ID code: '3OIJ' 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' --------------------------------------------------------------------------------- 3385 C1' G C 1 beta 3380 3386 3383 3408 C1' G C 2 beta 3403 3409 3406 3431 C1' G C 3 beta 3426 3432 3429 3454 C1' C C 4 beta 3449 3455 3452 3474 C1' U C 5 beta 3469 3475 3472 3494 C1' U C 6 beta 3489 3495 3492 3514 C1' C C 7 beta 3509 3515 3512 3534 C1' A C 8 beta 3529 3535 3532 3556 C1' A C 9 beta 3551 3557 3554 3578 C1' C C 10 beta 3573 3579 3576 3598 C1' G C 11 beta 3593 3599 3596 3621 C1' C C 12 beta 3616 3622 3619 3641 C1' C C 13 beta 3636 3642 3639 3661 C1' C C 14 beta 3656 3662 3659 3679 C1' G D 1 beta 3674 3680 3677 3702 C1' G D 2 beta 3697 3703 3700 3725 C1' G D 3 beta 3720 3726 3723 3748 C1' C D 4 beta 3743 3749 3746 3768 C1' U D 5 beta 3763 3769 3766 3788 C1' U D 6 beta 3783 3789 3786 3808 C1' C D 7 beta 3803 3809 3806 3828 C1' A D 8 beta 3823 3829 3826 3850 C1' A D 9 beta 3845 3851 3848 3872 C1' C D 10 beta 3867 3873 3870 3892 C1' G D 11 beta 3887 3893 3890 3915 C1' C D 12 beta 3910 3916 3913 3935 C1' C D 13 beta 3930 3936 3933 3955 C1' C D 14 beta 3950 3956 3953 3979 C1' SAH A 253 beta 3974 3980 3977 4004 C1' SAH B 253 beta 3999 4005 4002 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3383 C2' G C 1 OK 3385 3381 3384 3406 C2' G C 2 OK 3408 3404 3407 3429 C2' G C 3 OK 3431 3427 3430 3452 C2' C C 4 OK 3454 3450 3453 3472 C2' U C 5 OK 3474 3470 3473 3492 C2' U C 6 OK 3494 3490 3493 3512 C2' C C 7 OK 3514 3510 3513 3532 C2' A C 8 OK 3534 3530 3533 3554 C2' A C 9 OK 3556 3552 3555 3576 C2' C C 10 OK 3578 3574 3577 3596 C2' G C 11 OK 3598 3594 3597 3619 C2' C C 12 OK 3621 3617 3620 3639 C2' C C 13 OK 3641 3637 3640 3659 C2' C C 14 OK 3661 3657 3660 3677 C2' G D 1 OK 3679 3675 3678 3700 C2' G D 2 OK 3702 3698 3701 3723 C2' G D 3 OK 3725 3721 3724 3746 C2' C D 4 OK 3748 3744 3747 3766 C2' U D 5 OK 3768 3764 3767 3786 C2' U D 6 OK 3788 3784 3787 3806 C2' C D 7 OK 3808 3804 3807 3826 C2' A D 8 OK 3828 3824 3827 3848 C2' A D 9 OK 3850 3846 3849 3870 C2' C D 10 OK 3872 3868 3871 3890 C2' G D 11 OK 3892 3888 3891 3913 C2' C D 12 OK 3915 3911 3914 3933 C2' C D 13 OK 3935 3931 3934 3953 C2' C D 14 OK 3955 3951 3954 3977 C2' SAH A 253 OK 3979 3975 3978 4002 C2' SAH B 253 OK 4004 4000 4003 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3381 C3' G C 1 OK 3379 3382 3383 3404 C3' G C 2 OK 3402 3405 3406 3427 C3' G C 3 OK 3425 3428 3429 3450 C3' C C 4 OK 3448 3451 3452 3470 C3' U C 5 OK 3468 3471 3472 3490 C3' U C 6 OK 3488 3491 3492 3510 C3' C C 7 OK 3508 3511 3512 3530 C3' A C 8 OK 3528 3531 3532 3552 C3' A C 9 OK 3550 3553 3554 3574 C3' C C 10 OK 3572 3575 3576 3594 C3' G C 11 OK 3592 3595 3596 3617 C3' C C 12 OK 3615 3618 3619 3637 C3' C C 13 OK 3635 3638 3639 3657 C3' C C 14 OK 3655 3658 3659 3675 C3' G D 1 OK 3673 3676 3677 3698 C3' G D 2 OK 3696 3699 3700 3721 C3' G D 3 OK 3719 3722 3723 3744 C3' C D 4 OK 3742 3745 3746 3764 C3' U D 5 OK 3762 3765 3766 3784 C3' U D 6 OK 3782 3785 3786 3804 C3' C D 7 OK 3802 3805 3806 3824 C3' A D 8 OK 3822 3825 3826 3846 C3' A D 9 OK 3844 3847 3848 3868 C3' C D 10 OK 3866 3869 3870 3888 C3' G D 11 OK 3886 3889 3890 3911 C3' C D 12 OK 3909 3912 3913 3931 C3' C D 13 OK 3929 3932 3933 3951 C3' C D 14 OK 3949 3952 3953 3975 C3' SAH A 253 OK 3973 3976 3977 4000 C3' SAH B 253 OK 3998 4001 4002 