ID code: '3OIN' 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' --------------------------------------------------------------------------------- 3448 C1' G C 1 beta 3443 3449 3446 3471 C1' G C 2 beta 3466 3472 3469 3494 C1' G C 3 beta 3489 3495 3492 3517 C1' C C 4 beta 3512 3518 3515 3537 C1' U C 5 beta 3532 3538 3535 3557 C1' U C 6 beta 3552 3558 3555 3577 C1' C C 7 beta 3572 3578 3575 3597 C1' A C 8 beta 3592 3598 3595 3619 C1' A C 9 beta 3614 3620 3617 3641 C1' C C 10 beta 3636 3642 3639 3661 C1' G C 11 beta 3656 3662 3659 3684 C1' C C 12 beta 3679 3685 3682 3704 C1' C C 13 beta 3699 3705 3702 3724 C1' C C 14 beta 3719 3725 3722 3760 C1' SAH B 253 beta 3755 3761 3758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3446 C2' G C 1 OK 3448 3444 3447 3469 C2' G C 2 OK 3471 3467 3470 3492 C2' G C 3 OK 3494 3490 3493 3515 C2' C C 4 OK 3517 3513 3516 3535 C2' U C 5 OK 3537 3533 3536 3555 C2' U C 6 OK 3557 3553 3556 3575 C2' C C 7 OK 3577 3573 3576 3595 C2' A C 8 OK 3597 3593 3596 3617 C2' A C 9 OK 3619 3615 3618 3639 C2' C C 10 OK 3641 3637 3640 3659 C2' G C 11 OK 3661 3657 3660 3682 C2' C C 12 OK 3684 3680 3683 3702 C2' C C 13 OK 3704 3700 3703 3722 C2' C C 14 OK 3724 3720 3723 3758 C2' SAH B 253 OK 3760 3756 3759 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3444 C3' G C 1 OK 3442 3445 3446 3467 C3' G C 2 OK 3465 3468 3469 3490 C3' G C 3 OK 3488 3491 3492 3513 C3' C C 4 OK 3511 3514 3515 3533 C3' U C 5 OK 3531 3534 3535 3553 C3' U C 6 OK 3551 3554 3555 3573 C3' C C 7 OK 3571 3574 3575 3593 C3' A C 8 OK 3591 3594 3595 3615 C3' A C 9 OK 3613 3616 3617 3637 C3' C C 10 OK 3635 3638 3639 3657 C3' G C 11 OK 3655 3658 3659 3680 C3' C C 12 OK 3678 3681 3682 3700 C3' C C 13 OK 3698 3701 3702 3720 C3' C C 14 OK 3718 3721 3722 3756 C3' SAH B 253 OK 3754 3757 3758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3442 C4' G C 1 OK 3444 3441 3443 3465 C4' G C 2 OK 3467 3464 3466 3488 C4' G C 3 OK 3490 3487 3489 3511 C4' C C 4 OK 3513 3510 3512 3531 C4' U C 5 OK 3533 3530 3532 3551 C4' U C 6 OK 3553 3550 3552 3571 C4' C C 7 OK 3573 3570 3572 3591 C4' A C 8 OK 3593 3590 3592 3613 C4' A C 9 OK 3615 3612 3614 3635 C4' C C 10 OK 3637 3634 3636 3655 C4' G C 11 OK 3657 3654 3656 3678 C4' C C 12 OK 3680 3677 3679 3698 C4' C C 13 OK 3700 3697 3699 3718 C4' C C 14 OK 3720 3717 3719 3754 C4' SAH B 253 OK 3756 3753 3755 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3441 C5' G C 1 3440 3442 3464 C5' G C 2 3463 3465 3487 C5' G C 3 3486 3488 3510 C5' C C 4 3509 3511 3530 C5' U C 5 3529 3531 3550 C5' U C 6 3549 3551 3570 C5' C C 7 3569 3571 3590 C5' A C 8 3589 3591 3612 C5' A C 9 3611 3613 3634 C5' C C 10 3633 3635 3654 C5' G C 11 3653 3655 3677 C5' C C 12 3676 3678 3697 C5' C C 13 3696 3698 3717 C5' C C 14 3716 3718 3753 C5' SAH B 253 3754 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3460 P G C 2 distorted distorted 3445 3461 3462 3463 3483 P G C 3 distorted distorted 3468 3484 3485 3486 3506 P C C 4 distorted distorted 3491 3507 3508 3509 3526 P U C 5 distorted distorted 3514 3527 3528 3529 3546 P U C 6 distorted distorted 3534 3547 3548 3549 3566 P C C 7 distorted distorted 3554 3567 3568 3569 3586 P A C 8 distorted distorted 3574 3587 3588 3589 3608 P A C 9 distorted distorted 3594 3609 3610 3611 3630 P C C 10 distorted distorted 3616 3631 3632 3633 3650 P G C 11 distorted distorted 3638 3651 3652 3653 3673 P C C 12 distorted distorted 3658 3674 3675 3676 3693 P C C 13 distorted distorted 3681 3694 3695 3696 3713 P C C 14 distorted distorted 3701 3714 3715 3716 ---------------------------------------------------------------------------------