ID code: '4PTF' 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' --------------------------------------------------------------------------------- 8863 C1' DT P 2 beta 8859 8864 8862 8883 C1' DC P 3 beta 8879 8884 8882 8902 C1' DC P 4 beta 8898 8903 8901 8921 C1' DT P 5 beta 8917 8922 8920 8941 C1' DC P 6 beta 8937 8942 8940 8960 C1' DC P 7 beta 8956 8961 8959 8979 C1' DC P 8 beta 8975 8980 8978 8998 C1' DC P 9 beta 8994 8999 8997 9017 C1' DT P 10 beta 9013 9018 9016 9037 C1' DA P 11 beta 9033 9038 9036 9056 C1' DOC P 12 beta 9060 9048 9057 9074 C1' DT T 1 beta 9070 9075 9073 9094 C1' DA T 2 beta 9090 9095 9093 9115 C1' DA T 3 beta 9111 9116 9114 9136 C1' DG T 4 beta 9132 9137 9135 9158 C1' DG T 5 beta 9154 9159 9157 9180 C1' DT T 6 beta 9176 9181 9179 9200 C1' DA T 7 beta 9196 9201 9199 9221 C1' DG T 8 beta 9217 9222 9220 9243 C1' DG T 9 beta 9239 9244 9242 9265 C1' DG T 10 beta 9261 9266 9264 9287 C1' DG T 11 beta 9283 9288 9286 9309 C1' DA T 12 beta 9305 9310 9308 9330 C1' DG T 13 beta 9326 9331 9329 9352 C1' DG T 14 beta 9348 9353 9351 9374 C1' DA T 15 beta 9370 9375 9373 9394 C1' DCP A1201 beta 9398 9386 9395 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8862 C2' DT P 2 8863 8860 8882 C2' DC P 3 8883 8880 8901 C2' DC P 4 8902 8899 8920 C2' DT P 5 8921 8918 8940 C2' DC P 6 8941 8938 8959 C2' DC P 7 8960 8957 8978 C2' DC P 8 8979 8976 8997 C2' DC P 9 8998 8995 9016 C2' DT P 10 9017 9014 9036 C2' DA P 11 9037 9034 9057 C2' DOC P 12 9056 9058 9073 C2' DT T 1 9074 9071 9093 C2' DA T 2 9094 9091 9114 C2' DA T 3 9115 9112 9135 C2' DG T 4 9136 9133 9157 C2' DG T 5 9158 9155 9179 C2' DT T 6 9180 9177 9199 C2' DA T 7 9200 9197 9220 C2' DG T 8 9221 9218 9242 C2' DG T 9 9243 9240 9264 C2' DG T 10 9265 9262 9286 C2' DG T 11 9287 9284 9308 C2' DA T 12 9309 9306 9329 C2' DG T 13 9330 9327 9351 C2' DG T 14 9352 9349 9373 C2' DA T 15 9374 9371 9395 C2' DCP A1201 9394 9396 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8860 C3' DT P 2 OK 8858 8861 8862 8880 C3' DC P 3 OK 8878 8881 8882 8899 C3' DC P 4 OK 8897 8900 8901 8918 C3' DT P 5 OK 8916 8919 8920 8938 C3' DC P 6 OK 8936 8939 8940 8957 C3' DC P 7 OK 8955 8958 8959 8976 C3' DC P 8 OK 8974 8977 8978 8995 C3' DC P 9 OK 8993 8996 8997 9014 C3' DT P 10 OK 9012 9015 9016 9034 C3' DA P 11 OK 9032 9035 9036 9058 C3' DOC P 12 9059 9057 9071 C3' DT T 1 OK 9069 9072 9073 9091 C3' DA T 2 OK 9089 9092 9093 9112 C3' DA T 3 OK 9110 9113 9114 9133 C3' DG T 4 OK 9131 9134 9135 9155 C3' DG T 5 OK 9153 9156 9157 9177 C3' DT T 6 OK 9175 9178 9179 9197 C3' DA T 7 OK 9195 9198 9199 9218 C3' DG T 8 OK 9216 9219 9220 9240 C3' DG T 9 OK 9238 9241 9242 9262 C3' DG T 10 OK 9260 9263 9264 9284 C3' DG T 11 OK 9282 9285 9286 9306 C3' DA T 12 OK 9304 9307 9308 9327 C3' DG T 13 OK 9325 9328 9329 9349 C3' DG T 14 OK 9347 9350 9351 9371 C3' DA T 15 OK 9369 9372 9373 9396 C3' DCP A1201 OK 9397 9399 9395 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8858 C4' DT P 2 OK 8860 8857 8859 8878 C4' DC P 3 OK 8880 8877 8879 8897 C4' DC P 4 OK 8899 8896 8898 8916 C4' DT