ID code: '3SV4' 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' --------------------------------------------------------------------------------- 8632 C1' DG B 101 beta 8628 8633 8631 8654 C1' DA B 102 beta 8650 8655 8653 8675 C1' DC B 103 beta 8671 8676 8674 8694 C1' DC B 104 beta 8690 8695 8693 8713 C1' DA B 105 beta 8709 8714 8712 8734 C1' DC B 106 beta 8730 8735 8733 8753 C1' DG B 107 beta 8749 8754 8752 8775 C1' DG B 108 beta 8771 8776 8774 8797 C1' DC B 109 beta 8793 8798 8796 8816 C1' DG B 110 beta 8812 8817 8815 8838 C1' DC B 111 beta 8834 8839 8837 8855 C1' DOC B 112 alpha beta 8859 8869 8847 8856 8888 C1' DA C 202 beta 8884 8889 8887 8909 C1' DA C 203 beta 8905 8910 8908 8930 C1' DT C 204 beta 8926 8931 8929 8950 C1' DG C 205 beta 8946 8951 8949 8972 C1' DG C 206 beta 8968 8973 8971 8994 C1' DC C 207 beta 8990 8995 8993 9013 C1' DG C 208 beta 9009 9014 9012 9035 C1' DC C 209 beta 9031 9036 9034 9054 C1' DC C 210 beta 9050 9055 9053 9073 C1' DG C 211 beta 9069 9074 9072 9095 C1' DT C 212 beta 9091 9096 9094 9115 C1' DG C 213 beta 9111 9116 9114 9137 C1' DG C 214 beta 9133 9138 9136 9159 C1' DT C 215 beta 9155 9160 9158 9179 C1' DC C 216 beta 9175 9180 9178 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8631 C2' DG B 101 8632 8629 8653 C2' DA B 102 8654 8651 8674 C2' DC B 103 8675 8672 8693 C2' DC B 104 8694 8691 8712 C2' DA B 105 8713 8710 8733 C2' DC B 106 8734 8731 8752 C2' DG B 107 8753 8750 8774 C2' DG B 108 8775 8772 8796 C2' DC B 109 8797 8794 8815 C2' DG B 110 8816 8813 8837 C2' DC B 111 8838 8835 8856 C2' DOC B 112 OK OK 8855 8857 8870 8871 8887 C2' DA C 202 8888 8885 8908 C2' DA C 203 8909 8906 8929 C2' DT C 204 8930 8927 8949 C2' DG C 205 8950 8947 8971 C2' DG C 206 8972 8969 8993 C2' DC C 207 8994 8991 9012 C2' DG C 208 9013 9010 9034 C2' DC C 209 9035 9032 9053 C2' DC C 210 9054 9051 9072 C2' DG C 211 9073 9070 9094 C2' DT C 212 9095 9092 9114 C2' DG C 213 9115 9112 9136 C2' DG C 214 9137 9134 9158 C2' DT C 215 9159 9156 9178 C2' DC C 216 9179 9176 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8629 C3' DG B 101 OK 8627 8630 8631 8651 C3' DA B 102 OK 8649 8652 8653 8672 C3' DC B 103 OK 8670 8673 8674 8691 C3' DC B 104 OK 8689 8692 8693 8710 C3' DA B 105 OK 8708 8711 8712 8731 C3' DC B 106 OK 8729 8732 8733 8750 C3' DG B 107 OK 8748 8751 8752 8772 C3' DG B 108 OK 8770 8773 8774 8794 C3' DC B 109 OK 8792 8795 8796 8813 C3' DG B 110 OK 8811 8814 8815 8835 C3' DC B 111 OK 8833 8836 8837 8857 C3' DOC B 112 8858 8856 8885 C3' DA C 202 OK 8883 8886 8887 8906 C3' DA C 203 OK 8904 8907 8908 8927 C3' DT C 204 OK 8925 8928 8929 8947 C3' DG C 205 OK 8945 8948 8949 8969 C3' DG C 206 OK 8967 8970 8971 8991 C3' DC C 207 OK 8989 8992 8993 9010 C3' DG C 208 OK 9008 9011 9012 9032 C3' DC C 209 OK 9030 9033 9034 9051 C3' DC C 210 OK 9049 9052 9053 9070 C3' DG C 211 OK 9068 9071 9072 9092 C3' DT C 212 OK 9090 9093 9094 9112 C3' DG C 213 OK 9110 9113 9114 9134 C3' DG C 214 OK 9132 9135 9136 9156 C3' DT C 215 OK 9154 9157 9158 9176 C3' DC C 216 OK 9174 9177 9178 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8627 C4' DG B 101 OK 8629 8626 8628 8649 C4' DA B 102 OK 8651 8648 8650 8670 C4' DC B 103 OK 8672 8669 8671 8689 C4' DC B 104 OK 8691 8688 8690 8708 C4' DA B 