ID code: '4TZ6' 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' --------------------------------------------------------------------------------- 7544 C1' A B -1 alpha beta 7539 7561 7545 7542 7577 C1' A B 0 alpha beta 7572 7594 7578 7575 7610 C1' A B 1 alpha beta 7605 7627 7611 7608 7643 C1' A B 2 alpha beta 7638 7660 7644 7641 7676 C1' A B 3 alpha beta 7671 7693 7677 7674 7709 C1' A B 4 alpha beta 7704 7726 7710 7707 7742 C1' A B 5 alpha beta 7737 7760 7743 7740 7778 C1' UDP A 602 alpha beta 7783 7798 7770 7779 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7542 C2' A B -1 OK OK 7544 7540 7559 7543 7575 C2' A B 0 OK OK 7577 7573 7592 7576 7608 C2' A B 1 OK OK 7610 7606 7625 7609 7641 C2' A B 2 OK OK 7643 7639 7658 7642 7674 C2' A B 3 OK OK 7676 7672 7691 7675 7707 C2' A B 4 OK OK 7709 7705 7724 7708 7740 C2' A B 5 OK OK 7742 7738 7758 7741 7779 C2' UDP A 602 OK OK 7778 7781 7799 7780 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7540 C3' A B -1 OK OK 7538 7558 7541 7542 7573 C3' A B 0 OK OK 7571 7591 7574 7575 7606 C3' A B 1 OK OK 7604 7624 7607 7608 7639 C3' A B 2 OK OK 7637 7657 7640 7641 7672 C3' A B 3 OK OK 7670 7690 7673 7674 7705 C3' A B 4 OK OK 7703 7723 7706 7707 7738 C3' A B 5 OK OK 7736 7756 7739 7740 7781 C3' UDP A 602 OK OK 7782 7801 7784 7779 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7538 C4' A B -1 OK OK 7540 7557 7537 7539 7571 C4' A B 0 OK OK 7573 7590 7570 7572 7604 C4' A B 1 OK OK 7606 7623 7603 7605 7637 C4' A B 2 OK OK 7639 7656 7636 7638 7670 C4' A B 3 OK OK 7672 7689 7669 7671 7703 C4' A B 4 OK OK 7705 7722 7702 7704 7736 C4' A B 5 OK OK 7738 7755 7735 7737 7782 C4' UDP A 602 OK OK 7781 7802 7785 7783 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7537 C5' A B -1 OK OK 7536 7555 7556 7538 7570 C5' A B 0 OK OK 7569 7588 7589 7571 7603 C5' A B 1 OK OK 7602 7621 7622 7604 7636 C5' A B 2 OK OK 7635 7654 7655 7637 7669 C5' A B 3 OK OK 7668 7687 7688 7670 7702 C5' A B 4 OK OK 7701 7720 7721 7703 7735 C5' A B 5 OK OK 7734 7753 7754 7736 7785 C5' UDP A 602 OK OK 7786 7804 7805 7782 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7533 P A B -1 distorted distorted 7534 7535 7536 7566 P A B 0 distorted distorted 7541 7567 7568 7569 7599 P A B 1 distorted distorted 7574 7600 7601 7602 7632 P A B 2 distorted distorted 7607 7633 7634 7635 7665 P A B 3 distorted distorted 7640 7666 7667 7668 7698 P A B 4 distorted distorted 7673 7699 7700 7701 7731 P A B 5 distorted distorted 7706 7732 7733 7734 ---------------------------------------------------------------------------------