ID code: '2W36' 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' --------------------------------------------------------------------------------- 3584 C1' DG C 1 beta 3580 3585 3583 3606 C1' DC C 2 beta 3602 3607 3605 3624 C1' BRU C 3 beta 3629 3615 3625 3645 C1' DA C 4 beta 3641 3646 3644 3666 C1' DC C 5 beta 3662 3667 3665 3685 C1' DI C 6 beta 3681 3686 3684 3706 C1' DG C 7 beta 3702 3707 3705 3728 C1' DA C 8 beta 3724 3729 3727 3748 C1' BRU C 9 beta 3753 3739 3749 3769 C1' DC C 10 beta 3765 3770 3768 3788 C1' DG C 11 beta 3784 3789 3787 3808 C1' DG D 18 beta 3804 3809 3807 3830 C1' DT D 19 beta 3826 3831 3829 3850 C1' DA D 20 beta 3846 3851 3849 3871 C1' DG D 21 beta 3867 3872 3870 3893 C1' DC D 22 beta 3889 3894 3892 3910 C1' DG E 1 beta 3906 3911 3909 3932 C1' DC E 2 beta 3928 3933 3931 3950 C1' BRU E 3 beta 3955 3941 3951 3971 C1' DA E 4 beta 3967 3972 3970 3992 C1' DC E 5 beta 3988 3993 3991 4011 C1' DI E 6 beta 4007 4012 4010 4032 C1' DG E 7 beta 4028 4033 4031 4054 C1' DA E 8 beta 4050 4055 4053 4074 C1' BRU E 9 beta 4079 4065 4075 4095 C1' DC E 10 beta 4091 4096 4094 4114 C1' DG E 11 beta 4110 4115 4113 4134 C1' DG F 18 beta 4130 4135 4133 4156 C1' DT F 19 beta 4152 4157 4155 4176 C1' DA F 20 beta 4172 4177 4175 4197 C1' DG F 21 beta 4193 4198 4196 4219 C1' DC F 22 beta 4215 4220 4218 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3583 C2' DG C 1 3584 3581 3605 C2' DC C 2 3606 3603 3625 C2' BRU C 3 3624 3626 3644 C2' DA C 4 3645 3642 3665 C2' DC C 5 3666 3663 3684 C2' DI C 6 3685 3682 3705 C2' DG C 7 3706 3703 3727 C2' DA C 8 3728 3725 3749 C2' BRU C 9 3748 3750 3768 C2' DC C 10 3769 3766 3787 C2' DG C 11 3788 3785 3807 C2' DG D 18 3808 3805 3829 C2' DT D 19 3830 3827 3849 C2' DA D 20 3850 3847 3870 C2' DG D 21 3871 3868 3892 C2' DC D 22 3893 3890 3909 C2' DG E 1 3910 3907 3931 C2' DC E 2 3932 3929 3951 C2' BRU E 3 3950 3952 3970 C2' DA E 4 3971 3968 3991 C2' DC E 5 3992 3989 4010 C2' DI E 6 4011 4008 4031 C2' DG E 7 4032 4029 4053 C2' DA E 8 4054 4051 4075 C2' BRU E 9 4074 4076 4094 C2' DC E 10 4095 4092 4113 C2' DG E 11 4114 4111 4133 C2' DG F 18 4134 4131 4155 C2' DT F 19 4156 4153 4175 C2' DA F 20 4176 4173 4196 C2' DG F 21 4197 4194 4218 C2' DC F 22 4219 4216 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3581 C3' DG C 1 OK 3579 3582 3583 3603 C3' DC C 2 OK 3601 3604 3605 3626 C3' BRU C 3 OK 3627 3628 3625 3642 C3' DA C 4 OK 3640 3643 3644 3663 C3' DC C 5 OK 3661 3664 3665 3682 C3' DI C 6 OK 3680 3683 3684 3703 C3' DG C 7 OK 3701 3704 3705 3725 C3' DA C 8 OK 3723 3726 3727 3750 C3' BRU C 9 OK 3751 3752 3749 3766 C3' DC C 10 OK 3764 3767 3768 3785 C3' DG C 11 OK 3783 3786 3787 3805 C3' DG D 18 OK 3803 3806 3807 3827 C3' DT D 19 OK 3825 3828 3829 3847 C3' DA D 20 OK 3845 3848 3849 3868 C3' DG D 21 OK 3866 3869 3870 3890 C3' DC D 22 OK 3888 3891 3892 3907 C3' DG E 1 OK 3905 3908 3909 3929 C3' DC E 2 OK 3927 3930 3931 3952 C3' BRU E 3 OK 3953 3954 3951 3968 C3' DA E 4 OK 3966 3969 3970 3989 C3' DC E 5 OK 3987 3990 3991 4008 C3' DI E 6 OK 4006 4009 4010 4029 C3' DG E 7 OK 4027 4030 4031 4051 C3' DA E 8 OK 4049 4052 4053 4076 C3' BRU E 9 OK 4077 4078 4075 4092 C3' DC E 10 OK 4090 4093 4094 4111 C3' DG E 11 OK 4109 4112 4113 4131 C3' DG F 18 OK 4129 4132 4133 4153 C3' DT F 19 OK 4151 4154 4155 4173 C3' DA F 20 OK 4171 4174 4175 4194 C3' DG F 21 OK 4192 4195 4196 4216 C3' DC F 22 OK 4214 4217 4218 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3579 C4' DG C 1 OK 3581 3578 3580 3601 C4' DC C 2 OK 3603 3600 3602 3627 C4' BRU C 3 OK 3626 3630 3629 3640 C4' DA C 