ID code: '1AZ0' 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' --------------------------------------------------------------------------------- 3650 C1' A C 902 beta 3646 3651 3649 3671 C1' A C 903 beta 3667 3672 3670 3692 C1' G C 904 beta 3688 3693 3691 3714 C1' A C 905 beta 3710 3715 3713 3735 C1' T C 906 beta 3731 3736 3734 3755 C1' A C 907 beta 3751 3756 3754 3776 C1' T C 908 beta 3772 3777 3775 3796 C1' C C 909 beta 3792 3797 3795 3815 C1' T C 910 beta 3811 3816 3814 3835 C1' T C 911 beta 3831 3836 3834 3874 C1' A D 802 beta 3870 3875 3873 3895 C1' A D 803 beta 3891 3896 3894 3916 C1' G D 804 beta 3912 3917 3915 3938 C1' A D 805 beta 3934 3939 3937 3959 C1' T D 806 beta 3955 3960 3958 3979 C1' A D 807 beta 3975 3980 3978 4000 C1' T D 808 beta 3996 4001 3999 4020 C1' C D 809 beta 4016 4021 4019 4039 C1' T D 810 beta 4035 4040 4038 4059 C1' T D 811 beta 4055 4060 4058 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3649 C2' A C 902 3650 3647 3670 C2' A C 903 3671 3668 3691 C2' G C 904 3692 3689 3713 C2' A C 905 3714 3711 3734 C2' T C 906 3735 3732 3754 C2' A C 907 3755 3752 3775 C2' T C 908 3776 3773 3795 C2' C C 909 3796 3793 3814 C2' T C 910 3815 3812 3834 C2' T C 911 3835 3832 3873 C2' A D 802 3874 3871 3894 C2' A D 803 3895 3892 3915 C2' G D 804 3916 3913 3937 C2' A D 805 3938 3935 3958 C2' T D 806 3959 3956 3978 C2' A D 807 3979 3976 3999 C2' T D 808 4000 3997 4019 C2' C D 809 4020 4017 4038 C2' T D 810 4039 4036 4058 C2' T D 811 4059 4056 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3647 C3' A C 902 OK 3645 3648 3649 3668 C3' A C 903 OK 3666 3669 3670 3689 C3' G C 904 OK 3687 3690 3691 3711 C3' A C 905 OK 3709 3712 3713 3732 C3' T C 906 OK 3730 3733 3734 3752 C3' A C 907 OK 3750 3753 3754 3773 C3' T C 908 OK 3771 3774 3775 3793 C3' C C 909 OK 3791 3794 3795 3812 C3' T C 910 OK 3810 3813 3814 3832 C3' T C 911 OK 3830 3833 3834 3871 C3' A D 802 OK 3869 3872 3873 3892 C3' A D 803 OK 3890 3893 3894 3913 C3' G D 804 OK 3911 3914 3915 3935 C3' A D 805 OK 3933 3936 3937 3956 C3' T D 806 OK 3954 3957 3958 3976 C3' A D 807 OK 3974 3977 3978 3997 C3' T D 808 OK 3995 3998 3999 4017 C3' C D 809 OK 4015 4018 4019 4036 C3' T D 810 OK 4034 4037 4038 4056 C3' T D 811 OK 4054 4057 4058 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3645 C4' A C 902 OK 3647 3644 3646 3666 C4' A C 903 OK 3668 3665 3667 3687 C4' G C 904 OK 3689 3686 3688 3709 C4' A C 905 OK 3711 3708 3710 3730 C4' T C 906 OK 3732 3729 3731 3750 C4' A C 907 OK 3752 3749 3751 3771 C4' T C 908 OK 3773 3770 3772 3791 C4' C C 909 OK 3793 3790 3792 3810 C4' T C 910 OK 3812 3809 3811 3830 C4' T C 911 OK 3832 3829 3831 3869 C4' A D 802 OK 3871 3868 3870 3890 C4' A D 803 OK 3892 3889 3891 3911 C4' G D 804 OK 3913 3910 3912 3933 C4' A D 805 OK 3935 3932 3934 3954 C4' T D 806 OK 3956 3953 3955 3974 C4' A D 807 OK 3976 3973 3975 3995 C4' T D 808 OK 3997 3994 3996 4015 C4' C D 809 OK 4017 4014 4016 4034 C4' T D 810 OK 4036 4033 4035 4054 C4' T D 811 OK 4056 4053 4055 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3644 C5' A C 902 3643 3645 3665 C5' A C 903 3664 3666 3686 C5' G C 904 3685 3687 3708 C5' A C 905 3707 3709 3729 C5' T C 906 3728 3730 3749 C5' A C 907 3748 3750 3770 C5' T C 908 3769 3771 3790 C5' C C 909 3789 3791 3809 C5' T C 910 3808 3810 3829 C5' T C 911 3828 3830 3868 C5' A D 802 3867 3869 3889 C5' A D 803 3888 3890 3910 C5' G D 804 3909 3911 3932 C5' A D 805 3931 3933 3953 C5' T D 806 3952 3954 3973 C5' A D 807 3972 3974 3994 C5' T D 808 3993 3995 4014 C5' C D 809 4013 4015 4033 C5' T D 810 4032 4034 4053 C5' T D 811 4052 4054 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3661 P A C 903 OK OK 3648 3662 3663 3664 3682 P G C 904 OK OK 3669 3683 3684 3685 3704 P A C 905 OK OK 3690 3705 3706 3707 3725 P T C 906 OK OK 3712 3726 3727 3728 3745 P A C 907 OK OK 3733 3746 3747 3748 3766 P T C 908 OK OK 3753 3767 3768 3769 3786 P C C 909 OK OK 3774 3787 3788 3789 3805 P T C 910 OK OK 3794 3806 3807 3808 3825 P T C 911 OK OK 3813 3826 3827 3828 3885 P A D 803 OK OK 3872 3886 3887 3888 3906 P G D 804 OK OK 3893 3907 3908 3909 3928 P A D 805 OK OK 3914 3929 3930 3931 3949 P T D 806 OK OK 3936 3950 3951 3952 3969 P A D 807 OK OK 3957 3970 3971 3972 3990 P T D 808 OK OK 3977 3991 3992 3993 4010 P C D 809 OK OK 3998 4011 4012 4013 4029 P T D 810 OK OK 4018 4030 4031 4032 4049 P T D 811 OK OK 4037 4050 4051 4052 ---------------------------------------------------------------------------------