ID code: '5F8J' 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' --------------------------------------------------------------------------------- 3698 C1' G B 599 beta 3693 3699 3696 3721 C1' G B 600 beta 3716 3722 3719 3744 C1' U B 601 beta 3739 3745 3742 3764 C1' C B 602 beta 3759 3765 3762 3784 C1' U B 603 beta 3779 3785 3782 3804 C1' C B 604 beta 3799 3805 3802 3824 C1' U B 605 beta 3819 3825 3822 3844 C1' C B 606 beta 3839 3845 3842 3864 C1' U B 607 beta 3859 3865 3862 3884 C1' C B 608 beta 3879 3885 3882 3904 C1' G B 609 beta 3899 3905 3902 3927 C1' U B 610 beta 3922 3928 3925 3948 C1' A C 692 beta 3943 3949 3946 3970 C1' C C 693 beta 3965 3971 3968 3990 C1' G C 694 beta 3985 3991 3988 4013 C1' A C 695 beta 4008 4014 4011 4035 C1' G C 696 beta 4030 4036 4033 4058 C1' A C 697 beta 4053 4059 4056 4080 C1' G C 698 beta 4075 4081 4078 4103 C1' A C 699 beta 4098 4104 4101 4125 C1' G C 700 beta 4120 4126 4123 4148 C1' A C 701 beta 4143 4149 4146 4170 C1' C C 702 beta 4165 4171 4168 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3696 C2' G B 599 OK 3698 3694 3697 3719 C2' G B 600 OK 3721 3717 3720 3742 C2' U B 601 OK 3744 3740 3743 3762 C2' C B 602 OK 3764 3760 3763 3782 C2' U B 603 OK 3784 3780 3783 3802 C2' C B 604 OK 3804 3800 3803 3822 C2' U B 605 OK 3824 3820 3823 3842 C2' C B 606 OK 3844 3840 3843 3862 C2' U B 607 OK 3864 3860 3863 3882 C2' C B 608 OK 3884 3880 3883 3902 C2' G B 609 OK 3904 3900 3903 3925 C2' U B 610 OK 3927 3923 3926 3946 C2' A C 692 OK 3948 3944 3947 3968 C2' C C 693 OK 3970 3966 3969 3988 C2' G C 694 OK 3990 3986 3989 4011 C2' A C 695 OK 4013 4009 4012 4033 C2' G C 696 OK 4035 4031 4034 4056 C2' A C 697 OK 4058 4054 4057 4078 C2' G C 698 OK 4080 4076 4079 4101 C2' A C 699 OK 4103 4099 4102 4123 C2' G C 700 OK 4125 4121 4124 4146 C2' A C 701 OK 4148 4144 4147 4168 C2' C C 702 OK 4170 4166 4169 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3694 C3' G B 599 OK 3692 3695 3696 3717 C3' G B 600 OK 3715 3718 3719 3740 C3' U B 601 OK 3738 3741 3742 3760 C3' C B 602 OK 3758 3761 3762 3780 C3' U B 603 OK 3778 3781 3782 3800 C3' C B 604 OK 3798 3801 3802 3820 C3' U B 605 OK 3818 3821 3822 3840 C3' C B 606 OK 3838 3841 3842 3860 C3' U B 607 OK 3858 3861 3862 3880 C3' C B 608 OK 3878 3881 3882 3900 C3' G B 609 OK 3898 3901 3902 3923 C3' U B 610 OK 3921 3924 3925 3944 C3' A C 692 OK 3942 3945 3946 3966 C3' C C 693 OK 3964 3967 3968 3986 C3' G C 694 OK 3984 3987 3988 4009 C3' A C 695 OK 4007 4010 4011 4031 C3' G C 696 OK 4029 4032 4033 4054 C3' A C 697 OK 4052 4055 4056 4076 C3' G C 698 OK 4074 4077 4078 4099 C3' A C 699 OK 4097 4100 4101 4121 C3' G C 700 OK 4119 4122 4123 4144 C3' A C 701 OK 4142 4145 4146 4166 C3' C C 702 OK 4164 4167 4168 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3692 C4' G B 599 OK 3694 3691 3693 3715 C4' G B 