105 OK 8710 8707 8709 8729 C4' DC B 106 OK 8731 8728 8730 8748 C4' DG B 107 OK 8750 8747 8749 8770 C4' DG B 108 OK 8772 8769 8771 8792 C4' DC B 109 OK 8794 8791 8793 8811 C4' DG B 110 OK 8813 8810 8812 8833 C4' DC B 111 OK 8835 8832 8834 8858 C4' DOC B 112 OK OK 8857 8874 8860 8859 8883 C4' DA C 202 OK 8885 8882 8884 8904 C4' DA C 203 OK 8906 8903 8905 8925 C4' DT C 204 OK 8927 8924 8926 8945 C4' DG C 205 OK 8947 8944 8946 8967 C4' DG C 206 OK 8969 8966 8968 8989 C4' DC C 207 OK 8991 8988 8990 9008 C4' DG C 208 OK 9010 9007 9009 9030 C4' DC C 209 OK 9032 9029 9031 9049 C4' DC C 210 OK 9051 9048 9050 9068 C4' DG C 211 OK 9070 9067 9069 9090 C4' DT C 212 OK 9092 9089 9091 9110 C4' DG C 213 OK 9112 9109 9111 9132 C4' DG C 214 OK 9134 9131 9133 9154 C4' DT C 215 OK 9156 9153 9155 9174 C4' DC C 216 OK 9176 9173 9175 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8626 C5' DG B 101 8625 8627 8648 C5' DA B 102 8647 8649 8669 C5' DC B 103 8668 8670 8688 C5' DC B 104 8687 8689 8707 C5' DA B 105 8706 8708 8728 C5' DC B 106 8727 8729 8747 C5' DG B 107 8746 8748 8769 C5' DG B 108 8768 8770 8791 C5' DC B 109 8790 8792 8810 C5' DG B 110 8809 8811 8832 C5' DC B 111 8831 8833 8860 C5' DOC B 112 distorted distorted 8861 8875 8876 8858 8882 C5' DA C 202 8881 8883 8903 C5' DA C 203 8902 8904 8924 C5' DT C 204 8923 8925 8944 C5' DG C 205 8943 8945 8966 C5' DG C 206 8965 8967 8988 C5' DC C 207 8987 8989 9007 C5' DG C 208 9006 9008 9029 C5' DC C 209 9028 9030 9048 C5' DC C 210 9047 9049 9067 C5' DG C 211 9066 9068 9089 C5' DT C 212 9088 9090 9109 C5' DG C 213 9108 9110 9131 C5' DG C 214 9130 9132 9153 C5' DT C 215 9152 9154 9173 C5' DC C 216 9172 9174 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8644 P DA B 102 distorted distorted 8630 8645 8646 8647 8665 P DC B 103 distorted distorted 8652 8666 8667 8668 8684 P DC B 104 distorted distorted 8673 8685 8686 8687 8703 P DA B 105 distorted distorted 8692 8704 8705 8706 8724 P DC B 106 distorted distorted 8711 8725 8726 8727 8743 P DG B 107 distorted distorted 8732 8744 8745 8746 8765 P DG B 108 distorted distorted 8751 8766 8767 8768 8787 P DC B 109 distorted distorted 8773 8788 8789 8790 8806 P DG B 110 distorted distorted 8795 8807 8808 8809 8828 P DC B 111 distorted distorted 8814 8829 8830 8831 8862 P DOC B 112 distorted distorted 8836 8863 8864 8861 8878 P DA C 202 distorted distorted 8879 8880 8881 8899 P DA C 203 distorted distorted 8886 8900 8901 8902 8920 P DT C 204 distorted distorted 8907 8921 8922 8923 8940 P DG C 205 distorted distorted 8928 8941 8942 8943 8962 P DG C 206 distorted distorted 8948 8963 8964 8965 8984 P DC C 207 distorted distorted 8970 8985 8986 8987 9003 P DG C 208 distorted distorted 8992 9004 9005 9006 9025 P DC C 209 distorted distorted 9011 9026 9027 9028 9044 P DC C 210 distorted distorted 9033 9045 9046 9047 9063 P DG C 211 distorted distorted 9052 9064 9065 9066 9085 P DT C 212 distorted distorted 9071 9086 9087 9088 9105 P DG C 213 distorted distorted 9093 9106 9107 9108 9127 P DG C 214 distorted distorted 9113 9128 9129 9130 9149 P DT C 215 distorted distorted 9135 9150 9151 9152 9169 P DC C 216 distorted distorted 9157 9170 9171 9172 ---------------------------------------------------------------------------------