P 5 OK 8918 8915 8917 8936 C4' DC P 6 OK 8938 8935 8937 8955 C4' DC P 7 OK 8957 8954 8956 8974 C4' DC P 8 OK 8976 8973 8975 8993 C4' DC P 9 OK 8995 8992 8994 9012 C4' DT P 10 OK 9014 9011 9013 9032 C4' DA P 11 OK 9034 9031 9033 9059 C4' DOC P 12 OK 9058 9061 9060 9069 C4' DT T 1 OK 9071 9068 9070 9089 C4' DA T 2 OK 9091 9088 9090 9110 C4' DA T 3 OK 9112 9109 9111 9131 C4' DG T 4 OK 9133 9130 9132 9153 C4' DG T 5 OK 9155 9152 9154 9175 C4' DT T 6 OK 9177 9174 9176 9195 C4' DA T 7 OK 9197 9194 9196 9216 C4' DG T 8 OK 9218 9215 9217 9238 C4' DG T 9 OK 9240 9237 9239 9260 C4' DG T 10 OK 9262 9259 9261 9282 C4' DG T 11 OK 9284 9281 9283 9304 C4' DA T 12 OK 9306 9303 9305 9325 C4' DG T 13 OK 9327 9324 9326 9347 C4' DG T 14 OK 9349 9346 9348 9369 C4' DA T 15 OK 9371 9368 9370 9397 C4' DCP A1201 OK 9396 9400 9398 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8857 C5' DT P 2 8856 8858 8877 C5' DC P 3 8876 8878 8896 C5' DC P 4 8895 8897 8915 C5' DT P 5 8914 8916 8935 C5' DC P 6 8934 8936 8954 C5' DC P 7 8953 8955 8973 C5' DC P 8 8972 8974 8992 C5' DC P 9 8991 8993 9011 C5' DT P 10 9010 9012 9031 C5' DA P 11 9030 9032 9061 C5' DOC P 12 9062 9059 9068 C5' DT T 1 9067 9069 9088 C5' DA T 2 9087 9089 9109 C5' DA T 3 9108 9110 9130 C5' DG T 4 9129 9131 9152 C5' DG T 5 9151 9153 9174 C5' DT T 6 9173 9175 9194 C5' DA T 7 9193 9195 9215 C5' DG T 8 9214 9216 9237 C5' DG T 9 9236 9238 9259 C5' DG T 10 9258 9260 9281 C5' DG T 11 9280 9282 9303 C5' DA T 12 9302 9304 9324 C5' DG T 13 9323 9325 9346 C5' DG T 14 9345 9347 9368 C5' DA T 15 9367 9369 9400 C5' DCP A1201 9401 9397 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8853 P DT P 2 OK OK 8854 8855 8856 8873 P DC P 3 distorted distorted 8861 8874 8875 8876 8892 P DC P 4 distorted distorted 8881 8893 8894 8895 8911 P DT P 5 distorted distorted 8900 8912 8913 8914 8931 P DC P 6 distorted distorted 8919 8932 8933 8934 8950 P DC P 7 distorted distorted 8939 8951 8952 8953 8969 P DC P 8 distorted distorted 8958 8970 8971 8972 8988 P DC P 9 distorted distorted 8977 8989 8990 8991 9007 P DT P 10 distorted distorted 8996 9008 9009 9010 9027 P DA P 11 distorted distorted 9015 9028 9029 9030 9063 P DOC P 12 OK OK 9035 9064 9065 9062 9084 P DA T 2 distorted distorted 9072 9085 9086 9087 9105 P DA T 3 distorted distorted 9092 9106 9107 9108 9126 P DG T 4 distorted distorted 9113 9127 9128 9129 9148 P DG T 5 distorted distorted 9134 9149 9150 9151 9170 P DT T 6 distorted distorted 9156 9171 9172 9173 9190 P DA T 7 distorted distorted 9178 9191 9192 9193 9211 P DG T 8 distorted distorted 9198 9212 9213 9214 9233 P DG T 9 distorted distorted 9219 9234 9235 9236 9255 P DG T 10 distorted distorted 9241 9256 9257 9258 9277 P DG T 11 distorted distorted 9263 9278 9279 9280 9299 P DA T 12 distorted distorted 9285 9300 9301 9302 9320 P DG T 13 distorted distorted 9307 9321 9322 9323 9342 P DG T 14 distorted distorted 9328 9343 9344 9345 9364 P DA T 15 distorted distorted 9350 9365 9366 9367 ---------------------------------------------------------------------------------