ID code: '3OSP' 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' --------------------------------------------------------------------------------- 3428 C1' DT T 1 beta 3424 3429 3427 3448 C1' DA T 2 beta 3444 3449 3447 3469 C1' DA T 3 beta 3465 3470 3468 3488 C1' 3DR T 4 3487 3484 3501 C1' DG T 5 beta 3497 3502 3500 3523 C1' DT T 6 beta 3519 3524 3522 3543 C1' DA T 7 beta 3539 3544 3542 3564 C1' DG T 8 beta 3560 3565 3563 3586 C1' DG T 9 beta 3582 3587 3585 3608 C1' DG T 10 beta 3604 3609 3607 3630 C1' DG T 11 beta 3626 3631 3629 3652 C1' DA T 12 beta 3648 3653 3651 3673 C1' DG T 13 beta 3669 3674 3672 3695 C1' DG T 14 beta 3691 3696 3694 3717 C1' DA T 15 beta 3713 3718 3716 3738 C1' DT T 16 beta 3734 3739 3737 3756 C1' DA P 1 beta 3752 3757 3755 3777 C1' DT P 2 beta 3773 3778 3776 3797 C1' DC P 3 beta 3793 3798 3796 3816 C1' DC P 4 beta 3812 3817 3815 3835 C1' DT P 5 beta 3831 3836 3834 3855 C1' DC P 6 beta 3851 3856 3854 3874 C1' DC P 7 beta 3870 3875 3873 3893 C1' DC P 8 beta 3889 3894 3892 3912 C1' DC P 9 beta 3908 3913 3911 3931 C1' DT P 10 beta 3927 3932 3930 3951 C1' DA P 11 beta 3947 3952 3950 3970 C1' DOC P 12 beta 3974 3962 3971 3989 C1' DCP A 739 beta 3993 3981 3990 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3427 C2' DT T 1 3428 3425 3447 C2' DA T 2 3448 3445 3468 C2' DA T 3 3469 3466 3484 C2' 3DR T 4 3488 3489 3500 C2' DG T 5 3501 3498 3522 C2' DT T 6 3523 3520 3542 C2' DA T 7 3543 3540 3563 C2' DG T 8 3564 3561 3585 C2' DG T 9 3586 3583 3607 C2' DG T 10 3608 3605 3629 C2' DG T 11 3630 3627 3651 C2' DA T 12 3652 3649 3672 C2' DG T 13 3673 3670 3694 C2' DG T 14 3695 3692 3716 C2' DA T 15 3717 3714 3737 C2' DT T 16 3738 3735 3755 C2' DA P 1 3756 3753 3776 C2' DT P 2 3777 3774 3796 C2' DC P 3 3797 3794 3815 C2' DC P 4 3816 3813 3834 C2' DT P 5 3835 3832 3854 C2' DC P 6 3855 3852 3873 C2' DC P 7 3874 3871 3892 C2' DC P 8 3893 3890 3911 C2' DC P 9 3912 3909 3930 C2' DT P 10 3931 3928 3950 C2' DA P 11 3951 3948 3971 C2' DOC P 12 3970 3972 3990 C2' DCP A 739 3989 3991 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3425 C3' DT T 1 OK 3423 3426 3427 3445 C3' DA T 2 OK 3443 3446 3447 3466 C3' DA T 3 OK 3464 3467 3468 3489 C3' 3DR T 4 OK 3486 3490 3484 3498 C3' DG T 5 OK 3496 3499 3500 3520 C3' DT T 6 OK 3518 3521 3522 3540 C3' DA T 7 OK 3538 3541 3542 3561 C3' DG T 8 OK 3559 3562 3563 3583 C3' DG T 9 OK 3581 3584 3585 3605 C3' DG T 10 OK 3603 3606 3607 3627 C3' DG T 11 OK 3625 3628 3629 3649 C3' DA T 12 OK 3647 3650 3651 3670 C3' DG T 13 OK 3668 3671 3672 3692 C3' DG T 14 OK 3690 3693 3694 3714 C3' DA T 15 OK 3712 3715 3716 3735 C3' DT T 16 OK 3733 3736 3737 3753 C3' DA P 1 OK 3751 3754 3755 3774 C3' DT P 2 OK 3772 3775 3776 3794 C3' DC P 3 OK 3792 3795 3796 3813 C3' DC P 4 OK 3811 3814 3815 3832 C3' DT P 5 OK 3830 3833 3834 3852 C3' DC P 6 OK 3850 3853 3854 3871 C3' DC P 7 OK 3869 3872 3873 3890 C3' DC P 8 OK 3888 3891 3892 3909 C3' DC P 9 OK 3907 3910 3911 3928 C3' DT P 10 OK 3926 3929 3930 3948 C3' DA P 11 OK 3946 3949 3950 3972 C3' DOC P 12 3973 3971 3991 C3' DCP A 739 OK 3992 3994 3990 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3423 C4' DT T 1 OK 3425 3422 3424 3443 C4' DA T 2 OK 3445 3442 3444 3464 C4' DA T 3 OK 3466 3463 3465 3486 C4' 