ID code: '3OJU' 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' --------------------------------------------------------------------------------- 8621 C1' DG B 101 beta 8617 8622 8620 8643 C1' DA B 102 beta 8639 8644 8642 8664 C1' DC B 103 beta 8660 8665 8663 8683 C1' DC B 104 beta 8679 8684 8682 8702 C1' DA B 105 beta 8698 8703 8701 8723 C1' DC B 106 beta 8719 8724 8722 8742 C1' DG B 107 beta 8738 8743 8741 8764 C1' DG B 108 beta 8760 8765 8763 8786 C1' DC B 109 beta 8782 8787 8785 8805 C1' DG B 110 beta 8801 8806 8804 8827 C1' DC B 111 beta 8823 8828 8826 8844 C1' DOC B 112 alpha beta 8848 8858 8836 8845 8877 C1' DA C 203 beta 8873 8878 8876 8898 C1' DA C 204 beta 8894 8899 8897 8919 C1' DG C 205 beta 8915 8920 8918 8941 C1' DG C 206 beta 8937 8942 8940 8963 C1' DC C 207 beta 8959 8964 8962 8982 C1' DG C 208 beta 8978 8983 8981 9004 C1' DC C 209 beta 9000 9005 9003 9023 C1' DC C 210 beta 9019 9024 9022 9042 C1' DG C 211 beta 9038 9043 9041 9064 C1' DT C 212 beta 9060 9065 9063 9084 C1' DG C 213 beta 9080 9085 9083 9106 C1' DG C 214 beta 9102 9107 9105 9128 C1' DT C 215 beta 9124 9129 9127 9148 C1' DC C 216 beta 9144 9149 9147 9169 C1' SSJ A 1 beta 9193 9158 9173 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8620 C2' DG B 101 8621 8618 8642 C2' DA B 102 8643 8640 8663 C2' DC B 103 8664 8661 8682 C2' DC B 104 8683 8680 8701 C2' DA B 105 8702 8699 8722 C2' DC B 106 8723 8720 8741 C2' DG B 107 8742 8739 8763 C2' DG B 108 8764 8761 8785 C2' DC B 109 8786 8783 8804 C2' DG B 110 8805 8802 8826 C2' DC B 111 8827 8824 8845 C2' DOC B 112 OK OK 8844 8846 8859 8860 8876 C2' DA C 203 8877 8874 8897 C2' DA C 204 8898 8895 8918 C2' DG C 205 8919 8916 8940 C2' DG C 206 8941 8938 8962 C2' DC C 207 8963 8960 8981 C2' DG C 208 8982 8979 9003 C2' DC C 209 9004 9001 9022 C2' DC C 210 9023 9020 9041 C2' DG C 211 9042 9039 9063 C2' DT C 212 9064 9061 9083 C2' DG C 213 9084 9081 9105 C2' DG C 214 9106 9103 9127 C2' DT C 215 9128 9125 9147 C2' DC C 216 9148 9145 9173 C2' SSJ A 1 9169 9177 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8618 C3' DG B 101 OK 8616 8619 8620 8640 C3' DA B 102 OK 8638 8641 8642 8661 C3' DC B 103 OK 8659 8662 8663 8680 C3' DC B 104 OK 8678 8681 8682 8699 C3' DA B 105 OK 8697 8700 8701 8720 C3' DC B 106 OK 8718 8721 8722 8739 C3' DG B 107 OK 8737 8740 8741 8761 C3' DG B 108 OK 8759 8762 8763 8783 C3' DC B 109 OK 8781 8784 8785 8802 C3' DG B 110 OK 8800 8803 8804 8824 C3' DC B 111 OK 8822 8825 8826 8846 C3' DOC B 112 8847 8845 8874 C3' DA C 203 OK 8872 8875 8876 8895 C3' DA C 204 OK 8893 8896 8897 8916 C3' DG C 205 OK 8914 8917 8918 8938 C3' DG C 206 OK 8936 8939 8940 8960 C3' DC C 207 OK 8958 8961 8962 8979 C3' DG C 208 OK 8977 8980 8981 9001 C3' DC C 209 OK 8999 9002 9003 9020 C3' DC C 210 OK 9018 9021 9022 9039 C3' DG C 211 OK 9037 9040 9041 9061 C3' DT C 212 OK 9059 9062 9063 9081 C3' DG C 213 OK 9079 9082 9083 9103 C3' DG C 214 OK 9101 9104 9105 9125 C3' DT C 215 OK 9123 9126 9127 9145 C3' DC C 216 OK 9143 9146 9147 9177 C3' SSJ A 1 OK 9192 9178 9173 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8616 C4' DG B 101 OK 8618 8615 8617 8638 C4' DA B 102 OK 8640 8637 8639 8659 C4' DC B 103 OK 8661 8658 8660 8678 C4' DC B 104 OK 8680 