ID code: '4WAN' 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' --------------------------------------------------------------------------------- 971 C1' U B 3 beta 966 972 969 991 C1' A B 4 beta 986 992 989 1013 C1' C B 5 beta 1008 1014 1011 1033 C1' U B 6 beta 1028 1034 1031 1053 C1' A B 7 beta 1048 1054 1051 1075 C1' A B 8 beta 1070 1076 1073 1097 C1' C B 9 beta 1092 1098 1095 2086 C1' A D 2 2081 2084 2098 C1' U D 3 beta 2093 2099 2096 2118 C1' A D 4 beta 2113 2119 2116 2140 C1' C D 5 beta 2135 2141 2138 2160 C1' U D 6 beta 2155 2161 2158 2180 C1' A D 7 beta 2175 2181 2178 2202 C1' A D 8 beta 2197 2203 2200 2224 C1' C D 9 beta 2219 2225 2222 3182 C1' A F 2 3178 3181 3194 C1' U F 3 beta 3189 3195 3192 3214 C1' A F 4 beta 3209 3215 3212 3236 C1' C F 5 beta 3231 3237 3234 3256 C1' U F 6 beta 3251 3257 3254 3276 C1' A F 7 beta 3271 3277 3274 3298 C1' A F 8 beta 3293 3299 3296 3320 C1' C F 9 beta 3315 3321 3318 4253 C1' U H 3 beta 4248 4254 4251 4273 C1' A H 4 beta 4268 4274 4271 4295 C1' C H 5 beta 4290 4296 4293 4315 C1' U H 6 beta 4310 4316 4313 4335 C1' A H 7 beta 4330 4336 4333 4357 C1' A H 8 beta 4352 4358 4355 4379 C1' C H 9 beta 4374 4380 4377 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 969 C2' U B 3 OK 971 967 970 989 C2' A B 4 OK 991 987 990 1011 C2' C B 5 OK 1013 1009 1012 1031 C2' U B 6 OK 1033 1029 1032 1051 C2' A B 7 OK 1053 1049 1052 1073 C2' A B 8 OK 1075 1071 1074 1095 C2' C B 9 OK 1097 1093 1096 2084 C2' A D 2 OK 2086 2082 2085 2096 C2' U D 3 OK 2098 2094 2097 2116 C2' A D 4 OK 2118 2114 2117 2138 C2' C D 5 OK 2140 2136 2139 2158 C2' U D 6 OK 2160 2156 2159 2178 C2' A D 7 OK 2180 2176 2179 2200 C2' A D 8 OK 2202 2198 2201 2222 C2' C D 9 OK 2224 2220 2223 3181 C2' A F 2 3182 3179 3192 C2' U F 3 OK 3194 3190 3193 3212 C2' A F 4 OK 3214 3210 3213 3234 C2' C F 5 OK 3236 3232 3235 3254 C2' U F 6 OK 3256 3252 3255 3274 C2' A F 7 OK 3276 3272 3275 3296 C2' A F 8 OK 3298 3294 3297 3318 C2' C F 9 OK 3320 3316 3319 4251 C2' U H 3 OK 4253 4249 4252 4271 C2' A H 4 OK 4273 4269 4272 4293 C2' C H 5 OK 4295 4291 4294 4313 C2' U H 6 OK 4315 4311 4314 4333 C2' A H 7 OK 4335 4331 4334 4355 C2' A H 8 OK 4357 4353 4356 4377 C2' C H 9 OK 4379 4375 4378 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 967 C3' U B 3 OK 965 968 969 987 C3' A B 4 OK 985 988 989 1009 C3' C B 5 OK 1007 1010 1011 1029 C3' U B 6 OK 1027 1030 1031 1049 C3' A B 7 OK 1047 1050 1051 1071 C3' A B 8 OK 1069 1072 1073 1093 C3' C B 9 OK 1091 1094 1095 2082 C3' A D 2 OK 2080 2083 2084 2094 C3' U D 3 OK 2092 2095 2096 2114 C3' A D 4 OK 2112 2115 2116 2136 C3' C D 5 OK 2134 2137 2138 2156 C3' U D 6 OK 2154 2157 2158 2176 C3' A D 7 OK 2174 2177 2178 2198 C3' A D 8 OK 2196 2199 2200 2220 C3' C D 9 OK 2218 2221 2222 3179 C3' A F 2 OK 3177 3180 3181 3190 C3' U F 3 OK 3188 3191 3192 3210 C3' A F 4 OK 3208 3211 3212 3232 C3' C F 5 OK 3230 3233 3234 3252 C3' U F 6 OK 3250 3253 3254 3272 C3' A F 7 OK 3270 3273 3274 3294 C3' A F 8 OK 3292 3295 3296 3316 C3' C F 9 OK 3314 3317 3318 4249 C3' U H 3 OK 4247 4250 4251 4269 C3' A H 4 OK 4267 4270 4271 4291 C3' C H 5 OK 4289 4292 4293 4311 C3' U H 6 OK 4309 4312 4313 4331 C3' A H 7 OK 4329 4332 4333 4353 C3' A H 8 OK 4351 4354 4355 4375 C3' C H 9 OK 4373 4376 4377 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 965 C4' U B 3 OK 967 964 966 985 C4' A B 4 OK 987 984 986 1007 C4' C B 5 OK 1009 1006 1008 1027 C4' U B 6 OK 1029 1026 1028 1047 C4' A B 7 OK 1049 1046 1048 1069 C4' A B 8 OK 1071 1068 1070 1091 C4' C B 9 OK 