4 OK 3642 3639 3641 3661 C4' DC C 5 OK 3663 3660 3662 3680 C4' DI C 6 OK 3682 3679 3681 3701 C4' DG C 7 OK 3703 3700 3702 3723 C4' DA C 8 OK 3725 3722 3724 3751 C4' BRU C 9 OK 3750 3754 3753 3764 C4' DC C 10 OK 3766 3763 3765 3783 C4' DG C 11 OK 3785 3782 3784 3803 C4' DG D 18 OK 3805 3802 3804 3825 C4' DT D 19 OK 3827 3824 3826 3845 C4' DA D 20 OK 3847 3844 3846 3866 C4' DG D 21 OK 3868 3865 3867 3888 C4' DC D 22 OK 3890 3887 3889 3905 C4' DG E 1 OK 3907 3904 3906 3927 C4' DC E 2 OK 3929 3926 3928 3953 C4' BRU E 3 OK 3952 3956 3955 3966 C4' DA E 4 OK 3968 3965 3967 3987 C4' DC E 5 OK 3989 3986 3988 4006 C4' DI E 6 OK 4008 4005 4007 4027 C4' DG E 7 OK 4029 4026 4028 4049 C4' DA E 8 OK 4051 4048 4050 4077 C4' BRU E 9 OK 4076 4080 4079 4090 C4' DC E 10 OK 4092 4089 4091 4109 C4' DG E 11 OK 4111 4108 4110 4129 C4' DG F 18 OK 4131 4128 4130 4151 C4' DT F 19 OK 4153 4150 4152 4171 C4' DA F 20 OK 4173 4170 4172 4192 C4' DG F 21 OK 4194 4191 4193 4214 C4' DC F 22 OK 4216 4213 4215 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3578 C5' DG C 1 3577 3579 3600 C5' DC C 2 3599 3601 3630 C5' BRU C 3 3631 3627 3639 C5' DA C 4 3638 3640 3660 C5' DC C 5 3659 3661 3679 C5' DI C 6 3678 3680 3700 C5' DG C 7 3699 3701 3722 C5' DA C 8 3721 3723 3754 C5' BRU C 9 3755 3751 3763 C5' DC C 10 3762 3764 3782 C5' DG C 11 3781 3783 3802 C5' DG D 18 3801 3803 3824 C5' DT D 19 3823 3825 3844 C5' DA D 20 3843 3845 3865 C5' DG D 21 3864 3866 3887 C5' DC D 22 3886 3888 3904 C5' DG E 1 3903 3905 3926 C5' DC E 2 3925 3927 3956 C5' BRU E 3 3957 3953 3965 C5' DA E 4 3964 3966 3986 C5' DC E 5 3985 3987 4005 C5' DI E 6 4004 4006 4026 C5' DG E 7 4025 4027 4048 C5' DA E 8 4047 4049 4080 C5' BRU E 9 4081 4077 4089 C5' DC E 10 4088 4090 4108 C5' DG E 11 4107 4109 4128 C5' DG F 18 4127 4129 4150 C5' DT F 19 4149 4151 4170 C5' DA F 20 4169 4171 4191 C5' DG F 21 4190 4192 4213 C5' DC F 22 4212 4214 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3596 P DC C 2 distorted distorted 3582 3597 3598 3599 3632 P BRU C 3 distorted distorted 3604 3633 3634 3631 3635 P DA C 4 distorted distorted 3628 3636 3637 3638 3656 P DC C 5 distorted distorted 3643 3657 3658 3659 3675 P DI C 6 distorted distorted 3664 3676 3677 3678 3696 P DG C 7 distorted distorted 3683 3697 3698 3699 3718 P DA C 8 distorted distorted 3704 3719 3720 3721 3756 P BRU C 9 distorted distorted 3726 3757 3758 3755 3759 P DC C 10 distorted distorted 3752 3760 3761 3762 3778 P DG C 11 distorted distorted 3767 3779 3780 3781 3820 P DT D 19 distorted distorted 3806 3821 3822 3823 3840 P DA D 20 distorted distorted 3828 3841 3842 3843 3861 P DG D 21 distorted distorted 3848 3862 3863 3864 3883 P DC D 22 distorted distorted 3869 3884 3885 3886 3922 P DC E 2 distorted distorted 3908 3923 3924 3925 3958 P BRU E 3 distorted distorted 3930 3959 3960 3957 3961 P DA E 4 distorted distorted 3954 3962 3963 3964 3982 P DC E 5 distorted distorted 3969 3983 3984 3985 4001 P DI E 6 distorted distorted 3990 4002 4003 4004 4022 P DG E 7 distorted distorted 4009 4023 4024 4025 4044 P DA E 8 distorted distorted 4030 4045 4046 4047 4082 P BRU E 9 distorted distorted 4052 4083 4084 4081 4085 P DC E 10 distorted distorted 4078 4086 4087 4088 4104 P DG E 11 distorted distorted 4093 4105 4106 4107 4146 P DT F 19 distorted distorted 4132 4147 4148 4149 4166 P DA F 20 distorted distorted 4154 4167 4168 4169 4187 P DG F 21 distorted distorted 4174 4188 4189 4190 4209 P DC F 22 distorted distorted 4195 4210 4211 4212 ---------------------------------------------------------------------------------