ID code: '1QRH' 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' --------------------------------------------------------------------------------- 2557 C1' C M 2 beta 2553 2558 2556 2578 C1' G M 3 beta 2574 2579 2577 2603 C1' C M 4 beta 2599 2604 2602 2624 C1' G M 5 beta 2620 2625 2623 2649 C1' A M 6 beta 2645 2650 2648 2672 C1' A M 7 beta 2668 2673 2671 2695 C1' T M 8 beta 2691 2696 2694 2716 C1' T M 9 beta 2712 2717 2715 2737 C1' C M 10 beta 2733 2738 2736 2758 C1' G M 11 beta 2754 2759 2757 2783 C1' C M 12 beta 2779 2784 2782 2804 C1' G M 13 beta 2800 2805 2803 5378 C1' C C 2 beta 5374 5379 5377 5399 C1' G C 3 beta 5395 5400 5398 5424 C1' C C 4 beta 5420 5425 5423 5445 C1' G C 5 beta 5441 5446 5444 5470 C1' A C 6 beta 5466 5471 5469 5493 C1' A C 7 beta 5489 5494 5492 5516 C1' T C 8 beta 5512 5517 5515 5537 C1' T C 9 beta 5533 5538 5536 5558 C1' C C 10 beta 5554 5559 5557 5579 C1' G C 11 beta 5575 5580 5578 5604 C1' C C 12 beta 5600 5605 5603 5625 C1' G C 13 beta 5621 5626 5624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2556 C2' C M 2 2557 2554 2577 C2' G M 3 2578 2575 2602 C2' C M 4 2603 2600 2623 C2' G M 5 2624 2621 2648 C2' A M 6 2649 2646 2671 C2' A M 7 2672 2669 2694 C2' T M 8 2695 2692 2715 C2' T M 9 2716 2713 2736 C2' C M 10 2737 2734 2757 C2' G M 11 2758 2755 2782 C2' C M 12 2783 2780 2803 C2' G M 13 2804 2801 5377 C2' C C 2 5378 5375 5398 C2' G C 3 5399 5396 5423 C2' C C 4 5424 5421 5444 C2' G C 5 5445 5442 5469 C2' A C 6 5470 5467 5492 C2' A C 7 5493 5490 5515 C2' T C 8 5516 5513 5536 C2' T C 9 5537 5534 5557 C2' C C 10 5558 5555 5578 C2' G C 11 5579 5576 5603 C2' C C 12 5604 5601 5624 C2' G C 13 5625 5622 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2554 C3' C M 2 OK 2552 2555 2556 2575 C3' G M 3 OK 2573 2576 2577 2600 C3' C M 4 OK 2598 2601 2602 2621 C3' G M 5 OK 2619 2622 2623 2646 C3' A M 6 OK 2644 2647 2648 2669 C3' A M 7 OK 2667 2670 2671 2692 C3' T M 8 OK 2690 2693 2694 2713 C3' T M 9 OK 2711 2714 2715 2734 C3' C M 10 OK 2732 2735 2736 2755 C3' G M 11 OK 2753 2756 2757 2780 C3' C M 12 OK 2778 2781 2782 2801 C3' G M 13 OK 2799 2802 2803 5375 C3' C C 2 OK 5373 5376 5377 5396 C3' G C 3 OK 5394 5397 5398 5421 C3' C C 4 OK 5419 5422 5423 5442 C3' G C 5 OK 5440 5443 5444 5467 C3' A C 6 OK 5465 5468 5469 5490 C3' A C 7 OK 5488 5491 5492 5513 C3' T C 8 OK 5511 5514 5515 5534 C3' T C 9 OK 5532 5535 5536 5555 C3' C C 10 OK 5553 5556 5557 5576 C3' G C 11 OK 5574 5577 5578 5601 C3' C C 12 OK 5599 5602 5603 5622 C3' G C 13 OK 5620 5623 5624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2552 C4' C M 2 OK 2554 2551 2553 2573 C4' G M 3 OK 2575 2572 2574 2598 