ID code: '5F8N' 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' --------------------------------------------------------------------------------- 3690 C1' C B 599 beta 3685 3691 3688 3710 C1' A B 600 beta 3705 3711 3708 3732 C1' G B 601 beta 3727 3733 3730 3755 C1' G B 602 beta 3750 3756 3753 3778 C1' U B 603 beta 3773 3779 3776 3798 C1' C B 604 beta 3793 3799 3796 3818 C1' U B 605 beta 3813 3819 3816 3838 C1' C B 606 beta 3833 3839 3836 3858 C1' U B 607 beta 3853 3859 3856 3879 C1' A C 695 beta 3874 3880 3877 3901 C1' G C 696 beta 3896 3902 3899 3924 C1' A C 697 beta 3919 3925 3922 3946 C1' G C 698 beta 3941 3947 3944 3969 C1' A C 699 beta 3964 3970 3967 3991 C1' C C 700 beta 3986 3992 3989 4011 C1' C C 701 beta 4006 4012 4009 4031 C1' U C 702 beta 4026 4032 4029 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3688 C2' C B 599 OK 3690 3686 3689 3708 C2' A B 600 OK 3710 3706 3709 3730 C2' G B 601 OK 3732 3728 3731 3753 C2' G B 602 OK 3755 3751 3754 3776 C2' U B 603 OK 3778 3774 3777 3796 C2' C B 604 OK 3798 3794 3797 3816 C2' U B 605 OK 3818 3814 3817 3836 C2' C B 606 OK 3838 3834 3837 3856 C2' U B 607 OK 3858 3854 3857 3877 C2' A C 695 OK 3879 3875 3878 3899 C2' G C 696 OK 3901 3897 3900 3922 C2' A C 697 OK 3924 3920 3923 3944 C2' G C 698 OK 3946 3942 3945 3967 C2' A C 699 OK 3969 3965 3968 3989 C2' C C 700 OK 3991 3987 3990 4009 C2' C C 701 OK 4011 4007 4010 4029 C2' U C 702 OK 4031 4027 4030 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3686 C3' C B 599 OK 3684 3687 3688 3706 C3' A B 600 OK 3704 3707 3708 3728 C3' G B 601 OK 3726 3729 3730 3751 C3' G B 602 OK 3749 3752 3753 3774 C3' U B 603 OK 3772 3775 3776 3794 C3' C B 604 OK 3792 3795 3796 3814 C3' U B 605 OK 3812 3815 3816 3834 C3' C B 606 OK 3832 3835 3836 3854 C3' U B 607 OK 3852 3855 3856 3875 C3' A C 695 OK 3873 3876 3877 3897 C3' G C 696 OK 3895 3898 3899 3920 C3' A C 697 OK 3918 3921 3922 3942 C3' G C 698 OK 3940 3943 3944 3965 C3' A C 699 OK 3963 3966 3967 3987 C3' C C 700 OK 3985 3988 3989 4007 C3' C C 701 OK 4005 4008 4009 4027 C3' U C 702 OK 4025 4028 4029 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3684 C4' C B 599 OK 3686 3683 3685 3704 C4' A B 600 OK 3706 3703 3705 3726 C4' G B 601 OK 3728 3725 3727 3749 C4' G B 602 OK 3751 3748 3750 3772 C4' U B 603 OK 3774 3771 3773 3792 C4' C B 604 OK 3794 3791 3793 3812 C4' U B 605 OK 3814 3811 3813 3832 C4' C B 606 OK 3834 3831 3833 3852 C4' U B 607 OK 3854 3851 3853 3873 C4' A C 695 OK 3875 3872 3874 3895 C4' G C 696 OK 3897 3894 3896 3918 C4' A C 697 OK 3920 3917 3919 3940 C4' G C 698 OK 3942 3939 3941 3963 C4' A C 699 OK 3965 3962 3964 3985 C4' C C 700 OK 3987 3984 3986 4005 C4' C C 701 OK 4007 4004 4006 4025 C4' U C 702 OK 4027 4024 4026 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3683 C5' C B 599 3682 3684 3703 C5' A B 600 3702 3704 3725 C5' G B 601 3724 3726 3748 C5' G B 602 3747 3749 3771 C5' U B 603 3770 3772 3791 C5' C B 604 3790 3792 3811 C5' U B 605 3810 3812 3831 C5' C B 606 3830 3832 3851 C5' U B 607 3850 3852 3872 C5' A C 695 3871 3873 3894 C5' G C 696 3893 3895 3917 C5' A C 697 3916 3918 3939 C5' G C 698 3938 3940 3962 C5' A C 699 3961 3963 3984 C5' C C 700 3983 3985 4004 C5' C C 701 4003 4005 4024 C5' U C 702 4023 4025 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3679 P C B 599 distorted distorted 3680 3681 3682 3699 P A B 600 distorted distorted 3687 3700 3701 3702 3721 P G B 601 distorted distorted 3707 3722 3723 3724 3744 P G B 602 distorted distorted 3729 3745 3746 3747 3767 P U B 603 distorted distorted 3752 3768 3769 3770 3787 P C B 604 distorted distorted 3775 3788 3789 3790 3807 P U B 605 distorted distorted 3795 3808 3809 3810 3827 P C B 606 distorted distorted 3815 3828 3829 3830 3847 P U B 607 distorted distorted 3835 3848 3849 3850 3868 P A C 695 distorted distorted 3869 3870 3871 3890 P G C 696 distorted distorted 3876 3891 3892 3893 3913 P A C 697 distorted distorted 3898 3914 3915 3916 3935 P G C 698 distorted distorted 3921 3936 3937 3938 3958 P A C 699 distorted distorted 3943 3959 3960 3961 3980 P C C 700 distorted distorted 3966 3981 3982 3983 4000 P C C 701 distorted distorted 3988 4001 4002 4003 4020 P U C 702 distorted distorted 4008 4021 4022 4023 ---------------------------------------------------------------------------------