ID code: '4FTB' 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' --------------------------------------------------------------------------------- 7509 C1' U R 1 beta 7504 7510 7507 7529 C1' U R 2 beta 7524 7530 7527 7549 C1' U R 3 beta 7544 7550 7547 7569 C1' C R 4 beta 7564 7570 7567 7589 C1' U R 5 beta 7584 7590 7587 7609 C1' C R 6 beta 7604 7610 7607 7629 C1' U R 7 beta 7624 7630 7627 7649 C1' U R 8 beta 7644 7650 7647 7669 C1' U R 9 beta 7664 7670 7667 7689 C1' U R 10 beta 7684 7690 7687 7709 C1' A R 11 beta 7704 7710 7707 7731 C1' U R 12 beta 7726 7732 7729 7751 C1' C R 13 beta 7746 7752 7749 7771 C1' U R 14 beta 7766 7772 7769 7791 C1' U R 15 beta 7786 7792 7789 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7507 C2' U R 1 OK 7509 7505 7508 7527 C2' U R 2 OK 7529 7525 7528 7547 C2' U R 3 OK 7549 7545 7548 7567 C2' C R 4 OK 7569 7565 7568 7587 C2' U R 5 OK 7589 7585 7588 7607 C2' C R 6 OK 7609 7605 7608 7627 C2' U R 7 OK 7629 7625 7628 7647 C2' U R 8 OK 7649 7645 7648 7667 C2' U R 9 OK 7669 7665 7668 7687 C2' U R 10 OK 7689 7685 7688 7707 C2' A R 11 OK 7709 7705 7708 7729 C2' U R 12 OK 7731 7727 7730 7749 C2' C R 13 OK 7751 7747 7750 7769 C2' U R 14 OK 7771 7767 7770 7789 C2' U R 15 OK 7791 7787 7790 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7505 C3' U R 1 OK 7503 7506 7507 7525 C3' U R 2 OK 7523 7526 7527 7545 C3' U R 3 OK 7543 7546 7547 7565 C3' C R 4 OK 7563 7566 7567 7585 C3' U R 5 OK 7583 7586 7587 7605 C3' C R 6 OK 7603 7606 7607 7625 C3' U R 7 OK 7623 7626 7627 7645 C3' U R 8 OK 7643 7646 7647 7665 C3' U R 9 OK 7663 7666 7667 7685 C3' U R 10 OK 7683 7686 7687 7705 C3' A R 11 OK 7703 7706 7707 7727 C3' U R 12 OK 7725 7728 7729 7747 C3' C R 13 OK 7745 7748 7749 7767 C3' U R 14 OK 7765 7768 7769 7787 C3' U R 15 OK 7785 7788 7789 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7503 C4' U R 1 OK 7505 7502 7504 7523 C4' U R 2 OK 7525 7522 7524 7543 C4' U R 3 OK 7545 7542 7544 7563 C4' C R 4 OK 7565 7562 7564 7583 C4' U R 5 OK 7585 7582 7584 7603 C4' C R 6 OK 7605 7602 7604 7623 C4' U R 7 OK 7625 7622 7624 7643 C4' U R 8 OK 7645 7642 7644 7663 C4' U R 9 OK 7665 7662 7664 7683 C4' U R 10 OK 7685 7682 7684 7703 C4' A R 11 OK 7705 7702 7704 7725 C4' U R 12 OK 7727 7724 7726 7745 C4' C R 13 OK 7747 7744 7746 7765 C4' U R 14 OK 7767 7764 7766 7785 C4' U R 15 OK 7787 7784 7786 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7502 C5' U R 1 7501 7503 7522 C5' U R 2 7521 7523 7542 C5' U R 3 7541 7543 7562 C5' C R 4 7561 7563 7582 C5' U R 5 7581 7583 7602 C5' C R 6 7601 7603 7622 C5' U R 7 7621 7623 7642 C5' U R 8 7641 7643 7662 C5' U R 9 7661 7663 7682 C5' U R 10 7681 7683 7702 C5' A R 11 7701 7703 7724 C5' U R 12 7723 7725 7744 C5' C R 13 7743 7745 7764 C5' U R 14 7763 7765 7784 C5' U R 15 7783 7785 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7498 P U R 1 distorted distorted 7499 7500 7501 7518 P U R 2 distorted distorted 7506 7519 7520 7521 7538 P U R 3 distorted distorted 7526 7539 7540 7541 7558 P C R 4 distorted distorted 7546 7559 7560 7561 7578 P U R 5 distorted distorted 7566 7579 7580 7581 7598 P C R 6 distorted distorted 7586 7599 7600 7601 7618 P U R 7 distorted distorted 7606 7619 7620 7621 7638 P U R 8 distorted distorted 7626 7639 7640 7641 7658 P U R 9 distorted distorted 7646 7659 7660 7661 7678 P U R 10 distorted distorted 7666 7679 7680 7681 7698 P A R 11 distorted distorted 7686 7699 7700 7701 7720 P U R 12 distorted distorted 7706 7721 7722 7723 7740 P C R 13 distorted distorted 7728 7741 7742 7743 7760 P U R 14 distorted distorted 7748 7761 7762 7763 7780 P U R 15 distorted distorted 7768 7781 7782 7783 ---------------------------------------------------------------------------------