ID code: '4EBE' 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' --------------------------------------------------------------------------------- 2986 C1' DA P 1 beta 2982 2987 2985 3007 C1' DG P 2 beta 3003 3008 3006 3029 C1' DG P 3 beta 3025 3030 3028 3051 C1' DA P 4 beta 3047 3052 3050 3072 C1' DC P 5 beta 3068 3073 3071 3091 C1' DC P 6 beta 3087 3092 3090 3108 C1' DOC P 7 beta 3112 3100 3109 3129 C1' DC T 3 beta 3125 3130 3128 3148 C1' DT T 4 beta 3144 3149 3147 3168 C1' DG T 5 beta 3164 3169 3167 3190 C1' DG T 6 beta 3186 3191 3189 3212 C1' DG T 7 beta 3208 3213 3211 3234 C1' DT T 8 beta 3230 3235 3233 3254 C1' DC T 9 beta 3250 3255 3253 3273 C1' DC T 10 beta 3269 3274 3272 3292 C1' DT T 11 beta 3288 3293 3291 3322 C1' DTP A 501 beta 3318 3323 3321 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2985 C2' DA P 1 2986 2983 3006 C2' DG P 2 3007 3004 3028 C2' DG P 3 3029 3026 3050 C2' DA P 4 3051 3048 3071 C2' DC P 5 3072 3069 3090 C2' DC P 6 3091 3088 3109 C2' DOC P 7 3108 3110 3128 C2' DC T 3 3129 3126 3147 C2' DT T 4 3148 3145 3167 C2' DG T 5 3168 3165 3189 C2' DG T 6 3190 3187 3211 C2' DG T 7 3212 3209 3233 C2' DT T 8 3234 3231 3253 C2' DC T 9 3254 3251 3272 C2' DC T 10 3273 3270 3291 C2' DT T 11 3292 3289 3321 C2' DTP A 501 3322 3319 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2983 C3' DA P 1 OK 2981 2984 2985 3004 C3' DG P 2 OK 3002 3005 3006 3026 C3' DG P 3 OK 3024 3027 3028 3048 C3' DA P 4 OK 3046 3049 3050 3069 C3' DC P 5 OK 3067 3070 3071 3088 C3' DC P 6 OK 3086 3089 3090 3110 C3' DOC P 7 3111 3109 3126 C3' DC T 3 OK 3124 3127 3128 3145 C3' DT T 4 OK 3143 3146 3147 3165 C3' DG T 5 OK 3163 3166 3167 3187 C3' DG T 6 OK 3185 3188 3189 3209 C3' DG T 7 OK 3207 3210 3211 3231 C3' DT T 8 OK 3229 3232 3233 3251 C3' DC T 9 OK 3249 3252 3253 3270 C3' DC T 10 OK 3268 3271 3272 3289 C3' DT T 11 OK 3287 3290 3291 3319 C3' DTP A 501 OK 3317 3320 3321 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2981 C4' DA P 1 OK 2983 2980 2982 3002 C4' DG P 2 OK 3004 3001 3003 3024 C4' DG P 3 OK 3026 3023 3025 3046 C4' DA P 4 OK 3048 3045 3047 3067 C4' DC P 5 OK 3069 3066 3068 3086 C4' DC P 6 OK 3088 3085 3087 3111 C4' DOC P 7 OK 3110 3113 3112 3124 C4' DC T 3 OK 3126 3123 3125 3143 C4' DT T 4 OK 3145 3142 3144 3163 C4' DG T 5 OK 3165 3162 3164 3185 C4' DG T 6 OK 3187 3184 3186 3207 C4' DG T 7 OK 3209 3206 3208 3229 C4' DT T 8 OK 3231 3228 3230 3249 C4' DC T 9 OK 3251 3248 3250 3268 C4' DC T 10 OK 3270 3267 3269 3287 C4' DT T 11 OK 3289 3286 3288 3317 C4' DTP A 501 OK 3319 3316 3318 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2980 C5' DA P 1 2979 2981 3001 C5' DG P 2 3000 3002 3023 C5' DG P 3 3022 3024 3045 C5' DA P 4 3044 3046 3066 C5' DC P 5 3065 3067 3085 C5' DC P 6 3084 3086 3113 C5' DOC P 7 3114 3111 3123 C5' DC T 3 3122 3124 3142 C5' DT T 4 3141 3143 3162 C5' DG T 5 3161 3163 3184 C5' DG T 6 3183 3185 3206 C5' DG T 7 3205 3207 3228 C5' DT T 8 3227 3229 3248 C5' DC T 9 3247 3249 3267 C5' DC T 10 3266 3268 3286 C5' DT T 11 3285 3287 3316 C5' DTP A 501 3315 3317 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2976 P DA P 1 OK OK 2977 2978 2979 2997 P DG P 2 distorted distorted 2984 2998 2999 3000 3019 P DG P 3 distorted distorted 3005 3020 3021 3022 3041 P DA P 4 distorted distorted 3027 3042 3043 3044 3062 P DC P 5 distorted distorted 3049 3063 3064 3065 3081 P DC P 6 distorted distorted 3070 3082 3083 3084 3115 P DOC P 7 distorted distorted 3089 3116 3117 3114 3119 P DC T 3 distorted distorted 3120 3121 3122 3138 P DT T 4 distorted distorted 3127 3139 3140 3141 3158 P DG T 5 distorted distorted 3146 3159 3160 3161 3180 P DG T 6 distorted distorted 3166 3181 3182 3183 3202 P DG T 7 distorted distorted 3188 3203 3204 3205 3224 P DT T 8 distorted distorted 3210 3225 3226 3227 3244 P DC T 9 distorted distorted 3232 3245 3246 3247 3263 P DC T 10 distorted distorted 3252 3264 3265 3266 3282 P DT T 11 distorted distorted 3271 3283 3284 3285 ---------------------------------------------------------------------------------