3DR T 4 OK 3489 3485 3487 3496 C4' DG T 5 OK 3498 3495 3497 3518 C4' DT T 6 OK 3520 3517 3519 3538 C4' DA T 7 OK 3540 3537 3539 3559 C4' DG T 8 OK 3561 3558 3560 3581 C4' DG T 9 OK 3583 3580 3582 3603 C4' DG T 10 OK 3605 3602 3604 3625 C4' DG T 11 OK 3627 3624 3626 3647 C4' DA T 12 OK 3649 3646 3648 3668 C4' DG T 13 OK 3670 3667 3669 3690 C4' DG T 14 OK 3692 3689 3691 3712 C4' DA T 15 OK 3714 3711 3713 3733 C4' DT T 16 OK 3735 3732 3734 3751 C4' DA P 1 OK 3753 3750 3752 3772 C4' DT P 2 OK 3774 3771 3773 3792 C4' DC P 3 OK 3794 3791 3793 3811 C4' DC P 4 OK 3813 3810 3812 3830 C4' DT P 5 OK 3832 3829 3831 3850 C4' DC P 6 OK 3852 3849 3851 3869 C4' DC P 7 OK 3871 3868 3870 3888 C4' DC P 8 OK 3890 3887 3889 3907 C4' DC P 9 OK 3909 3906 3908 3926 C4' DT P 10 OK 3928 3925 3927 3946 C4' DA P 11 OK 3948 3945 3947 3973 C4' DOC P 12 OK 3972 3975 3974 3992 C4' DCP A 739 OK 3991 3995 3993 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3422 C5' DT T 1 3421 3423 3442 C5' DA T 2 3441 3443 3463 C5' DA T 3 3462 3464 3485 C5' 3DR T 4 3480 3486 3495 C5' DG T 5 3494 3496 3517 C5' DT T 6 3516 3518 3537 C5' DA T 7 3536 3538 3558 C5' DG T 8 3557 3559 3580 C5' DG T 9 3579 3581 3602 C5' DG T 10 3601 3603 3624 C5' DG T 11 3623 3625 3646 C5' DA T 12 3645 3647 3667 C5' DG T 13 3666 3668 3689 C5' DG T 14 3688 3690 3711 C5' DA T 15 3710 3712 3732 C5' DT T 16 3731 3733 3750 C5' DA P 1 3749 3751 3771 C5' DT P 2 3770 3772 3791 C5' DC P 3 3790 3792 3810 C5' DC P 4 3809 3811 3829 C5' DT P 5 3828 3830 3849 C5' DC P 6 3848 3850 3868 C5' DC P 7 3867 3869 3887 C5' DC P 8 3886 3888 3906 C5' DC P 9 3905 3907 3925 C5' DT P 10 3924 3926 3945 C5' DA P 11 3944 3946 3975 C5' DOC P 12 3976 3973 3995 C5' DCP A 739 3996 3992 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3438 P DA T 2 distorted distorted 3426 3439 3440 3441 3459 P DA T 3 distorted distorted 3446 3460 3461 3462 3481 P 3DR T 4 OK OK 3467 3482 3483 3480 3491 P DG T 5 distorted distorted 3490 3492 3493 3494 3513 P DT T 6 distorted distorted 3499 3514 3515 3516 3533 P DA T 7 distorted distorted 3521 3534 3535 3536 3554 P DG T 8 distorted distorted 3541 3555 3556 3557 3576 P DG T 9 distorted distorted 3562 3577 3578 3579 3598 P DG T 10 distorted distorted 3584 3599 3600 3601 3620 P DG T 11 distorted distorted 3606 3621 3622 3623 3642 P DA T 12 distorted distorted 3628 3643 3644 3645 3663 P DG T 13 distorted distorted 3650 3664 3665 3666 3685 P DG T 14 distorted distorted 3671 3686 3687 3688 3707 P DA T 15 distorted distorted 3693 3708 3709 3710 3728 P DT T 16 distorted distorted 3715 3729 3730 3731 3767 P DT P 2 distorted distorted 3754 3768 3769 3770 3787 P DC P 3 distorted distorted 3775 3788 3789 3790 3806 P DC P 4 distorted distorted 3795 3807 3808 3809 3825 P DT P 5 distorted distorted 3814 3826 3827 3828 3845 P DC P 6 distorted distorted 3833 3846 3847 3848 3864 P DC P 7 distorted distorted 3853 3865 3866 3867 3883 P DC P 8 distorted distorted 3872 3884 3885 3886 3902 P DC P 9 distorted distorted 3891 3903 3904 3905 3921 P DT P 10 distorted distorted 3910 3922 3923 3924 3941 P DA P 11 distorted distorted 3929 3942 3943 3944 3977 P DOC P 12 OK OK 3949 3978 3979 3976 ---------------------------------------------------------------------------------