8677 8679 8697 C4' DA B 105 OK 8699 8696 8698 8718 C4' DC B 106 OK 8720 8717 8719 8737 C4' DG B 107 OK 8739 8736 8738 8759 C4' DG B 108 OK 8761 8758 8760 8781 C4' DC B 109 OK 8783 8780 8782 8800 C4' DG B 110 OK 8802 8799 8801 8822 C4' DC B 111 OK 8824 8821 8823 8847 C4' DOC B 112 OK OK 8846 8863 8849 8848 8872 C4' DA C 203 OK 8874 8871 8873 8893 C4' DA C 204 OK 8895 8892 8894 8914 C4' DG C 205 OK 8916 8913 8915 8936 C4' DG C 206 OK 8938 8935 8937 8958 C4' DC C 207 OK 8960 8957 8959 8977 C4' DG C 208 OK 8979 8976 8978 8999 C4' DC C 209 OK 9001 8998 9000 9018 C4' DC C 210 OK 9020 9017 9019 9037 C4' DG C 211 OK 9039 9036 9038 9059 C4' DT C 212 OK 9061 9058 9060 9079 C4' DG C 213 OK 9081 9078 9080 9101 C4' DG C 214 OK 9103 9100 9102 9123 C4' DT C 215 OK 9125 9122 9124 9143 C4' DC C 216 OK 9145 9142 9144 9192 C4' SSJ A 1 OK 9177 9196 9193 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8615 C5' DG B 101 8614 8616 8637 C5' DA B 102 8636 8638 8658 C5' DC B 103 8657 8659 8677 C5' DC B 104 8676 8678 8696 C5' DA B 105 8695 8697 8717 C5' DC B 106 8716 8718 8736 C5' DG B 107 8735 8737 8758 C5' DG B 108 8757 8759 8780 C5' DC B 109 8779 8781 8799 C5' DG B 110 8798 8800 8821 C5' DC B 111 8820 8822 8849 C5' DOC B 112 distorted distorted 8850 8864 8865 8847 8871 C5' DA C 203 8870 8872 8892 C5' DA C 204 8891 8893 8913 C5' DG C 205 8912 8914 8935 C5' DG C 206 8934 8936 8957 C5' DC C 207 8956 8958 8976 C5' DG C 208 8975 8977 8998 C5' DC C 209 8997 8999 9017 C5' DC C 210 9016 9018 9036 C5' DG C 211 9035 9037 9058 C5' DT C 212 9057 9059 9078 C5' DG C 213 9077 9079 9100 C5' DG C 214 9099 9101 9122 C5' DT C 215 9121 9123 9142 C5' DC C 216 9141 9143 9196 C5' SSJ A 1 9197 9192 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8633 P DA B 102 distorted distorted 8619 8634 8635 8636 8654 P DC B 103 distorted distorted 8641 8655 8656 8657 8673 P DC B 104 distorted distorted 8662 8674 8675 8676 8692 P DA B 105 distorted distorted 8681 8693 8694 8695 8713 P DC B 106 distorted distorted 8700 8714 8715 8716 8732 P DG B 107 distorted distorted 8721 8733 8734 8735 8754 P DG B 108 distorted distorted 8740 8755 8756 8757 8776 P DC B 109 distorted distorted 8762 8777 8778 8779 8795 P DG B 110 distorted distorted 8784 8796 8797 8798 8817 P DC B 111 distorted distorted 8803 8818 8819 8820 8851 P DOC B 112 distorted distorted 8825 8852 8853 8850 8867 P DA C 203 distorted distorted 8868 8869 8870 8888 P DA C 204 distorted distorted 8875 8889 8890 8891 8909 P DG C 205 distorted distorted 8896 8910 8911 8912 8931 P DG C 206 distorted distorted 8917 8932 8933 8934 8953 P DC C 207 distorted distorted 8939 8954 8955 8956 8972 P DG C 208 distorted distorted 8961 8973 8974 8975 8994 P DC C 209 distorted distorted 8980 8995 8996 8997 9013 P DC C 210 distorted distorted 9002 9014 9015 9016 9032 P DG C 211 distorted distorted 9021 9033 9034 9035 9054 P DT C 212 distorted distorted 9040 9055 9056 9057 9074 P DG C 213 distorted distorted 9062 9075 9076 9077 9096 P DG C 214 distorted distorted 9082 9097 9098 9099 9118 P DT C 215 distorted distorted 9104 9119 9120 9121 9138 P DC C 216 distorted distorted 9126 9139 9140 9141 ---------------------------------------------------------------------------------