ID code: '1DGC' 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' --------------------------------------------------------------------------------- 485 C1' G B -9 beta 481 486 484 507 C1' G B -8 beta 503 508 506 529 C1' A B -7 beta 525 530 528 550 C1' G B -6 beta 546 551 549 572 C1' A B -5 beta 568 573 571 593 C1' T B -4 beta 589 594 592 613 C1' G B -3 beta 609 614 612 635 C1' A B -2 beta 631 636 634 656 C1' C B -1 beta 652 657 655 675 C1' G B 1 beta 671 676 674 697 C1' T B 2 beta 693 698 696 717 C1' C B 3 beta 713 718 716 736 C1' A B 4 beta 732 737 735 757 C1' T B 5 beta 753 758 756 777 C1' C B 6 beta 773 778 776 796 C1' T B 7 beta 792 797 795 816 C1' C B 8 beta 812 817 815 835 C1' C B 9 beta 831 836 834 485 C1' G B -9 beta 481 486 484 507 C1' G B -8 beta 503 508 506 529 C1' A B -7 beta 525 530 528 550 C1' G B -6 beta 546 551 549 572 C1' A B -5 beta 568 573 571 593 C1' T B -4 beta 589 594 592 613 C1' G B -3 beta 609 614 612 635 C1' A B -2 beta 631 636 634 656 C1' C B -1 beta 652 657 655 675 C1' G B 1 beta 671 676 674 697 C1' T B 2 beta 693 698 696 717 C1' C B 3 beta 713 718 716 736 C1' A B 4 beta 732 737 735 757 C1' T B 5 beta 753 758 756 777 C1' C B 6 beta 773 778 776 796 C1' T B 7 beta 792 797 795 816 C1' C B 8 beta 812 817 815 835 C1' C B 9 beta 831 836 834 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 484 C2' G B -9 485 482 506 C2' G B -8 507 504 528 C2' A B -7 529 526 549 C2' G B -6 550 547 571 C2' A B -5 572 569 592 C2' T B -4 593 590 612 C2' G B -3 613 610 634 C2' A B -2 635 632 655 C2' C B -1 656 653 674 C2' G B 1 675 672 696 C2' T B 2 697 694 716 C2' C B 3 717 714 735 C2' A B 4 736 733 756 C2' T B 5 757 754 776 C2' C B 6 777 774 795 C2' T B 7 796 793 815 C2' C B 8 816 813 834 C2' C B 9 835 832 484 C2' G B -9 485 482 506 C2' G B -8 507 504 528 C2' A B -7 529 526 549 C2' G B -6 550 547 571 C2' A B -5 572 569 592 C2' T B -4 593 590 612 C2' G B -3 613 610 634 C2' A B -2 635 632 655 C2' C B -1 656 653 674 C2' G B 1 675 672 696 C2' T B 2 697 694 716 C2' C B 3 717 714 735 C2' A B 4 736 733 756 C2' T B 5 757 754 776 C2' C B 6 777 774 795 C2' T B 7 796 793 815 C2' C B 8 816 813 834 C2' C B 9 835 832 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 482 C3' G B -9 OK 480 483 484 504 C3' G B -8 OK 502 505 506 526 C3' A B -7 OK 524 527 528 547 C3' G B -6 OK 545 548 549 569 C3' A B -5 OK 567 570 571 590 C3' T B -4 OK 588 591 592 610 C3' G B -3 OK 608 611 612 632 C3' A B -2 OK 630 633 634 653 C3' C B -1 OK 651 654 655 672 C3' G B 1 OK 670 673 674 694 C3' T B 2 OK 692 695 696 714 C3' C B 3 OK 712 715 716 733 C3' A B 4 OK 731 734 735 754 C3' T B 5 OK 752 755 756 774 C3' C B 6 OK 772 775 776 793 C3' T B 7 OK 791 794 795 813 C3' C B 8 OK 811 814 815 832 C3' C B 9 OK 830 833 834 482 C3' G B -9 OK 480 483 484 504 C3' G B -8 OK 502 505 506 526 C3' A B -7 OK 524 527 528 547 C3' G B -6 OK 545 548 549 569 C3' A B -5 OK 567 570 571 590 C3' T B -4 OK 588 591 592 610 C3' G B -3 OK 608 611 612 632 C3' A B -2 OK 630 633 634 653 C3' C B -1 OK 651 654 655 672 C3' G B 1 OK 670 673 674 694 C3' T B 2 OK 692 695 696 714 C3' C B 3 OK 712 715 716 733 C3' A B 4 OK 731 734 735 754 C3' T B 5 OK 752 755 756 774 C3' C B 6 OK 772 775 776 793 C3' T B 7 OK 791 794 795 813 C3' C B 8 OK 811 814 815 832 C3' C B 9 OK 830 833 834 