5 beta 3107 3113 3110 3132 C1' G C 6 beta 3127 3133 3130 3155 C1' U C 7 beta 3150 3156 3153 3175 C1' A C 8 beta 3170 3176 3173 3197 C1' A C 9 beta 3192 3198 3195 3219 C1' U C 10 beta 3214 3220 3217 3239 C1' U C 11 beta 3234 3240 3237 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3028 C2' U C 1 OK 3030 3026 3029 3048 C2' A C 2 OK 3050 3046 3049 3070 C2' U C 3 OK 3072 3068 3071 3090 C2' U C 4 OK 3092 3088 3091 3110 C2' U C 5 OK 3112 3108 3111 3130 C2' G C 6 OK 3132 3128 3131 3153 C2' U C 7 OK 3155 3151 3154 3173 C2' A C 8 OK 3175 3171 3174 3195 C2' A C 9 OK 3197 3193 3196 3217 C2' U C 10 OK 3219 3215 3218 3237 C2' U C 11 OK 3239 3235 3238 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3026 C3' U C 1 OK 3024 3027 3028 3046 C3' A C 2 OK 3044 3047 3048 3068 C3' U C 3 OK 3066 3069 3070 3088 C3' U C 4 OK 3086 3089 3090 3108 C3' U C 5 OK 3106 3109 3110 3128 C3' G C 6 OK 3126 3129 3130 3151 C3' U C 7 OK 3149 3152 3153 3171 C3' A C 8 OK 3169 3172 3173 3193 C3' A C 9 OK 3191 3194 3195 3215 C3' U C 10 OK 3213 3216 3217 3235 C3' U C 11 OK 3233 3236 3237 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3024 C4' U C 1 OK 3026 3023 3025 3044 C4' A C 2 OK 3046 3043 3045 3066 C4' U C 3 OK 3068 3065 3067 3086 C4' U C 4 OK 3088 3085 3087 3106 C4' U C 5 OK 3108 3105 3107 3126 C4' G C 6 OK 3128 3125 3127 3149 C4' U C 7 OK 3151 3148 3150 3169 C4' A C 8 OK 3171 3168 3170 3191 C4' A C 9 OK 3193 3190 3192 3213 C4' U C 10 OK 3215 3212 3214 3233 C4' U C 11 OK 3235 3232 3234 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3023 C5' U C 1 3022 3024 3043 C5' A C 2 3042 3044 3065 C5' U C 3 3064 3066 3085 C5' U C 4 3084 3086 3105 C5' U C 5 3104 3106 3125 C5' G C 6 3124 3126 3148 C5' U C 7 3147 3149 3168 C5' A C 8 3167 3169 3190 C5' A C 9 3189 3191 3212 C5' U C 10 3211 3213 3232 C5' U C 11 3231 3233 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3039 P A C 2 distorted distorted 3027 3040 3041 3042 3061 P U C 3 distorted distorted 3047 3062 3063 3064 3081 P U C 4 distorted distorted 3069 3082 3083 3084 3101 P U C 5 distorted distorted 3089 3102 3103 3104 3121 P G C 6 distorted distorted 3109 3122 3123 3124 3144 P U C 7 distorted distorted 3129 3145 3146 3147 3164 P A C 8 distorted distorted 3152 3165 3166 3167 3186 P A C 9 distorted distorted 3172 3187 3188 3189 3208 P U C 10 distorted distorted 3194 3209 3210 3211 3228 P U C 11 distorted distorted 3216 3229 3230 3231 ---------------------------------------------------------------------------------