ID code: '5F8M' 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' --------------------------------------------------------------------------------- 3694 C1' C B 599 beta 3689 3695 3692 3714 C1' A B 600 beta 3709 3715 3712 3736 C1' G B 601 beta 3731 3737 3734 3759 C1' G B 602 beta 3754 3760 3757 3782 C1' U B 603 beta 3777 3783 3780 3802 C1' C B 604 beta 3797 3803 3800 3822 C1' U B 605 beta 3817 3823 3820 3842 C1' C B 606 beta 3837 3843 3840 3862 C1' U B 607 beta 3857 3863 3860 3882 C1' C B 608 beta 3877 3883 3880 3902 C1' U B 609 beta 3897 3903 3900 3922 C1' C B 610 beta 3917 3923 3920 3943 C1' A C 693 beta 3938 3944 3941 3965 C1' G C 694 beta 3960 3966 3963 3988 C1' A C 695 beta 3983 3989 3986 4010 C1' G C 696 beta 4005 4011 4008 4033 C1' A C 697 beta 4028 4034 4031 4055 C1' G C 698 beta 4050 4056 4053 4078 C1' A C 699 beta 4073 4079 4076 4100 C1' C C 700 beta 4095 4101 4098 4120 C1' C C 701 beta 4115 4121 4118 4140 C1' U C 702 beta 4135 4141 4138 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3692 C2' C B 599 OK 3694 3690 3693 3712 C2' A B 600 OK 3714 3710 3713 3734 C2' G B 601 OK 3736 3732 3735 3757 C2' G B 602 OK 3759 3755 3758 3780 C2' U B 603 OK 3782 3778 3781 3800 C2' C B 604 OK 3802 3798 3801 3820 C2' U B 605 OK 3822 3818 3821 3840 C2' C B 606 OK 3842 3838 3841 3860 C2' U B 607 OK 3862 3858 3861 3880 C2' C B 608 OK 3882 3878 3881 3900 C2' U B 609 OK 3902 3898 3901 3920 C2' C B 610 OK 3922 3918 3921 3941 C2' A C 693 OK 3943 3939 3942 3963 C2' G C 694 OK 3965 3961 3964 3986 C2' A C 695 OK 3988 3984 3987 4008 C2' G C 696 OK 4010 4006 4009 4031 C2' A C 697 OK 4033 4029 4032 4053 C2' G C 698 OK 4055 4051 4054 4076 C2' A C 699 OK 4078 4074 4077 4098 C2' C C 700 OK 4100 4096 4099 4118 C2' C C 701 OK 4120 4116 4119 4138 C2' U C 702 OK 4140 4136 4139 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3690 C3' C B 599 OK 3688 3691 3692 3710 C3' A B 600 OK 3708 3711 3712 3732 C3' G B 601 OK 3730 3733 3734 3755 C3' G B 602 OK 3753 3756 3757 3778 C3' U B 603 OK 3776 3779 3780 3798 C3' C B 604 OK 3796 3799 3800 3818 C3' U B 605 OK 3816 3819 3820 3838 C3' C B 606 OK 3836 3839 3840 3858 C3' U B 607 OK 3856 3859 3860 3878 C3' C B 608 OK 3876 3879 3880 3898 C3' U B 609 OK 3896 3899 3900 3918 C3' C B 610 OK 3916 3919 3920 3939 C3' A C 693 OK 3937 3940 3941 3961 C3' G C 694 OK 3959 3962 3963 3984 C3' A C 695 OK 3982 3985 3986 4006 C3' G C 696 OK 4004 4007 4008 4029 C3' A C 697 OK 4027 4030 4031 4051 C3' G C 698 OK 4049 4052 4053 4074 C3' A C 699 OK 4072 4075 4076 4096 C3' C C 700 OK 4094 4097 4098 4116 C3' C C 701 OK 4114 4117 4118 4136 C3' U C 702 OK 4134 4137 4138 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3688 C4' C B 599 OK 3690 3687 3689 3708 C4' A B 600 OK 3710 3707 3709 3730 C4' G B 601 OK 3732 3729 3731 3753 C4' G B 602 OK 3755 3752 3754 3776 C4' U B 603 OK 3778 3775 3777 3796 C4' C B 604 OK 3798 3795 3797 3816 C4' U B 605 OK 3818 3815 3817 3836 C4' C B 606 OK 3838 3835 3837 3856 C4' U B 607 OK 3858 3855 3857 3876 C4' C B 608 OK 3878 3875 3877 3896 C4' U B 609 OK 3898 3895 3897 3916 C4' C B 610 OK 3918 3915 3917 3937 C4' A C 693 OK 3939 3936 3938 3959 C4' G C 694 OK 3961 3958 3960 3982 C4' A C 695 OK 3984 3981 3983 4004 C4' G C 696 OK 4006 4003 4005 4027 C4' A C 697 OK 4029 4026 4028 4049 C4' G C 698 OK 4051 4048 4050 4072 C4' A C 699 OK 4074 4071 4073 4094 C4' C C 700 OK 4096 4093 4095 4114 C4' C C 701 OK 4116 4113 4115 4134 C4' U C 702 OK 4136 4133 4135 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3687 C5' C B 599 3686 3688 3707 C5' A B 600 3706 3708 3729 C5' G B 601 3728 3730 3752 C5' G B 602 3751 3753 3775 C5' U B 603 3774 3776 3795 C5' C B 604 3794 3796 3815 C5' U B 605 3814 3816 3835 C5' C B 606 3834 3836 3855 C5' U B 607 3854 3856 3875 C5' C B 608 3874 3876 3895 C5' U B 609 3894 3896 3915 C5' C B 610 3914 3916 3936 C5' A C 693 3935 3937 3958 C5' G C 694 3957 3959 3981 C5' A C 695 3980 3982 4003 C5' G C 696 4002 4004 4026 C5' A C 697 4025 4027 4048 C5' G C 698 4047 4049 4071 C5' A C 699 4070 4072 4093 C5' C C 700 4092 4094 4113 C5' C C 701 4112 4114 4133 C5' U C 702 4132 4134 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3683 P C B 599 distorted distorted 3684 3685 3686 3703 P A B 600 distorted distorted 3691 3704 3705 3706 3725 P G B 601 distorted distorted 3711 3726 3727 3728 3748 P G B 602 distorted distorted 3733 3749 3750 3751 3771 P U B 603 distorted distorted 3756 3772 3773 3774 3791 P C B 604 distorted distorted 3779 3792 3793 3794 3811 P U B 605 distorted distorted 3799 3812 3813 3814 3831 P C B 606 distorted distorted 3819 3832 3833 3834 3851 P U B 607 distorted distorted 3839 3852 3853 3854 3871 P C B 608 distorted distorted 3859 3872 3873 3874 3891 P U B 609 distorted distorted 3879 3892 3893 3894 3911 P C B 610 distorted distorted 3899 3912 3913 3914 3932 P A C 693 distorted distorted 3933 3934 3935 3954 P G C 694 distorted distorted 3940 3955 3956 3957 3977 P A C 695 distorted distorted 3962 3978 3979 3980 3999 P G C 696 distorted distorted 3985 4000 4001 4002 4022 P A C 697 distorted distorted 4007 4023 4024 4025 4044 P G C 698 distorted distorted 4030 4045 4046 4047 4067 P A C 699 distorted distorted 4052 4068 4069 4070 4089 P C C 700 distorted distorted 4075 4090 4091 4092 4109 P C C 701 distorted distorted 4097 4110 4111 4112 4129 P U C 702 distorted distorted 4117 4130 4131 4132 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