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 480 C4' G B -9 OK 482 479 481 502 C4' G B -8 OK 504 501 503 524 C4' A B -7 OK 526 523 525 545 C4' G B -6 OK 547 544 546 567 C4' A B -5 OK 569 566 568 588 C4' T B -4 OK 590 587 589 608 C4' G B -3 OK 610 607 609 630 C4' A B -2 OK 632 629 631 651 C4' C B -1 OK 653 650 652 670 C4' G B 1 OK 672 669 671 692 C4' T B 2 OK 694 691 693 712 C4' C B 3 OK 714 711 713 731 C4' A B 4 OK 733 730 732 752 C4' T B 5 OK 754 751 753 772 C4' C B 6 OK 774 771 773 791 C4' T B 7 OK 793 790 792 811 C4' C B 8 OK 813 810 812 830 C4' C B 9 OK 832 829 831 480 C4' G B -9 OK 482 479 481 502 C4' G B -8 OK 504 501 503 524 C4' A B -7 OK 526 523 525 545 C4' G B -6 OK 547 544 546 567 C4' A B -5 OK 569 566 568 588 C4' T B -4 OK 590 587 589 608 C4' G B -3 OK 610 607 609 630 C4' A B -2 OK 632 629 631 651 C4' C B -1 OK 653 650 652 670 C4' G B 1 OK 672 669 671 692 C4' T B 2 OK 694 691 693 712 C4' C B 3 OK 714 711 713 731 C4' A B 4 OK 733 730 732 752 C4' T B 5 OK 754 751 753 772 C4' C B 6 OK 774 771 773 791 C4' T B 7 OK 793 790 792 811 C4' C B 8 OK 813 810 812 830 C4' C B 9 OK 832 829 831 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 479 C5' G B -9 478 480 501 C5' G B -8 500 502 523 C5' A B -7 522 524 544 C5' G B -6 543 545 566 C5' A B -5 565 567 587 C5' T B -4 586 588 607 C5' G B -3 606 608 629 C5' A B -2 628 630 650 C5' C B -1 649 651 669 C5' G B 1 668 670 691 C5' T B 2 690 692 711 C5' C B 3 710 712 730 C5' A B 4 729 731 751 C5' T B 5 750 752 771 C5' C B 6 770 772 790 C5' T B 7 789 791 810 C5' C B 8 809 811 829 C5' C B 9 828 830 479 C5' G B -9 478 480 501 C5' G B -8 500 502 523 C5' A B -7 522 524 544 C5' G B -6 543 545 566 C5' A B -5 565 567 587 C5' T B -4 586 588 607 C5' G B -3 606 608 629 C5' A B -2 628 630 650 C5' C B -1 649 651 669 C5' G B 1 668 670 691 C5' T B 2 690 692 711 C5' C B 3 710 712 730 C5' A B 4 729 731 751 C5' T B 5 750 752 771 C5' C B 6 770 772 790 C5' T B 7 789 791 810 C5' C B 8 809 811 829 C5' C B 9 828 830 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 497 P G B -8 OK OK 483 498 499 500 519 P A B -7 OK OK 505 520 521 522 540 P G B -6 OK OK 527 541 542 543 562 P A B -5 OK OK 548 563 564 565 583 P T B -4 OK OK 570 584 585 586 603 P G B -3 OK OK 591 604 605 606 625 P A B -2 OK OK 611 626 627 628 646 P C B -1 OK OK 633 647 648 649 665 P G B 1 OK OK 654 666 667 668 687 P T B 2 OK OK 673 688 689 690 707 P C B 3 OK OK 695 708 709 710 726 P A B 4 OK OK 715 727 728 729 747 P T B 5 OK OK 734 748 749 750 767 P C B 6 OK OK 755 768 769 770 786 P T B 7 OK OK 775 787 788 789 806 P C B 8 OK OK 794 807 808 809 825 P C B 9 OK OK 814 826 827 828 497 P G B -8 OK OK 483 498 499 500 519 P A B -7 OK OK 505 520 521 522 540 P G B -6 OK OK 527 541 542 543 562 P A B -5 OK OK 548 563 564 565 583 P T B -4 OK OK 570 584 585 586 603 P G B -3 OK OK 591 604 605 606 625 P A B -2 OK OK 611 626 627 628 646 P C B -1 OK OK 633 647 648 649 665 P G B 1 OK OK 654 666 667 668 687 P T B 2 OK OK 673 688 689 690 707 P C B 3 OK OK 695 708 709 710 726 P A B 4 OK OK 715 727 728 729 747 P T B 5 OK OK 734 748 749 750 767 P C B 6 OK OK 755 768 769 770 786 P T B 7 OK OK 775 787 788 789 806 P C B 8 OK OK 794 807 808 809 825 P C B 9 OK OK 814 826 827 828 ---------------------------------------------------------------------------------