ID code: '2RVE' 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' --------------------------------------------------------------------------------- 4024 C1' C F 1 beta 4020 4025 4023 4043 C1' G F 2 beta 4039 4044 4042 4065 C1' A F 3 beta 4061 4066 4064 4086 C1' G F 4 beta 4082 4087 4085 4108 C1' C F 5 beta 4104 4109 4107 4127 C1' T F 6 beta 4123 4128 4126 4147 C1' C F 7 beta 4143 4148 4146 4166 C1' G F 8 beta 4162 4167 4165 3538 C1' C C 1 beta 3534 3539 3537 3557 C1' G C 2 beta 3553 3558 3556 3579 C1' A C 3 beta 3575 3580 3578 3600 C1' G C 4 beta 3596 3601 3599 3622 C1' C C 5 beta 3618 3623 3621 3641 C1' T C 6 beta 3637 3642 3640 3661 C1' C C 7 beta 3657 3662 3660 3680 C1' G C 8 beta 3676 3681 3679 3700 C1' C D 1 beta 3696 3701 3699 3719 C1' G D 2 beta 3715 3720 3718 3741 C1' A D 3 beta 3737 3742 3740 3762 C1' G D 4 beta 3758 3763 3761 3784 C1' C D 5 beta 3780 3785 3783 3803 C1' T D 6 beta 3799 3804 3802 3823 C1' C D 7 beta 3819 3824 3822 3842 C1' G D 8 beta 3838 3843 3841 3862 C1' C E 1 beta 3858 3863 3861 3881 C1' G E 2 beta 3877 3882 3880 3903 C1' A E 3 beta 3899 3904 3902 3924 C1' G E 4 beta 3920 3925 3923 3946 C1' C E 5 beta 3942 3947 3945 3965 C1' T E 6 beta 3961 3966 3964 3985 C1' C E 7 beta 3981 3986 3984 4004 C1' G E 8 beta 4000 4005 4003 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4023 C2' C F 1 4024 4021 4042 C2' G F 2 4043 4040 4064 C2' A F 3 4065 4062 4085 C2' G F 4 4086 4083 4107 C2' C F 5 4108 4105 4126 C2' T F 6 4127 4124 4146 C2' C F 7 4147 4144 4165 C2' G F 8 4166 4163 3537 C2' C C 1 3538 3535 3556 C2' G C 2 3557 3554 3578 C2' A C 3 3579 3576 3599 C2' G C 4 3600 3597 3621 C2' C C 5 3622 3619 3640 C2' T C 6 3641 3638 3660 C2' C C 7 3661 3658 3679 C2' G C 8 3680 3677 3699 C2' C D 1 3700 3697 3718 C2' G D 2 3719 3716 3740 C2' A D 3 3741 3738 3761 C2' G D 4 3762 3759 3783 C2' C D 5 3784 3781 3802 C2' T D 6 3803 3800 3822 C2' C D 7 3823 3820 3841 C2' G D 8 3842 3839 3861 C2' C E 1 3862 3859 3880 C2' G E 2 3881 3878 3902 C2' A E 3 3903 3900 3923 C2' G E 4 3924 3921 3945 C2' C E 5 3946 3943 3964 C2' T E 6 3965 3962 3984 C2' C E 7 3985 3982 4003 C2' G E 8 4004 4001 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4021 C3' C F 1 OK 4019 4022 4023 4040 C3' G F 2 OK 4038 4041 4042 4062 C3' A F 3 OK 4060 4063 4064 4083 C3' G F 4 OK 4081 4084 4085 4105 C3' C F 5 OK 4103 4106 4107 4124 C3' T F 6 OK 4122 4125 4126 4144 C3' C F 7 OK 4142 4145 4146 4163 C3' G F 8 OK 4161 4164 4165 3535 C3' C C 1 OK 3533 3536 3537 3554 C3' G C 2 OK 3552 3555 3556 3576 C3' A C 3 OK 3574 3577 3578 3597 C3' G C 4 OK 3595 3598 3599 3619 C3' C C 5 OK 3617 3620 3621 3638 C3' T C 6 OK 3636 3639 3640 3658 C3' C C 7 OK 3656 3659 3660 3677 C3' G C 8 OK 3675 3678 3679 3697 C3' C D 1 OK 3695 3698 3699 3716 C3' G D 2 OK 3714 3717 3718 3738 C3' A D 3 OK 3736 3739 3740 3759 C3' G D 4 OK 3757 3760 3761 3781 C3' C D 5 OK 3779 3782 3783 3800 C3' T D 6 OK 3798 3801 3802 3820 C3' C D 7 OK 3818 3821 3822 3839 C3' G D 8 OK 3837 3840 3841 3859 C3' C E 1 OK 3857 3860 3861 3878 C3' G E 2 OK 3876 3879 3880 3900 C3' A E 3 OK 3898 3901 3902 3921 C3' G E 4 OK 3919 3922 3923 3943 C3' C E 5 OK 3941 3944 3945 3962 C3' T E 6 OK 3960 3963 3964 3982 C3' C E 7 OK 3980 3983 3984 4001 C3' G E 8 OK 3999 4002 4003 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4019 C4' C F 1 OK 4021 4018 4020 4038 C4' G F 2 OK 4040 4037 4039 4060 C4' A F 3 OK 4062 4059 4061 4081 C4' G F 4 OK 