ID code: '3SV3' 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' --------------------------------------------------------------------------------- 8701 C1' DG B 101 beta 8697 8702 8700 8723 C1' DA B 102 beta 8719 8724 8722 8744 C1' DC B 103 beta 8740 8745 8743 8763 C1' DC B 104 beta 8759 8764 8762 8782 C1' DA B 105 beta 8778 8783 8781 8803 C1' DC B 106 beta 8799 8804 8802 8822 C1' DG B 107 beta 8818 8823 8821 8844 C1' DG B 108 beta 8840 8845 8843 8866 C1' DC B 109 beta 8862 8867 8865 8885 C1' DG B 110 beta 8881 8886 8884 8907 C1' DC B 111 beta 8903 8908 8906 8924 C1' DOC B 112 beta 8928 8916 8925 8942 C1' BMN C 204 8953 8943 8968 C1' DG C 205 beta 8964 8969 8967 8990 C1' DG C 206 beta 8986 8991 8989 9012 C1' DC C 207 beta 9008 9013 9011 9031 C1' DG C 208 beta 9027 9032 9030 9053 C1' DC C 209 beta 9049 9054 9052 9072 C1' DC C 210 beta 9068 9073 9071 9091 C1' DG C 211 beta 9087 9092 9090 9113 C1' DT C 212 beta 9109 9114 9112 9133 C1' DG C 213 beta 9129 9134 9132 9155 C1' DG C 214 beta 9151 9156 9154 9177 C1' DT C 215 beta 9173 9178 9176 9197 C1' DC C 216 beta 9193 9198 9196 9216 C1' 5SI A 1 beta 9234 9207 9220 9248 C1' 5SI A 833 beta 9266 9239 9252 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8700 C2' DG B 101 8701 8698 8722 C2' DA B 102 8723 8720 8743 C2' DC B 103 8744 8741 8762 C2' DC B 104 8763 8760 8781 C2' DA B 105 8782 8779 8802 C2' DC B 106 8803 8800 8821 C2' DG B 107 8822 8819 8843 C2' DG B 108 8844 8841 8865 C2' DC B 109 8866 8863 8884 C2' DG B 110 8885 8882 8906 C2' DC B 111 8907 8904 8925 C2' DOC B 112 8924 8926 8943 C2' BMN C 204 8942 8949 8967 C2' DG C 205 8968 8965 8989 C2' DG C 206 8990 8987 9011 C2' DC C 207 9012 9009 9030 C2' DG C 208 9031 9028 9052 C2' DC C 209 9053 9050 9071 C2' DC C 210 9072 9069 9090 C2' DG C 211 9091 9088 9112 C2' DT C 212 9113 9110 9132 C2' DG C 213 9133 9130 9154 C2' DG C 214 9155 9152 9176 C2' DT C 215 9177 9174 9196 C2' DC C 216 9197 9194 9220 C2' 5SI A 1 9216 9224 9252 C2' 5SI A 833 9248 9256 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8698 C3' DG B 101 OK 8696 8699 8700 8720 C3' DA B 102 OK 8718 8721 8722 8741 C3' DC B 103 OK 8739 8742 8743 8760 C3' DC B 104 OK 8758 8761 8762 8779 C3' DA B 105 OK 8777 8780 8781 8800 C3' DC B 106 OK 8798 8801 8802 8819 C3' DG B 107 OK 8817 8820 8821 8841 C3' DG B 108 OK 8839 8842 8843 8863 C3' DC B 109 OK 8861 8864 8865 8882 C3' DG B 110 OK 8880 8883 8884 8904 C3' DC B 111 OK 8902 8905 8906 8926 C3' DOC B 112 8927 8925 8949 C3' BMN C 204 OK 8952 8945 8943 8965 C3' DG C 205 OK 8963 8966 8967 8987 C3' DG C 206 OK 8985 8988 8989 9009 C3' DC C 207 OK 9007 9010 9011 9028 C3' DG C 208 OK 9026 9029 9030 9050 C3' DC C 209 OK 9048 9051 9052 9069 C3' DC C 210 OK 9067 9070 9071 9088 C3' DG C 211 OK 9086 9089 9090 9110 C3' DT C 212 OK 9108 9111 9112 9130 C3' DG C 213 OK 9128 9131 9132 9152 C3' DG C 214 OK 9150 9153 9154 9174 C3' DT C 215 OK 9172 9175 9176 9194 C3' DC C 216 OK 9192 9195 9196 9224 C3' 5SI A 1 OK 9233 9225 9220 9256 C3' 5SI A 833 OK 9265 9257 9252 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8696 C4' DG B 101 OK 8698 8695 8697 8718 C4' DA B 102 OK 8720 8717 8719 8739 C4' DC B 103 