1093 1090 1092 2080 C4' A D 2 OK 2082 2079 2081 2092 C4' U D 3 OK 2094 2091 2093 2112 C4' A D 4 OK 2114 2111 2113 2134 C4' C D 5 OK 2136 2133 2135 2154 C4' U D 6 OK 2156 2153 2155 2174 C4' A D 7 OK 2176 2173 2175 2196 C4' A D 8 OK 2198 2195 2197 2218 C4' C D 9 OK 2220 2217 2219 3177 C4' A F 2 OK 3179 3176 3178 3188 C4' U F 3 OK 3190 3187 3189 3208 C4' A F 4 OK 3210 3207 3209 3230 C4' C F 5 OK 3232 3229 3231 3250 C4' U F 6 OK 3252 3249 3251 3270 C4' A F 7 OK 3272 3269 3271 3292 C4' A F 8 OK 3294 3291 3293 3314 C4' C F 9 OK 3316 3313 3315 4247 C4' U H 3 OK 4249 4246 4248 4267 C4' A H 4 OK 4269 4266 4268 4289 C4' C H 5 OK 4291 4288 4290 4309 C4' U H 6 OK 4311 4308 4310 4329 C4' A H 7 OK 4331 4328 4330 4351 C4' A H 8 OK 4353 4350 4352 4373 C4' C H 9 OK 4375 4372 4374 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 964 C5' U B 3 963 965 984 C5' A B 4 983 985 1006 C5' C B 5 1005 1007 1026 C5' U B 6 1025 1027 1046 C5' A B 7 1045 1047 1068 C5' A B 8 1067 1069 1090 C5' C B 9 1089 1091 2079 C5' A D 2 2078 2080 2091 C5' U D 3 2090 2092 2111 C5' A D 4 2110 2112 2133 C5' C D 5 2132 2134 2153 C5' U D 6 2152 2154 2173 C5' A D 7 2172 2174 2195 C5' A D 8 2194 2196 2217 C5' C D 9 2216 2218 3176 C5' A F 2 3175 3177 3187 C5' U F 3 3186 3188 3207 C5' A F 4 3206 3208 3229 C5' C F 5 3228 3230 3249 C5' U F 6 3248 3250 3269 C5' A F 7 3268 3270 3291 C5' A F 8 3290 3292 3313 C5' C F 9 3312 3314 4246 C5' U H 3 4245 4247 4266 C5' A H 4 4265 4267 4288 C5' C H 5 4287 4289 4308 C5' U H 6 4307 4309 4328 C5' A H 7 4327 4329 4350 C5' A H 8 4349 4351 4372 C5' C H 9 4371 4373 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 960 P U B 3 distorted distorted 959 961 962 963 980 P A B 4 distorted distorted 968 981 982 983 1002 P C B 5 distorted distorted 988 1003 1004 1005 1022 P U B 6 distorted distorted 1010 1023 1024 1025 1042 P A B 7 distorted distorted 1030 1043 1044 1045 1064 P A B 8 distorted distorted 1050 1065 1066 1067 1086 P C B 9 distorted distorted 1072 1087 1088 1089 1106 P A B 10 distorted distorted 1094 1107 1108 1109 2075 P A D 2 distorted distorted 2074 2076 2077 2078 2087 P U D 3 distorted distorted 2083 2088 2089 2090 2107 P A D 4 distorted distorted 2095 2108 2109 2110 2129 P C D 5 distorted distorted 2115 2130 2131 2132 2149 P U D 6 distorted distorted 2137 2150 2151 2152 2169 P A D 7 distorted distorted 2157 2170 2171 2172 2191 P A D 8 distorted distorted 2177 2192 2193 2194 2213 P C D 9 distorted distorted 2199 2214 2215 2216 2233 P A D 10 distorted distorted 2221 2234 2235 2236 3172 P A F 2 distorted distorted 3171 3173 3174 3175 3183 P U F 3 distorted distorted 3180 3184 3185 3186 3203 P A F 4 distorted distorted 3191 3204 3205 3206 3225 P C F 5 distorted distorted 3211 3226 3227 3228 3245 P U F 6 distorted distorted 3233 3246 3247 3248 3265 P A F 7 distorted distorted 3253 3266 3267 3268 3287 P A F 8 distorted distorted 3273 3288 3289 3290 3309 P C F 9 distorted distorted 3295 3310 3311 3312 3329 P A F 10 distorted distorted 3317 3330 3331 3332 4242 P U H 3 distorted distorted 4241 4243 4244 4245 4262 P A H 4 distorted distorted 4250 4263 4264 4265 4284 P C H 5 distorted distorted 4270 4285 4286 4287 4304 P U H 6 distorted distorted 4292 4305 4306 4307 4324 P A H 7 distorted distorted 4312 4325 4326 4327 4346 P A H 8 distorted distorted 4332 4347 4348 4349 4368 P C H 9 distorted distorted 4354 4369 4370 4371 4388 P A H 10 distorted distorted 4376 4389 4390 4391 ---------------------------------------------------------------------------------