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3379 C4' G C 1 OK 3381 3378 3380 3402 C4' G C 2 OK 3404 3401 3403 3425 C4' G C 3 OK 3427 3424 3426 3448 C4' C C 4 OK 3450 3447 3449 3468 C4' U C 5 OK 3470 3467 3469 3488 C4' U C 6 OK 3490 3487 3489 3508 C4' C C 7 OK 3510 3507 3509 3528 C4' A C 8 OK 3530 3527 3529 3550 C4' A C 9 OK 3552 3549 3551 3572 C4' C C 10 OK 3574 3571 3573 3592 C4' G C 11 OK 3594 3591 3593 3615 C4' C C 12 OK 3617 3614 3616 3635 C4' C C 13 OK 3637 3634 3636 3655 C4' C C 14 OK 3657 3654 3656 3673 C4' G D 1 OK 3675 3672 3674 3696 C4' G D 2 OK 3698 3695 3697 3719 C4' G D 3 OK 3721 3718 3720 3742 C4' C D 4 OK 3744 3741 3743 3762 C4' U D 5 OK 3764 3761 3763 3782 C4' U D 6 OK 3784 3781 3783 3802 C4' C D 7 OK 3804 3801 3803 3822 C4' A D 8 OK 3824 3821 3823 3844 C4' A D 9 OK 3846 3843 3845 3866 C4' C D 10 OK 3868 3865 3867 3886 C4' G D 11 OK 3888 3885 3887 3909 C4' C D 12 OK 3911 3908 3910 3929 C4' C D 13 OK 3931 3928 3930 3949 C4' C D 14 OK 3951 3948 3950 3973 C4' SAH A 253 OK 3975 3972 3974 3998 C4' SAH B 253 OK 4000 3997 3999 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3378 C5' G C 1 3377 3379 3401 C5' G C 2 3400 3402 3424 C5' G C 3 3423 3425 3447 C5' C C 4 3446 3448 3467 C5' U C 5 3466 3468 3487 C5' U C 6 3486 3488 3507 C5' C C 7 3506 3508 3527 C5' A C 8 3526 3528 3549 C5' A C 9 3548 3550 3571 C5' C C 10 3570 3572 3591 C5' G C 11 3590 3592 3614 C5' C C 12 3613 3615 3634 C5' C C 13 3633 3635 3654 C5' C C 14 3653 3655 3672 C5' G D 1 3671 3673 3695 C5' G D 2 3694 3696 3718 C5' G D 3 3717 3719 3741 C5' C D 4 3740 3742 3761 C5' U D 5 3760 3762 3781 C5' U D 6 3780 3782 3801 C5' C D 7 3800 3802 3821 C5' A D 8 3820 3822 3843 C5' A D 9 3842 3844 3865 C5' C D 10 3864 3866 3885 C5' G D 11 3884 3886 3908 C5' C D 12 3907 3909 3928 C5' C D 13 3927 3929 3948 C5' C D 14 3947 3949 3972 C5' SAH A 253 3973 3997 C5' SAH B 253 3998 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3397 P G C 2 distorted distorted 3382 3398 3399 3400 3420 P G C 3 distorted distorted 3405 3421 3422 3423 3443 P C C 4 distorted distorted 3428 3444 3445 3446 3463 P U C 5 distorted distorted 3451 3464 3465 3466 3483 P U C 6 distorted distorted 3471 3484 3485 3486 3503 P C C 7 distorted distorted 3491 3504 3505 3506 3523 P A C 8 distorted distorted 3511 3524 3525 3526 3545 P A C 9 distorted distorted 3531 3546 3547 3548 3567 P C C 10 distorted distorted 3553 3568 3569 3570 3587 P G C 11 distorted distorted 3575 3588 3589 3590 3610 P C C 12 distorted distorted 3595 3611 3612 3613 3630 P C C 13 distorted distorted 3618 3631 3632 3633 3650 P C C 14 distorted distorted 3638 3651 3652 3653 3691 P G D 2 distorted distorted 3676 3692 3693 3694 3714 P G D 3 distorted distorted 3699 3715 3716 3717 3737 P C D 4 distorted distorted 3722 3738 3739 3740 3757 P U D 5 distorted distorted 3745 3758 3759 3760 3777 P U D 6 distorted distorted 3765 3778 3779 3780 3797 P C D 7 distorted distorted 3785 3798 3799 3800 3817 P A D 8 distorted distorted 3805 3818 3819 3820 3839 P A D 9 distorted distorted 3825 3840 3841 3842 3861 P C D 10 distorted distorted 3847 3862 3863 3864 3881 P G D 11 distorted distorted 3869 3882 3883 3884 3904 P C D 12 distorted distorted 3889 3905 3906 3907 3924 P C D 13 distorted distorted 3912 3925 3926 3927 3944 P C D 14 distorted distorted 3932 3945 3946 3947 ---------------------------------------------------------------------------------