ID code: '5L2L' 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' --------------------------------------------------------------------------------- 2319 C1' A C 3 alpha beta 2314 2336 2320 2317 2352 C1' A C 4 alpha beta 2347 2369 2353 2350 2385 C1' A C 5 alpha beta 2380 2402 2386 2383 2418 C1' A C 6 alpha beta 2413 2435 2419 2416 2451 C1' A C 7 alpha beta 2446 2468 2452 2449 2484 C1' A C 8 alpha beta 2479 2501 2485 2482 2517 C1' A C 9 alpha beta 2512 2534 2518 2515 2550 C1' A C 10 alpha beta 2545 2567 2551 2548 2583 C1' A C 11 alpha beta 2578 2600 2584 2581 2616 C1' G C 12 alpha beta 2611 2635 2617 2614 2652 C1' A D 2 alpha beta 2647 2669 2653 2650 2685 C1' A D 3 alpha beta 2680 2702 2686 2683 2718 C1' A D 4 alpha beta 2713 2735 2719 2716 2751 C1' A D 5 alpha beta 2746 2768 2752 2749 2784 C1' A D 6 alpha beta 2779 2801 2785 2782 2817 C1' A D 7 alpha beta 2812 2834 2818 2815 2916 C1' A D 9 alpha beta 2911 2933 2917 2914 2949 C1' A D 10 alpha beta 2944 2966 2950 2947 2982 C1' A D 11 alpha beta 2977 2999 2983 2980 3015 C1' G D 12 alpha beta 3010 3034 3016 3013 5376 C1' A G 3 alpha beta 5371 5393 5377 5374 5409 C1' A G 4 alpha beta 5404 5426 5410 5407 5442 C1' A G 5 alpha beta 5437 5459 5443 5440 5475 C1' A G 6 alpha beta 5470 5492 5476 5473 5508 C1' A G 7 alpha beta 5503 5525 5509 5506 5607 C1' A G 9 alpha beta 5602 5624 5608 5605 5640 C1' A G 10 alpha beta 5635 5657 5641 5638 5673 C1' A G 11 alpha beta 5668 5690 5674 5671 5706 C1' G G 12 alpha beta 5701 5725 5707 5704 5742 C1' A H 3 alpha beta 5737 5759 5743 5740 5775 C1' A H 4 alpha beta 5770 5792 5776 5773 5808 C1' A H 5 alpha beta 5803 5825 5809 5806 5841 C1' A H 6 alpha beta 5836 5858 5842 5839 5874 C1' A H 7 alpha beta 5869 5891 5875 5872 5973 C1' A H 9 alpha beta 5968 5990 5974 5971 6006 C1' A H 10 alpha beta 6001 6023 6007 6004 6039 C1' A H 11 alpha beta 6034 6056 6040 6037 6072 C1' G H 12 alpha beta 6067 6091 6073 6070 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2317 C2' A C 3 OK OK 2319 2315 2334 2318 2350 C2' A C 4 OK OK 2352 2348 2367 2351 2383 C2' A C 5 OK OK 2385 2381 2400 2384 2416 C2' A C 6 OK OK 2418 2414 2433 2417 2449 C2' A C 7 OK OK 2451 2447 2466 2450 2482 C2' A C 8 OK OK 2484 2480 2499 2483 2515 C2' A C 9 OK OK 2517 2513 2532 2516 2548 C2' A C 10 OK OK 2550 2546 2565 2549 2581 C2' A C 11 OK OK 2583 2579 2598 2582 2614 C2' G C 12 OK OK 2616 2612 2633 2615 2650 C2' A D 2 OK OK 2652 2648 2667 2651 2683 C2' A D 3 OK OK 2685 2681 2700 2684 2716 C2' A D 4 OK OK 2718 2714 2733 2717 2749 C2' A D 5 OK OK 2751 2747 2766 2750 2782 C2' A D 6 OK OK 2784 2780 2799 2783 2815 C2' A D 7 OK OK 2817 2813 2832 2816 2914 C2' A D 9 OK OK 2916 2912 2931 2915 2947 C2' A D 10 OK OK 2949 2945 2964 2948 2980 C2' A D 11 OK OK 2982 2978 2997 2981 3013 C2' G D 12 OK OK 3015 3011 3032 3014 5374 C2' A G 3 OK OK 5376 5372 5391 5375 5407 C2' A G 4 OK OK 5409 5405 5424 5408 5440 C2' A G 5 OK OK 5442 5438 5457 5441 5473 C2' A G 6 OK OK 5475 5471 5490 5474 5506 C2' A G 7 OK OK 5508 5504 5523 5507 5605 