ID code: '3OJS' 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' --------------------------------------------------------------------------------- 8652 C1' DG B 101 beta 8648 8653 8651 8674 C1' DA B 102 beta 8670 8675 8673 8695 C1' DC B 103 beta 8691 8696 8694 8714 C1' DC B 104 beta 8710 8715 8713 8733 C1' DA B 105 beta 8729 8734 8732 8754 C1' DC B 106 beta 8750 8755 8753 8773 C1' DG B 107 beta 8769 8774 8772 8795 C1' DG B 108 beta 8791 8796 8794 8817 C1' DC B 109 beta 8813 8818 8816 8836 C1' DG B 110 beta 8832 8837 8835 8858 C1' DC B 111 beta 8854 8859 8857 8875 C1' DOC B 112 alpha beta 8879 8889 8867 8876 8905 C1' DA C 201 beta 8901 8906 8904 8926 C1' DA C 202 beta 8922 8927 8925 8947 C1' DA C 203 beta 8943 8948 8946 8968 C1' DA C 204 beta 8964 8969 8967 8989 C1' DG C 205 beta 8985 8990 8988 9011 C1' DG C 206 beta 9007 9012 9010 9033 C1' DC C 207 beta 9029 9034 9032 9052 C1' DG C 208 beta 9048 9053 9051 9074 C1' DC C 209 beta 9070 9075 9073 9093 C1' DC C 210 beta 9089 9094 9092 9112 C1' DG C 211 beta 9108 9113 9111 9134 C1' DT C 212 beta 9130 9135 9133 9154 C1' DG C 213 beta 9150 9155 9153 9176 C1' DG C 214 beta 9172 9177 9175 9198 C1' DT C 215 beta 9194 9199 9197 9218 C1' DC C 216 beta 9214 9219 9217 9257 C1' XJS A 1 beta 9294 9229 9277 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8651 C2' DG B 101 8652 8649 8673 C2' DA B 102 8674 8671 8694 C2' DC B 103 8695 8692 8713 C2' DC B 104 8714 8711 8732 C2' DA B 105 8733 8730 8753 C2' DC B 106 8754 8751 8772 C2' DG B 107 8773 8770 8794 C2' DG B 108 8795 8792 8816 C2' DC B 109 8817 8814 8835 C2' DG B 110 8836 8833 8857 C2' DC B 111 8858 8855 8876 C2' DOC B 112 OK OK 8875 8877 8890 8891 8904 C2' DA C 201 8905 8902 8925 C2' DA C 202 8926 8923 8946 C2' DA C 203 8947 8944 8967 C2' DA C 204 8968 8965 8988 C2' DG C 205 8989 8986 9010 C2' DG C 206 9011 9008 9032 C2' DC C 207 9033 9030 9051 C2' DG C 208 9052 9049 9073 C2' DC C 209 9074 9071 9092 C2' DC C 210 9093 9090 9111 C2' DG C 211 9112 9109 9133 C2' DT C 212 9134 9131 9153 C2' DG C 213 9154 9151 9175 C2' DG C 214 9176 9173 9197 C2' DT C 215 9198 9195 9217 C2' DC C 216 9218 9215 9277 C2' XJS A 1 9257 9288 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8649 C3' DG B 101 OK 8647 8650 8651 8671 C3' DA B 102 OK 8669 8672 8673 8692 C3' DC B 103 OK 8690 8693 8694 8711 C3' DC B 104 OK 8709 8712 8713 8730 C3' DA B 105 OK 8728 8731 8732 8751 C3' DC B 106 OK 8749 8752 8753 8770 C3' DG B 107 OK 8768 8771 8772 8792 C3' DG B 108 OK 8790 8793 8794 8814 C3' DC B 109 OK 8812 8815 8816 8833 C3' DG B 110 OK 8831 8834 8835 8855 C3' DC B 111 OK 8853 8856 8857 8877 C3' DOC B 112 8878 8876 8902 C3' DA C 201 OK 8900 8903 8904 8923 C3' DA C 202 OK 8921 8924 8925 8944 C3' DA C 203 OK 8942 8945 8946 8965 C3' DA C 204 OK 8963 8966 8967 8986 C3' DG C 205 OK 8984 8987 8988 9008 C3' DG C 206 OK 9006 9009 9010 9030 C3' DC C 207 OK 9028 9031 9032 9049 C3' DG C 208 OK 9047 9050 9051 9071 C3' DC C 209 OK 9069 9072 9073 9090 C3' DC C 210 OK 9088 9091 9092 9109 C3' DG C 211 OK 9107 9110 9111 9131 C3' DT C 212 OK 9129 9132 9133 9151 C3' DG C 213 OK 9149 9152 9153 9173 C3' DG C 214 OK 9171 9174 9175 9195 C3' DT C 215 OK 9193 9196 9197 9215 C3' DC C 216 OK 9213 9216 9217 9288 C3' XJS A 1 9293 9277 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8647 C4' DG B 101 OK 8649 8646 8648 8669 C4' DA B 102 OK 8671 8668 8670 8690 C4' DC B 103 OK 8692 8689 8691 8709 C4' DC B 