600 OK 3717 3714 3716 3738 C4' U B 601 OK 3740 3737 3739 3758 C4' C B 602 OK 3760 3757 3759 3778 C4' U B 603 OK 3780 3777 3779 3798 C4' C B 604 OK 3800 3797 3799 3818 C4' U B 605 OK 3820 3817 3819 3838 C4' C B 606 OK 3840 3837 3839 3858 C4' U B 607 OK 3860 3857 3859 3878 C4' C B 608 OK 3880 3877 3879 3898 C4' G B 609 OK 3900 3897 3899 3921 C4' U B 610 OK 3923 3920 3922 3942 C4' A C 692 OK 3944 3941 3943 3964 C4' C C 693 OK 3966 3963 3965 3984 C4' G C 694 OK 3986 3983 3985 4007 C4' A C 695 OK 4009 4006 4008 4029 C4' G C 696 OK 4031 4028 4030 4052 C4' A C 697 OK 4054 4051 4053 4074 C4' G C 698 OK 4076 4073 4075 4097 C4' A C 699 OK 4099 4096 4098 4119 C4' G C 700 OK 4121 4118 4120 4142 C4' A C 701 OK 4144 4141 4143 4164 C4' C C 702 OK 4166 4163 4165 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3691 C5' G B 599 3690 3692 3714 C5' G B 600 3713 3715 3737 C5' U B 601 3736 3738 3757 C5' C B 602 3756 3758 3777 C5' U B 603 3776 3778 3797 C5' C B 604 3796 3798 3817 C5' U B 605 3816 3818 3837 C5' C B 606 3836 3838 3857 C5' U B 607 3856 3858 3877 C5' C B 608 3876 3878 3897 C5' G B 609 3896 3898 3920 C5' U B 610 3919 3921 3941 C5' A C 692 3940 3942 3963 C5' C C 693 3962 3964 3983 C5' G C 694 3982 3984 4006 C5' A C 695 4005 4007 4028 C5' G C 696 4027 4029 4051 C5' A C 697 4050 4052 4073 C5' G C 698 4072 4074 4096 C5' A C 699 4095 4097 4118 C5' G C 700 4117 4119 4141 C5' A C 701 4140 4142 4163 C5' C C 702 4162 4164 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3687 P G B 599 distorted distorted 3688 3689 3690 3710 P G B 600 distorted distorted 3695 3711 3712 3713 3733 P U B 601 distorted distorted 3718 3734 3735 3736 3753 P C B 602 distorted distorted 3741 3754 3755 3756 3773 P U B 603 distorted distorted 3761 3774 3775 3776 3793 P C B 604 distorted distorted 3781 3794 3795 3796 3813 P U B 605 distorted distorted 3801 3814 3815 3816 3833 P C B 606 distorted distorted 3821 3834 3835 3836 3853 P U B 607 distorted distorted 3841 3854 3855 3856 3873 P C B 608 distorted distorted 3861 3874 3875 3876 3893 P G B 609 distorted distorted 3881 3894 3895 3896 3916 P U B 610 distorted distorted 3901 3917 3918 3919 3937 P A C 692 distorted distorted 3938 3939 3940 3959 P C C 693 distorted distorted 3945 3960 3961 3962 3979 P G C 694 distorted distorted 3967 3980 3981 3982 4002 P A C 695 distorted distorted 3987 4003 4004 4005 4024 P G C 696 distorted distorted 4010 4025 4026 4027 4047 P A C 697 distorted distorted 4032 4048 4049 4050 4069 P G C 698 distorted distorted 4055 4070 4071 4072 4092 P A C 699 distorted distorted 4077 4093 4094 4095 4114 P G C 700 distorted distorted 4100 4115 4116 4117 4137 P A C 701 distorted distorted 4122 4138 4139 4140 4159 P C C 702 distorted distorted 4145 4160 4161 4162 ---------------------------------------------------------------------------------