ID code: '5WTY' 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' --------------------------------------------------------------------------------- 8948 C1' G C1140 beta 8943 8949 8946 8971 C1' G C1141 beta 8966 8972 8969 8994 C1' A C1142 beta 8989 8995 8992 9016 C1' A C1143 beta 9011 9017 9014 9038 C1' U C1144 beta 9033 9039 9036 9058 C1' U C1145 beta 9053 9059 9056 9078 C1' G C1146 beta 9073 9079 9076 9101 C1' A C1147 beta 9096 9102 9099 9123 C1' C C1148 beta 9118 9124 9121 9143 C1' G C1149 beta 9138 9144 9141 9166 C1' G C1150 beta 9161 9167 9164 9190 C1' G D1140 beta 9185 9191 9188 9213 C1' G D1141 beta 9208 9214 9211 9236 C1' A D1142 beta 9231 9237 9234 9258 C1' A D1143 beta 9253 9259 9256 9280 C1' U D1144 beta 9275 9281 9278 9300 C1' U D1145 beta 9295 9301 9298 9320 C1' G D1146 beta 9315 9321 9318 9343 C1' A D1147 beta 9338 9344 9341 9365 C1' C D1148 beta 9360 9366 9363 9385 C1' G D1149 beta 9380 9386 9383 9408 C1' G D1150 beta 9403 9409 9406 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8946 C2' G C1140 OK 8948 8944 8947 8969 C2' G C1141 OK 8971 8967 8970 8992 C2' A C1142 OK 8994 8990 8993 9014 C2' A C1143 OK 9016 9012 9015 9036 C2' U C1144 OK 9038 9034 9037 9056 C2' U C1145 OK 9058 9054 9057 9076 C2' G C1146 OK 9078 9074 9077 9099 C2' A C1147 OK 9101 9097 9100 9121 C2' C C1148 OK 9123 9119 9122 9141 C2' G C1149 OK 9143 9139 9142 9164 C2' G C1150 OK 9166 9162 9165 9188 C2' G D1140 OK 9190 9186 9189 9211 C2' G D1141 OK 9213 9209 9212 9234 C2' A D1142 OK 9236 9232 9235 9256 C2' A D1143 OK 9258 9254 9257 9278 C2' U D1144 OK 9280 9276 9279 9298 C2' U D1145 OK 9300 9296 9299 9318 C2' G D1146 OK 9320 9316 9319 9341 C2' A D1147 OK 9343 9339 9342 9363 C2' C D1148 OK 9365 9361 9364 9383 C2' G D1149 OK 9385 9381 9384 9406 C2' G D1150 OK 9408 9404 9407 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8944 C3' G C1140 OK 8942 8945 8946 8967 C3' G C1141 OK 8965 8968 8969 8990 C3' A C1142 OK 8988 8991 8992 9012 C3' A C1143 OK 9010 9013 9014 9034 C3' U C1144 OK 9032 9035 9036 9054 C3' U C1145 OK 9052 9055 9056 9074 C3' G C1146 OK 9072 9075 9076 9097 C3' A C1147 OK 9095 9098 9099 9119 C3' C C1148 OK 9117 9120 9121 9139 C3' G C1149 OK 9137 9140 9141 9162 C3' G C1150 OK 9160 9163 9164 9186 C3' G D1140 OK 9184 9187 9188 9209 C3' G D1141 OK 9207 9210 9211 9232 C3' A D1142 OK 9230 9233 9234 9254 C3' A D1143 OK 9252 9255 9256 9276 C3' U D1144 OK 9274 9277 9278 9296 C3' U D1145 OK 9294 9297 9298 9316 C3' G D1146 OK 9314 9317 9318 9339 C3' A D1147 OK 9337 9340 9341 9361 C3' C D1148 OK 9359 9362 9363 9381 C3' G D1149 OK 9379 9382 9383 9404 C3' G D1150 OK 9402 9405 9406 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8942 C4' G C1140 OK 8944 8941 8943 8965 C4' G C1141 OK 8967 8964 8966 8988 C4' A C1142 OK 8990 8987 8989 9010 C4' A C1143 OK 9012 9009 9011 9032 C4' U C1144 OK 9034 9031 9033 9052 C4' U C1145 OK 9054 9051 9053 9072 C4' G C1146 OK 9074 9071 9073 9095 C4' A C1147 OK 9097 9094 9096 9117 C4' C C1148 OK 9119 9116 9118 9137 C4' G C1149 OK 9139 9136 9138 9160 C4' G C1150 OK 9162 9159 9161 9184 C4' G D1140 OK 9186 9183 9185 9207 C4' G D1141 OK 9209 9206 9208 9230 C4' A D1142 OK 9232 9229 9231 9252 C4' A D1143 OK 9254 9251 9253 9274 C4' U D1144 OK 9276 9273 9275 9294 C4' U D1145 OK 9296 9293 9295 9314 C4' G D1146 OK 9316 9313 9315 9337 C4' A D1147 OK 9339 9336 9338 9359 C4' C D1148 OK 9361 9358 9360 9379 C4' G D1149 OK 9381 9378 9380 9402 C4' G D1150 OK 9404 9401 9403 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8941 C5' G C1140 8940 8942 8964 C5' G C1141 8963 8965 8987 C5' A C1142 8986 8988 9009 C5' A C1143 9008 9010 9031 C5' U C1144 9030 9032 9051 C5' U C1145 9050 9052 9071 C5' G C1146 9070 9072 9094 C5' A C1147 9093 9095 9116 C5' C C1148 9115 9117 9136 C5' G C1149 9135 9137 9159 C5' G C1150 9158 9160 9183 C5' G D1140 9182 9184 9206 C5' G D1141 9205 9207 9229 C5' A D1142 9228 9230 9251 C5' A D1143 9250 9252 9273 C5' U D1144 9272 9274 9293 C5' U D1145 9292 9294 9313 C5' G D1146 9312 9314 9336 C5' A D1147 9335 9337 9358 C5' C D1148 9357 9359 9378 C5' G D1149 9377 9379 9401 C5' G D1150 9400 9402 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8937 P G C1140 distorted distorted 8938 8939 8940 8960 P G C1141 distorted distorted 8945 8961 8962 8963 8983 P A C1142 distorted distorted 8968 8984 8985 8986 9005 P A C1143 distorted distorted 8991 9006 9007 9008 9027 P U C1144 distorted distorted 9013 9028 9029 9030 9047 P U C1145 distorted distorted 9035 9048 9049 9050 9067 P G C1146 distorted distorted 9055 9068 9069 9070 9090 P A C1147 distorted distorted 9075 9091 9092 9093 9112 P C C1148 distorted distorted 9098 9113 9114 9115 9132 P G C1149 distorted distorted 9120 9133 9134 9135 9155 P G C1150 distorted distorted 9140 9156 9157 9158 9179 P G D1140 distorted distorted 9180 9181 9182 9202 P G D1141 distorted distorted 9187 9203 9204 9205 9225 P A D1142 distorted distorted 9210 9226 9227 9228 9247 P A D1143 distorted distorted 9233 9248 9249 9250 9269 P U D1144 distorted distorted 9255 9270 9271 9272 9289 P U D1145 distorted distorted 9277 9290 9291 9292 9309 P G D1146 distorted distorted 9297 9310 9311 9312 9332 P A D1147 distorted distorted 9317 9333 9334 9335 9354 P C D1148 distorted distorted 9340 9355 9356 9357 9374 P G D1149 distorted distorted 9362 9375 9376 9377 9397 P G D1150 distorted distorted 9382 9398 9399 9400 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