ID code: '5F8H' 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' G B 599 beta 3689 3695 3692 3717 C1' G B 600 beta 3712 3718 3715 3740 C1' U B 601 beta 3735 3741 3738 3760 C1' C B 602 beta 3755 3761 3758 3780 C1' U B 603 beta 3775 3781 3778 3800 C1' C B 604 beta 3795 3801 3798 3820 C1' U B 605 beta 3815 3821 3818 3840 C1' C B 606 beta 3835 3841 3838 3860 C1' U B 607 beta 3855 3861 3858 3880 C1' C B 608 beta 3875 3881 3878 3900 C1' G B 609 beta 3895 3901 3898 3923 C1' U B 610 beta 3918 3924 3921 3944 C1' A C 692 beta 3939 3945 3942 3966 C1' C C 693 beta 3961 3967 3964 3986 C1' G C 694 beta 3981 3987 3984 4009 C1' A C 695 beta 4004 4010 4007 4031 C1' G C 696 beta 4026 4032 4029 4054 C1' A C 697 beta 4049 4055 4052 4076 C1' G C 698 beta 4071 4077 4074 4099 C1' A C 699 beta 4094 4100 4097 4121 C1' G C 700 beta 4116 4122 4119 4144 C1' A C 701 beta 4139 4145 4142 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3692 C2' G B 599 OK 3694 3690 3693 3715 C2' G B 600 OK 3717 3713 3716 3738 C2' U B 601 OK 3740 3736 3739 3758 C2' C B 602 OK 3760 3756 3759 3778 C2' U B 603 OK 3780 3776 3779 3798 C2' C B 604 OK 3800 3796 3799 3818 C2' U B 605 OK 3820 3816 3819 3838 C2' C B 606 OK 3840 3836 3839 3858 C2' U B 607 OK 3860 3856 3859 3878 C2' C B 608 OK 3880 3876 3879 3898 C2' G B 609 OK 3900 3896 3899 3921 C2' U B 610 OK 3923 3919 3922 3942 C2' A C 692 OK 3944 3940 3943 3964 C2' C C 693 OK 3966 3962 3965 3984 C2' G C 694 OK 3986 3982 3985 4007 C2' A C 695 OK 4009 4005 4008 4029 C2' G C 696 OK 4031 4027 4030 4052 C2' A C 697 OK 4054 4050 4053 4074 C2' G C 698 OK 4076 4072 4075 4097 C2' A C 699 OK 4099 4095 4098 4119 C2' G C 700 OK 4121 4117 4120 4142 C2' A C 701 OK 4144 4140 4143 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3690 C3' G B 599 OK 3688 3691 3692 3713 C3' G B 600 OK 3711 3714 3715 3736 C3' U B 601 OK 3734 3737 3738 3756 C3' C B 602 OK 3754 3757 3758 3776 C3' U B 603 OK 3774 3777 3778 3796 C3' C B 604 OK 3794 3797 3798 3816 C3' U B 605 OK 3814 3817 3818 3836 C3' C B 606 OK 3834 3837 3838 3856 C3' U B 607 OK 3854 3857 3858 3876 C3' C B 608 OK 3874 3877 3878 3896 C3' G B 609 OK 3894 3897 3898 3919 C3' U B 610 OK 3917 3920 3921 3940 C3' A C 692 OK 3938 3941 3942 3962 C3' C C 693 OK 3960 3963 3964 3982 C3' G C 694 OK 3980 3983 3984 4005 C3' A C 695 OK 4003 4006 4007 4027 C3' G C 696 OK 4025 4028 4029 4050 C3' A C 697 OK 4048 4051 4052 4072 C3' G C 698 OK 4070 4073 4074 4095 C3' A C 699 OK 4093 4096 4097 4117 C3' G C 700 OK 4115 4118 4119 4140 C3' A C 701 OK 4138 4141 4142 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3688 C4' G B 599 OK 3690 3687 3689 3711 C4' G B 600 OK 3713 3710 3712 3734 C4' U B 601 OK 3736 3733 3735 3754 C4' C B 602 OK 3756 3753 3755 3774 C4' U B 603 OK 3776 3773 3775 3794 C4' C B 604 OK 3796 3793 3795 3814 C4' U B 605 OK 3816 3813 3815 3834 C4' C B 606 OK 3836 3833 3835 3854 C4' U B 607 OK 3856 3853 3855 3874 C4' C B 608 OK 3876 3873 3875 3894 C4' G B 609 OK 3896 3893 3895 3917 C4' U B 610 OK 3919 3916 3918 3938 C4' A C 692 OK 3940 3937 3939 3960 C4' C C 693 OK 3962 3959 3961 3980 C4' G C 694 OK 3982 3979 3981 4003 C4' A C 695 OK 4005 4002 4004 4025 C4' G C 696 OK 4027 4024 4026 4048 C4' A C 697 OK 4050 4047 4049 4070 C4' G C 698 OK 4072 4069 4071 4093 C4' A C 699 OK 4095 4092 4094 4115 C4' G C 700 OK 4117 4114 4116 4138 C4' A C 701 OK 4140 4137 4139 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3687 C5' G B 599 3686 3688 3710 C5' G B 600 3709 3711 3733 C5' U B 601 3732 3734 3753 C5' C B 602 3752 3754 3773 C5' U B 603 3772 3774 3793 C5' C B 604 3792 3794 3813 C5' U B 605 3812 3814 3833 C5' C B 606 3832 3834 3853 C5' U B 607 3852 3854 3873 C5' C B 608 3872 3874 3893 C5' G B 609 3892 3894 3916 C5' U B 610 3915 3917 3937 C5' A C 692 3936 3938 3959 C5' C C 693 3958 3960 3979 C5' G C 694 3978 3980 4002 C5' A C 695 4001 4003 4024 C5' G C 696 4023 4025 4047 C5' A C 697 4046 4048 4069 C5' G C 698 4068 4070 4092 C5' A C 699 4091 4093 4114 C5' G C 700 4113 4115 4137 C5' A C 701 4136 4138 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3683 P G B 599 distorted distorted 3684 3685 3686 3706 P G B 600 distorted distorted 3691 3707 3708 3709 3729 P U B 601 distorted distorted 3714 3730 3731 3732 3749 P C B 602 distorted distorted 3737 3750 3751 3752 3769 P U B 603 distorted distorted 3757 3770 3771 3772 3789 P C B 604 distorted distorted 3777 3790 3791 3792 3809 P U B 605 distorted distorted 3797 3810 3811 3812 3829 P C B 606 distorted distorted 3817 3830 3831 3832 3849 P U B 607 distorted distorted 3837 3850 3851 3852 3869 P C B 608 distorted distorted 3857 3870 3871 3872 3889 P G B 609 distorted distorted 3877 3890 3891 3892 3912 P U B 610 distorted distorted 3897 3913 3914 3915 3933 P A C 692 distorted distorted 3934 3935 3936 3955 P C C 693 distorted distorted 3941 3956 3957 3958 3975 P G C 694 distorted distorted 3963 3976 3977 3978 3998 P A C 695 distorted distorted 3983 3999 4000 4001 4020 P G C 696 distorted distorted 4006 4021 4022 4023 4043 P A C 697 distorted distorted 4028 4044 4045 4046 4065 P G C 698 distorted distorted 4051 4066 4067 4068 4088 P A C 699 distorted distorted 4073 4089 4090 4091 4110 P G C 700 distorted distorted 4096 4111 4112 4113 4133 P A C 701 distorted distorted 4118 4134 4135 4136 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