ID code: '3BAM' 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' --------------------------------------------------------------------------------- 3389 C1' A C 2 beta 3385 3390 3388 3410 C1' T C 3 beta 3406 3411 3409 3430 C1' G C 4 beta 3426 3431 3429 3452 C1' G C 5 beta 3448 3453 3451 3474 C1' A C 6 beta 3470 3475 3473 3495 C1' T C 7 beta 3491 3496 3494 3515 C1' C C 8 beta 3511 3516 3514 3534 C1' C C 9 beta 3530 3535 3533 3553 C1' A C 10 beta 3549 3554 3552 3574 C1' T C 11 beta 3570 3575 3573 3633 C1' A D 2 beta 3629 3634 3632 3654 C1' T D 3 beta 3650 3655 3653 3674 C1' G D 4 beta 3670 3675 3673 3697 C1' G E 1 beta 3693 3698 3696 3720 C1' A E 2 beta 3716 3721 3719 3741 C1' T E 3 beta 3737 3742 3740 3761 C1' C E 4 beta 3757 3762 3760 3780 C1' C E 5 beta 3776 3781 3779 3799 C1' A E 6 beta 3795 3800 3798 3820 C1' T E 7 beta 3816 3821 3819 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3388 C2' A C 2 3389 3386 3409 C2' T C 3 3410 3407 3429 C2' G C 4 3430 3427 3451 C2' G C 5 3452 3449 3473 C2' A C 6 3474 3471 3494 C2' T C 7 3495 3492 3514 C2' C C 8 3515 3512 3533 C2' C C 9 3534 3531 3552 C2' A C 10 3553 3550 3573 C2' T C 11 3574 3571 3632 C2' A D 2 3633 3630 3653 C2' T D 3 3654 3651 3673 C2' G D 4 3674 3671 3696 C2' G E 1 3697 3694 3719 C2' A E 2 3720 3717 3740 C2' T E 3 3741 3738 3760 C2' C E 4 3761 3758 3779 C2' C E 5 3780 3777 3798 C2' A E 6 3799 3796 3819 C2' T E 7 3820 3817 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3386 C3' A C 2 OK 3384 3387 3388 3407 C3' T C 3 OK 3405 3408 3409 3427 C3' G C 4 OK 3425 3428 3429 3449 C3' G C 5 OK 3447 3450 3451 3471 C3' A C 6 OK 3469 3472 3473 3492 C3' T C 7 OK 3490 3493 3494 3512 C3' C C 8 OK 3510 3513 3514 3531 C3' C C 9 OK 3529 3532 3533 3550 C3' A C 10 OK 3548 3551 3552 3571 C3' T C 11 OK 3569 3572 3573 3630 C3' A D 2 OK 3628 3631 3632 3651 C3' T D 3 OK 3649 3652 3653 3671 C3' G D 4 OK 3669 3672 3673 3694 C3' G E 1 OK 3692 3695 3696 3717 C3' A E 2 OK 3715 3718 3719 3738 C3' T E 3 OK 3736 3739 3740 3758 C3' C E 4 OK 3756 3759 3760 3777 C3' C E 5 OK 3775 3778 3779 3796 C3' A E 6 OK 3794 3797 3798 3817 C3' T E 7 OK 3815 3818 3819 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3384 C4' A C 2 OK 3386 3383 3385 3405 C4' T C 3 OK 3407 3404 3406 3425 C4' G C 4 OK 3427 3424 3426 3447 C4' G C 5 OK 3449 3446 3448 3469 C4' A C 6 OK 3471 3468 3470 3490 C4' T C 7 OK 3492 3489 3491 3510 C4' C C 8 OK 3512 3509 3511 3529 C4' C C 9 OK 3531 3528 3530 3548 C4' A C 10 OK 3550 3547 3549 3569 C4' T C 11 OK 3571 3568 3570 3628 C4' A D 2 OK 3630 3627 3629 3649 C4' T D 3 OK 3651 3648 3650 3669 C4' G D 4 OK 3671 3668 3670 3692 C4' G E 1 OK 3694 3691 3693 3715 C4' A E 2 OK 3717 3714 3716 3736 C4' T E 3 OK 3738 3735 3737 3756 C4' C E 4 OK 3758 3755 3757 3775 C4' C E 5 OK 3777 3774 3776 3794 C4' A E 6 OK 3796 3793 3795 3815 C4' T E 7 OK 3817 3814 3816 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3383 C5' A C 2 3382 3384 3404 C5' T C 3 3403 3405 3424 C5' G C 4 3423 3425 3446 C5' G C 5 3445 3447 3468 C5' A C 6 3467 3469 3489 C5' T C 7 3488 3490 3509 C5' C C 8 3508 3510 3528 C5' C C 9 3527 3529 3547 C5' A C 10 3546 3548 3568 C5' T C 11 3567 3569 3627 C5' A D 2 3626 3628 3648 C5' T D 3 3647 3649 3668 C5' G D 4 3667 3669 3691 C5' G E 1 3690 3692 3714 C5' A E 2 3713 3715 3735 C5' T E 3 3734 3736 3755 C5' C E 4 3754 3756 3774 C5' C E 5 3773 3775 3793 C5' A E 6 3792 3794 3814 C5' T E 7 3813 3815 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3400 P T C 3 OK OK 3387 3401 3402 3403 3420 P G C 4 OK OK 3408 3421 3422 3423 3442 P G C 5 OK OK 3428 3443 3444 3445 3464 P A C 6 OK OK 3450 3465 3466 3467 3485 P T C 7 OK OK 3472 3486 3487 3488 3505 P C C 8 OK OK 3493 3506 3507 3508 3524 P C C 9 OK OK 3513 3525 3526 3527 3543 P A C 10 OK OK 3532 3544 3545 3546 3564 P T C 11 OK OK 3551 3565 3566 3567 3644 P T D 3 OK OK 3631 3645 3646 3647 3664 P G D 4 OK OK 3652 3665 3666 3667 3687 P G E 1 OK OK 3688 3689 3690 3710 P A E 2 OK OK 3695 3711 3712 3713 3731 P T E 3 OK OK 3718 3732 3733 3734 3751 P C E 4 OK OK 3739 3752 3753 3754 3770 P C E 5 OK OK 3759 3771 3772 3773 3789 P A E 6 OK OK 3778 3790 3791 3792 3810 P T E 7 OK OK 3797 3811 3812 3813 ---------------------------------------------------------------------------------