ID code: '5SUP' 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' --------------------------------------------------------------------------------- 9662 C1' U D 1 beta 9657 9663 9660 9682 C1' U D 2 beta 9677 9683 9680 9702 C1' U D 3 beta 9697 9703 9700 9722 C1' U D 4 beta 9717 9723 9720 9742 C1' U D 5 beta 9737 9743 9740 9762 C1' U D 6 beta 9757 9763 9760 9783 C1' U E 1 beta 9778 9784 9781 9803 C1' U E 2 beta 9798 9804 9801 9823 C1' U E 3 beta 9818 9824 9821 9843 C1' U E 4 beta 9838 9844 9841 9863 C1' U E 5 beta 9858 9864 9861 9883 C1' U E 6 beta 9878 9884 9881 9904 C1' U F 1 beta 9899 9905 9902 9924 C1' U F 2 beta 9919 9925 9922 9944 C1' U F 3d beta 9939 9945 9942 9964 C1' U F 4 beta 9959 9965 9962 9984 C1' U F 5 beta 9979 9985 9982 10004 C1' U F 6•Çp beta 9999 10005 10002 10030 C1' ADP A1000 beta 10025 10031 10028 10062 C1' ADP B2000 beta 10057 10063 10060 10094 C1' ADP C3000 beta 10089 10095 10092 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 9660 C2' U D 1 OK 9662 9658 9661 9680 C2' U D 2 OK 9682 9678 9681 9700 C2' U D 3 OK 9702 9698 9701 9720 C2' U D 4 OK 9722 9718 9721 9740 C2' U D 5 OK 9742 9738 9741 9760 C2' U D 6 OK 9762 9758 9761 9781 C2' U E 1 OK 9783 9779 9782 9801 C2' U E 2 OK 9803 9799 9802 9821 C2' U E 3 OK 9823 9819 9822 9841 C2' U E 4 OK 9843 9839 9842 9861 C2' U E 5 OK 9863 9859 9862 9881 C2' U E 6 OK 9883 9879 9882 9902 C2' U F 1 OK 9904 9900 9903 9922 C2' U F 2 OK 9924 9920 9923 9942 C2' U F 3 OK 9944 9940 9943 9962 C2' U F 4•Çp OK 9964 9960 9963 9982 C2' U F 5 OK 9984 9980 9983 10002 C2' U F 6 OK 10004 10000 10003 10028 C2' ADP A1000 ü OK 10030 10026 10029 10060 C2' ADP B2000 OK 10062 10058 10061 10092 C2' ADP C3000 OK 10094 10090 10093 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9658 C3' U D 1 OK 9656 9659 9660 9678 C3' U D 2 OK 9676 9679 9680 9698 C3' U D 3 OK 9696 9699 9700 9718 C3' U D 4 OK 9716 9719 9720 9738 C3' U D 5 OK 9736 9739 9740 9758 C3' U D 6 OK 9756 9759 9760 9779 C3' U E 1 OK 9777 9780 9781 9799 C3' U E 2 OK 9797 9800 9801 9819 C3' U E 3 OK 9817 9820 9821 9839 C3' U E 4 OK 9837 9840 9841 9859 C3' U E 5 OK 9857 9860 9861 9879 C3' U E 6 OK 9877 9880 9881 9900 C3' U F 1 OK 9898 9901 9902 9920 C3' U F 2 OK 9918 9921 9922 9940 C3' U F 3 OK 9938 9941 9942 9960 C3' U F 4 OK 9958 9961 9962 9980 C3' U F 5 OK 9978 9981 9982 10000 C3' U F 6  OK 9998 10001 10002 10026 C3' ADP A1000 ü OK 10024 10027 10028 10058 C3' ADP B2000 OK 10056 10059 10060 10090 C3' ADP C3000 OK 10088 10091 10092 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 9656 C4' U D 1 OK 9658 9655 9657 9676 C4' U D 2 OK 9678 9675 9677 9696 C4' U D 3 OK 9698 9695 9697 9716 C4' U D 4 OK 9718 9715 9717 9736 C4' U D 5 OK 9738 9735 9737 9756 C4' U D 6 OK 9758 9755 9757 9777 C4' U E 1 OK 9779 9776 9778 9797 C4' U E 2 OK 9799 9796 9798 9817 C4' U E 3 OK 9819 9816 9818 9837 C4' U E 4 OK 9839 9836 9838 9857 C4' U E 5 OK 9859 9856 9858 9877 C4' U E 6 OK 9879 9876 9878 9898 C4' U F 1 OK 9900 9897 9899 9918 C4' U F 2 OK 9920 9917 9919 9938 C4' U F 3 OK 9940 9937 9939 9958 C4' U F 4 OK 9960 9957 9959 9978 C4' U F 5 ü OK 9980 9977 9979 9998 C4' U F 6 OK 10000 9997 9999 10024 C4' ADP A1000 OK 10026 10023 10025 10056 C4' ADP B2000 OK 10058 10055 10057 10088 C4' ADP C3000 OK 10090 10087 10089 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 9655 C5' U D 1 9654 9656 9675 C5' U D 2 9674 9676 9695 C5' U D 3 9694 9696 9715 C5' U D 4 9714 9716 9735 C5' U D 5 9734 9736 9755 C5' U D 6 9754 9756 9776 C5' U E 1 9775 9777 9796 C5' U E 2 9795 9797 9816 C5' U E 3 9815 9817 9836 C5' U E 4 9835 9837 9856 C5' U E 5 9855 9857 9876 C5' U E 6 9875 9877 9897 C5' U F 1 9896 9898 9917 C5' U F 2 9916 9918 9937 C5' U F 3 9936 9938 9957 C5' U F 4 9956 9958 9977 C5' U F 5•Çp 9976 9978 9997 C5' U F 6•Çp 9996