4083 4080 4082 4103 C4' C F 5 OK 4105 4102 4104 4122 C4' T F 6 OK 4124 4121 4123 4142 C4' C F 7 OK 4144 4141 4143 4161 C4' G F 8 OK 4163 4160 4162 3533 C4' C C 1 OK 3535 3532 3534 3552 C4' G C 2 OK 3554 3551 3553 3574 C4' A C 3 OK 3576 3573 3575 3595 C4' G C 4 OK 3597 3594 3596 3617 C4' C C 5 OK 3619 3616 3618 3636 C4' T C 6 OK 3638 3635 3637 3656 C4' C C 7 OK 3658 3655 3657 3675 C4' G C 8 OK 3677 3674 3676 3695 C4' C D 1 OK 3697 3694 3696 3714 C4' G D 2 OK 3716 3713 3715 3736 C4' A D 3 OK 3738 3735 3737 3757 C4' G D 4 OK 3759 3756 3758 3779 C4' C D 5 OK 3781 3778 3780 3798 C4' T D 6 OK 3800 3797 3799 3818 C4' C D 7 OK 3820 3817 3819 3837 C4' G D 8 OK 3839 3836 3838 3857 C4' C E 1 OK 3859 3856 3858 3876 C4' G E 2 OK 3878 3875 3877 3898 C4' A E 3 OK 3900 3897 3899 3919 C4' G E 4 OK 3921 3918 3920 3941 C4' C E 5 OK 3943 3940 3942 3960 C4' T E 6 OK 3962 3959 3961 3980 C4' C E 7 OK 3982 3979 3981 3999 C4' G E 8 OK 4001 3998 4000 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4018 C5' C F 1 4017 4019 4037 C5' G F 2 4036 4038 4059 C5' A F 3 4058 4060 4080 C5' G F 4 4079 4081 4102 C5' C F 5 4101 4103 4121 C5' T F 6 4120 4122 4141 C5' C F 7 4140 4142 4160 C5' G F 8 4159 4161 3532 C5' C C 1 3531 3533 3551 C5' G C 2 3550 3552 3573 C5' A C 3 3572 3574 3594 C5' G C 4 3593 3595 3616 C5' C C 5 3615 3617 3635 C5' T C 6 3634 3636 3655 C5' C C 7 3654 3656 3674 C5' G C 8 3673 3675 3694 C5' C D 1 3693 3695 3713 C5' G D 2 3712 3714 3735 C5' A D 3 3734 3736 3756 C5' G D 4 3755 3757 3778 C5' C D 5 3777 3779 3797 C5' T D 6 3796 3798 3817 C5' C D 7 3816 3818 3836 C5' G D 8 3835 3837 3856 C5' C E 1 3855 3857 3875 C5' G E 2 3874 3876 3897 C5' A E 3 3896 3898 3918 C5' G E 4 3917 3919 3940 C5' C E 5 3939 3941 3959 C5' T E 6 3958 3960 3979 C5' C E 7 3978 3980 3998 C5' G E 8 3997 3999 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4033 P G F 2 distorted distorted 4022 4034 4035 4036 4055 P A F 3 distorted distorted 4041 4056 4057 4058 4076 P G F 4 distorted distorted 4063 4077 4078 4079 4098 P C F 5 distorted distorted 4084 4099 4100 4101 4117 P T F 6 distorted distorted 4106 4118 4119 4120 4137 P C F 7 distorted distorted 4125 4138 4139 4140 4156 P G F 8 distorted distorted 4145 4157 4158 4159 3547 P G C 2 distorted distorted 3536 3548 3549 3550 3569 P A C 3 distorted distorted 3555 3570 3571 3572 3590 P G C 4 distorted distorted 3577 3591 3592 3593 3612 P C C 5 distorted distorted 3598 3613 3614 3615 3631 P T C 6 distorted distorted 3620 3632 3633 3634 3651 P C C 7 distorted distorted 3639 3652 3653 3654 3670 P G C 8 distorted distorted 3659 3671 3672 3673 3709 P G D 2 distorted distorted 3698 3710 3711 3712 3731 P A D 3 distorted distorted 3717 3732 3733 3734 3752 P G D 4 distorted distorted 3739 3753 3754 3755 3774 P C D 5 distorted distorted 3760 3775 3776 3777 3793 P T D 6 distorted distorted 3782 3794 3795 3796 3813 P C D 7 distorted distorted 3801 3814 3815 3816 3832 P G D 8 distorted distorted 3821 3833 3834 3835 3871 P G E 2 distorted distorted 3860 3872 3873 3874 3893 P A E 3 distorted distorted 3879 3894 3895 3896 3914 P G E 4 distorted distorted 3901 3915 3916 3917 3936 P C E 5 distorted distorted 3922 3937 3938 3939 3955 P T E 6 distorted distorted 3944 3956 3957 3958 3975 P C E 7 distorted distorted 3963 3976 3977 3978 3994 P G E 8 distorted distorted 3983 3995 3996 3997 ---------------------------------------------------------------------------------