104 OK 8711 8708 8710 8728 C4' DA B 105 OK 8730 8727 8729 8749 C4' DC B 106 OK 8751 8748 8750 8768 C4' DG B 107 OK 8770 8767 8769 8790 C4' DG B 108 OK 8792 8789 8791 8812 C4' DC B 109 OK 8814 8811 8813 8831 C4' DG B 110 OK 8833 8830 8832 8853 C4' DC B 111 OK 8855 8852 8854 8878 C4' DOC B 112 OK OK 8877 8894 8880 8879 8900 C4' DA C 201 OK 8902 8899 8901 8921 C4' DA C 202 OK 8923 8920 8922 8942 C4' DA C 203 OK 8944 8941 8943 8963 C4' DA C 204 OK 8965 8962 8964 8984 C4' DG C 205 OK 8986 8983 8985 9006 C4' DG C 206 OK 9008 9005 9007 9028 C4' DC C 207 OK 9030 9027 9029 9047 C4' DG C 208 OK 9049 9046 9048 9069 C4' DC C 209 OK 9071 9068 9070 9088 C4' DC C 210 OK 9090 9087 9089 9107 C4' DG C 211 OK 9109 9106 9108 9129 C4' DT C 212 OK 9131 9128 9130 9149 C4' DG C 213 OK 9151 9148 9150 9171 C4' DG C 214 OK 9173 9170 9172 9193 C4' DT C 215 OK 9195 9192 9194 9213 C4' DC C 216 OK 9215 9212 9214 9293 C4' XJS A 1 OK 9288 9295 9294 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8646 C5' DG B 101 8645 8647 8668 C5' DA B 102 8667 8669 8689 C5' DC B 103 8688 8690 8708 C5' DC B 104 8707 8709 8727 C5' DA B 105 8726 8728 8748 C5' DC B 106 8747 8749 8767 C5' DG B 107 8766 8768 8789 C5' DG B 108 8788 8790 8811 C5' DC B 109 8810 8812 8830 C5' DG B 110 8829 8831 8852 C5' DC B 111 8851 8853 8880 C5' DOC B 112 distorted distorted 8881 8895 8896 8878 8899 C5' DA C 201 8898 8900 8920 C5' DA C 202 8919 8921 8941 C5' DA C 203 8940 8942 8962 C5' DA C 204 8961 8963 8983 C5' DG C 205 8982 8984 9005 C5' DG C 206 9004 9006 9027 C5' DC C 207 9026 9028 9046 C5' DG C 208 9045 9047 9068 C5' DC C 209 9067 9069 9087 C5' DC C 210 9086 9088 9106 C5' DG C 211 9105 9107 9128 C5' DT C 212 9127 9129 9148 C5' DG C 213 9147 9149 9170 C5' DG C 214 9169 9171 9192 C5' DT C 215 9191 9193 9212 C5' DC C 216 9211 9213 9295 C5' XJS A 1 9296 9293 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8664 P DA B 102 distorted distorted 8650 8665 8666 8667 8685 P DC B 103 distorted distorted 8672 8686 8687 8688 8704 P DC B 104 distorted distorted 8693 8705 8706 8707 8723 P DA B 105 distorted distorted 8712 8724 8725 8726 8744 P DC B 106 distorted distorted 8731 8745 8746 8747 8763 P DG B 107 distorted distorted 8752 8764 8765 8766 8785 P DG B 108 distorted distorted 8771 8786 8787 8788 8807 P DC B 109 distorted distorted 8793 8808 8809 8810 8826 P DG B 110 distorted distorted 8815 8827 8828 8829 8848 P DC B 111 distorted distorted 8834 8849 8850 8851 8882 P DOC B 112 OK OK 8856 8883 8884 8881 8916 P DA C 202 distorted distorted 8903 8917 8918 8919 8937 P DA C 203 distorted distorted 8924 8938 8939 8940 8958 P DA C 204 distorted distorted 8945 8959 8960 8961 8979 P DG C 205 distorted distorted 8966 8980 8981 8982 9001 P DG C 206 distorted distorted 8987 9002 9003 9004 9023 P DC C 207 distorted distorted 9009 9024 9025 9026 9042 P DG C 208 distorted distorted 9031 9043 9044 9045 9064 P DC C 209 distorted distorted 9050 9065 9066 9067 9083 P DC C 210 distorted distorted 9072 9084 9085 9086 9102 P DG C 211 distorted distorted 9091 9103 9104 9105 9124 P DT C 212 distorted distorted 9110 9125 9126 9127 9144 P DG C 213 distorted distorted 9132 9145 9146 9147 9166 P DG C 214 distorted distorted 9152 9167 9168 9169 9188 P DT C 215 distorted distorted 9174 9189 9190 9191 9208 P DC C 216 distorted distorted 9196 9209 9210 9211 ---------------------------------------------------------------------------------