C4' C M 4 OK 2600 2597 2599 2619 C4' G M 5 OK 2621 2618 2620 2644 C4' A M 6 OK 2646 2643 2645 2667 C4' A M 7 OK 2669 2666 2668 2690 C4' T M 8 OK 2692 2689 2691 2711 C4' T M 9 OK 2713 2710 2712 2732 C4' C M 10 OK 2734 2731 2733 2753 C4' G M 11 OK 2755 2752 2754 2778 C4' C M 12 OK 2780 2777 2779 2799 C4' G M 13 OK 2801 2798 2800 5373 C4' C C 2 OK 5375 5372 5374 5394 C4' G C 3 OK 5396 5393 5395 5419 C4' C C 4 OK 5421 5418 5420 5440 C4' G C 5 OK 5442 5439 5441 5465 C4' A C 6 OK 5467 5464 5466 5488 C4' A C 7 OK 5490 5487 5489 5511 C4' T C 8 OK 5513 5510 5512 5532 C4' T C 9 OK 5534 5531 5533 5553 C4' C C 10 OK 5555 5552 5554 5574 C4' G C 11 OK 5576 5573 5575 5599 C4' C C 12 OK 5601 5598 5600 5620 C4' G C 13 OK 5622 5619 5621 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2551 C5' C M 2 2550 2552 2572 C5' G M 3 2571 2573 2597 C5' C M 4 2596 2598 2618 C5' G M 5 2617 2619 2643 C5' A M 6 2642 2644 2666 C5' A M 7 2665 2667 2689 C5' T M 8 2688 2690 2710 C5' T M 9 2709 2711 2731 C5' C M 10 2730 2732 2752 C5' G M 11 2751 2753 2777 C5' C M 12 2776 2778 2798 C5' G M 13 2797 2799 5372 C5' C C 2 5371 5373 5393 C5' G C 3 5392 5394 5418 C5' C C 4 5417 5419 5439 C5' G C 5 5438 5440 5464 C5' A C 6 5463 5465 5487 C5' A C 7 5486 5488 5510 C5' T C 8 5509 5511 5531 C5' T C 9 5530 5532 5552 C5' C C 10 5551 5553 5573 C5' G C 11 5572 5574 5598 C5' C C 12 5597 5599 5619 C5' G C 13 5618 5620 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2568 P G M 3 distorted distorted 2555 2569 2570 2571 2593 P C M 4 distorted distorted 2576 2594 2595 2596 2614 P G M 5 OK OK 2601 2615 2616 2617 2639 P A M 6 distorted distorted 2622 2640 2641 2642 2662 P A M 7 distorted distorted 2647 2663 2664 2665 2685 P T M 8 distorted distorted 2670 2686 2687 2688 2706 P T M 9 distorted distorted 2693 2707 2708 2709 2727 P C M 10 OK OK 2714 2728 2729 2730 2748 P G M 11 distorted distorted 2735 2749 2750 2751 2773 P C M 12 distorted distorted 2756 2774 2775 2776 2794 P G M 13 distorted distorted 2781 2795 2796 2797 5389 P G C 3 distorted distorted 5376 5390 5391 5392 5414 P C C 4 distorted distorted 5397 5415 5416 5417 5435 P G C 5 OK OK 5422 5436 5437 5438 5460 P A C 6 distorted distorted 5443 5461 5462 5463 5483 P A C 7 distorted distorted 5468 5484 5485 5486 5506 P T C 8 distorted distorted 5491 5507 5508 5509 5527 P T C 9 distorted distorted 5514 5528 5529 5530 5548 P C C 10 OK OK 5535 5549 5550 5551 5569 P G C 11 distorted distorted 5556 5570 5571 5572 5594 P C C 12 distorted distorted 5577 5595 5596 5597 5615 P G C 13 distorted distorted 5602 5616 5617 5618 ---------------------------------------------------------------------------------