OK 8741 8738 8740 8758 C4' DC B 104 OK 8760 8757 8759 8777 C4' DA B 105 OK 8779 8776 8778 8798 C4' DC B 106 OK 8800 8797 8799 8817 C4' DG B 107 OK 8819 8816 8818 8839 C4' DG B 108 OK 8841 8838 8840 8861 C4' DC B 109 OK 8863 8860 8862 8880 C4' DG B 110 OK 8882 8879 8881 8902 C4' DC B 111 OK 8904 8901 8903 8927 C4' DOC B 112 OK 8926 8929 8928 8952 C4' BMN C 204 OK 8949 8954 8953 8963 C4' DG C 205 OK 8965 8962 8964 8985 C4' DG C 206 OK 8987 8984 8986 9007 C4' DC C 207 OK 9009 9006 9008 9026 C4' DG C 208 OK 9028 9025 9027 9048 C4' DC C 209 OK 9050 9047 9049 9067 C4' DC C 210 OK 9069 9066 9068 9086 C4' DG C 211 OK 9088 9085 9087 9108 C4' DT C 212 OK 9110 9107 9109 9128 C4' DG C 213 OK 9130 9127 9129 9150 C4' DG C 214 OK 9152 9149 9151 9172 C4' DT C 215 OK 9174 9171 9173 9192 C4' DC C 216 OK 9194 9191 9193 9233 C4' 5SI A 1 OK 9224 9237 9234 9265 C4' 5SI A 833 OK 9256 9269 9266 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8695 C5' DG B 101 8694 8696 8717 C5' DA B 102 8716 8718 8738 C5' DC B 103 8737 8739 8757 C5' DC B 104 8756 8758 8776 C5' DA B 105 8775 8777 8797 C5' DC B 106 8796 8798 8816 C5' DG B 107 8815 8817 8838 C5' DG B 108 8837 8839 8860 C5' DC B 109 8859 8861 8879 C5' DG B 110 8878 8880 8901 C5' DC B 111 8900 8902 8929 C5' DOC B 112 8930 8927 8954 C5' BMN C 204 8955 8952 8962 C5' DG C 205 8961 8963 8984 C5' DG C 206 8983 8985 9006 C5' DC C 207 9005 9007 9025 C5' DG C 208 9024 9026 9047 C5' DC C 209 9046 9048 9066 C5' DC C 210 9065 9067 9085 C5' DG C 211 9084 9086 9107 C5' DT C 212 9106 9108 9127 C5' DG C 213 9126 9128 9149 C5' DG C 214 9148 9150 9171 C5' DT C 215 9170 9172 9191 C5' DC C 216 9190 9192 9237 C5' 5SI A 1 9238 9233 9269 C5' 5SI A 833 9270 9265 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8713 P DA B 102 distorted distorted 8699 8714 8715 8716 8734 P DC B 103 distorted distorted 8721 8735 8736 8737 8753 P DC B 104 distorted distorted 8742 8754 8755 8756 8772 P DA B 105 distorted distorted 8761 8773 8774 8775 8793 P DC B 106 distorted distorted 8780 8794 8795 8796 8812 P DG B 107 distorted distorted 8801 8813 8814 8815 8834 P DG B 108 distorted distorted 8820 8835 8836 8837 8856 P DC B 109 distorted distorted 8842 8857 8858 8859 8875 P DG B 110 distorted distorted 8864 8876 8877 8878 8897 P DC B 111 distorted distorted 8883 8898 8899 8900 8931 P DOC B 112 OK OK 8905 8932 8933 8930 8936 P BMN C 204 OK OK 8956 8957 8955 8958 P DG C 205 distorted distorted 8945 8959 8960 8961 8980 P DG C 206 distorted distorted 8966 8981 8982 8983 9002 P DC C 207 distorted distorted 8988 9003 9004 9005 9021 P DG C 208 distorted distorted 9010 9022 9023 9024 9043 P DC C 209 distorted distorted 9029 9044 9045 9046 9062 P DC C 210 distorted distorted 9051 9063 9064 9065 9081 P DG C 211 distorted distorted 9070 9082 9083 9084 9103 P DT C 212 distorted distorted 9089 9104 9105 9106 9123 P DG C 213 distorted distorted 9111 9124 9125 9126 9145 P DG C 214 distorted distorted 9131 9146 9147 9148 9167 P DT C 215 distorted distorted 9153 9168 9169 9170 9187 P DC C 216 distorted distorted 9175 9188 9189 9190 ---------------------------------------------------------------------------------