ID code: '5F8L' 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 3878 C1' C B 608 beta 3873 3879 3876 3898 C1' U B 609 beta 3893 3899 3896 3918 C1' C B 610 beta 3913 3919 3916 3939 C1' G C 692 beta 3934 3940 3937 3962 C1' A C 693 beta 3957 3963 3960 3984 C1' G C 694 beta 3979 3985 3982 4007 C1' A C 695 beta 4002 4008 4005 4029 C1' G C 696 beta 4024 4030 4027 4052 C1' A C 697 beta 4047 4053 4050 4074 C1' G C 698 beta 4069 4075 4072 4097 C1' A C 699 beta 4092 4098 4095 4119 C1' C C 700 beta 4114 4120 4117 4139 C1' C C 701 beta 4134 4140 4137 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 3876 C2' C B 608 OK 3878 3874 3877 3896 C2' U B 609 OK 3898 3894 3897 3916 C2' C B 610 OK 3918 3914 3917 3937 C2' G C 692 OK 3939 3935 3938 3960 C2' A C 693 OK 3962 3958 3961 3982 C2' G C 694 OK 3984 3980 3983 4005 C2' A C 695 OK 4007 4003 4006 4027 C2' G C 696 OK 4029 4025 4028 4050 C2' A C 697 OK 4052 4048 4051 4072 C2' G C 698 OK 4074 4070 4073 4095 C2' A C 699 OK 4097 4093 4096 4117 C2' C C 700 OK 4119 4115 4118 4137 C2' C C 701 OK 4139 4135 4138 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3874 C3' C B 608 OK 3872 3875 3876 3894 C3' U B 609 OK 3892 3895 3896 3914 C3' C B 610 OK 3912 3915 3916 3935 C3' G C 692 OK 3933 3936 3937 3958 C3' A C 693 OK 3956 3959 3960 3980 C3' G C 694 OK 3978 3981 3982 4003 C3' A C 695 OK 4001 4004 4005 4025 C3' G C 696 OK 4023 4026 4027 4048 C3' A C 697 OK 4046 4049 4050 4070 C3' G C 698 OK 4068 4071 4072 4093 C3' A C 699 OK 4091 4094 4095 4115 C3' C C 700 OK 4113 4116 4117 4135 C3' C C 701 OK 4133 4136 4137 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3872 C4' C B 608 OK 3874 3871 3873 3892 C4' U B 609 OK 3894 3891 3893 3912 C4' C B 610 OK 3914 3911 3913 3933 C4' G C 692 OK 3935 3932 3934 3956 C4' A C 693 OK 3958 3955 3957 3978 C4' G C 694 OK 3980 3977 3979 4001 C4' A C 695 OK 4003 4000 4002 4023 C4' G C 696 OK 4025 4022 4024 4046 C4' A C 697 OK 4048 4045 4047 4068 C4' G C 698 OK 4070 4067 4069 4091 C4' A C 699 OK 4093 4090 4092 4113 C4' C C 700 OK 4115 4112 4114 4133 C4' C C 701 OK 4135 4132 4134 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3871 C5' C B 608 3870 3872 3891 C5' U B 609 3890 3892 3911 C5' C B 610 3910 3912 3932 C5' G C 692 3931 3933 3955 C5' A C 693 3954 3956 3977 C5' G C 694 3976 3978 4000 C5' A C 695 3999 4001 4022 C5' G C 696 4021 4023 4045 C5' A C 697 4044 4046 4067 C5' G C 698 4066 4068 4090 C5' A C 699 4089 4091 4112 C5' C C 700 4111 4113 4132 C5' C C 701 4131 4133 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3867 P C B 608 distorted distorted 3855 3868 3869 3870 3887 P U B 609 distorted distorted 3875 3888 3889 3890 3907 P C B 610 distorted distorted 3895 3908 3909 3910 3928 P G C 692 distorted distorted 3929 3930 3931 3951 P A C 693 distorted distorted 3936 3952 3953 3954 3973 P G C 694 distorted distorted 3959 3974 3975 3976 3996 P A C 695 distorted distorted 3981 3997 3998 3999 4018 P G C 696 distorted distorted 4004 4019 4020 4021 4041 P A C 697 distorted distorted 4026 4042 4043 4044 4063 P G C 698 distorted distorted 4049 4064 4065 4066 4086 P A C 699 distorted distorted 4071 4087 4088 4089 4108 P C C 700 distorted distorted 4094 4109 4110 4111 4128 P C C 701 distorted distorted 4116 4129 4130 4131 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