C2' A G 9 OK OK 5607 5603 5622 5606 5638 C2' A G 10 OK OK 5640 5636 5655 5639 5671 C2' A G 11 OK OK 5673 5669 5688 5672 5704 C2' G G 12 OK OK 5706 5702 5723 5705 5740 C2' A H 3 OK OK 5742 5738 5757 5741 5773 C2' A H 4 OK OK 5775 5771 5790 5774 5806 C2' A H 5 OK OK 5808 5804 5823 5807 5839 C2' A H 6 OK OK 5841 5837 5856 5840 5872 C2' A H 7 OK OK 5874 5870 5889 5873 5971 C2' A H 9 OK OK 5973 5969 5988 5972 6004 C2' A H 10 OK OK 6006 6002 6021 6005 6037 C2' A H 11 OK OK 6039 6035 6054 6038 6070 C2' G H 12 OK OK 6072 6068 6089 6071 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2315 C3' A C 3 OK OK 2313 2333 2316 2317 2348 C3' A C 4 OK OK 2346 2366 2349 2350 2381 C3' A C 5 OK OK 2379 2399 2382 2383 2414 C3' A C 6 OK OK 2412 2432 2415 2416 2447 C3' A C 7 OK OK 2445 2465 2448 2449 2480 C3' A C 8 OK OK 2478 2498 2481 2482 2513 C3' A C 9 OK OK 2511 2531 2514 2515 2546 C3' A C 10 OK OK 2544 2564 2547 2548 2579 C3' A C 11 OK OK 2577 2597 2580 2581 2612 C3' G C 12 OK OK 2610 2631 2613 2614 2648 C3' A D 2 OK OK 2646 2666 2649 2650 2681 C3' A D 3 OK OK 2679 2699 2682 2683 2714 C3' A D 4 OK OK 2712 2732 2715 2716 2747 C3' A D 5 OK OK 2745 2765 2748 2749 2780 C3' A D 6 OK OK 2778 2798 2781 2782 2813 C3' A D 7 OK OK 2811 2831 2814 2815 2912 C3' A D 9 OK OK 2910 2930 2913 2914 2945 C3' A D 10 OK OK 2943 2963 2946 2947 2978 C3' A D 11 OK OK 2976 2996 2979 2980 3011 C3' G D 12 OK OK 3009 3030 3012 3013 5372 C3' A G 3 OK OK 5370 5390 5373 5374 5405 C3' A G 4 OK OK 5403 5423 5406 5407 5438 C3' A G 5 OK OK 5436 5456 5439 5440 5471 C3' A G 6 OK OK 5469 5489 5472 5473 5504 C3' A G 7 OK OK 5502 5522 5505 5506 5603 C3' A G 9 OK OK 5601 5621 5604 5605 5636 C3' A G 10 OK OK 5634 5654 5637 5638 5669 C3' A G 11 OK OK 5667 5687 5670 5671 5702 C3' G G 12 OK OK 5700 5721 5703 5704 5738 C3' A H 3 OK OK 5736 5756 5739 5740 5771 C3' A H 4 OK OK 5769 5789 5772 5773 5804 C3' A H 5 OK OK 5802 5822 5805 5806 5837 C3' A H 6 OK OK 5835 5855 5838 5839 5870 C3' A H 7 OK OK 5868 5888 5871 5872 5969 C3' A H 9 OK OK 5967 5987 5970 5971 6002 C3' A H 10 OK OK 6000 6020 6003 6004 6035 C3' A H 11 OK OK 6033 6053 6036 6037 6068 C3' G H 12 OK OK 6066 6087 6069 6070 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2313 C4' A C 3 OK OK 2315 2332 2312 2314 2346 C4' A C 4 OK OK 2348 2365 2345 2347 2379 C4' A C 5 OK OK 2381 2398 2378 2380 2412 C4' A C 6 OK OK 2414 2431 2411 2413 2445 C4' A C 7 OK OK 2447 2464 2444 2446 2478 C4' A C 8 OK OK 2480 2497 2477 2479 2511 C4' A C 9 OK OK 2513 2530 2510 2512 2544 C4' A C 10 OK OK 2546 2563 2543 2545 2577 C4' A C 11 OK OK 2579 2596 2576 2578 2610 C4' G C 12 OK OK 2612 2630 2609 2611 2646 C4' A D 2 OK OK 2648 2665 2645 2647 2679 C4' A D 3 OK OK 2681 2698 2678 2680 2712 C4' A D 4 OK OK 2714 2731 2711 2713 2745 C4' A D 5 OK OK 2747 2764 2744 2746 2778 C4' A D 6 OK OK 2780 2797 2777 2779 2811 C4' A D 7 OK OK 2813 2830 2810 2812 2910 C4' A D 9 OK OK 2912 2929 2909 2911 2943 C4' A D 10 OK OK 2945 2962 2942 2944 2976 C4' A D 11 OK OK 2978 2995 2975 2977 3009 C4' G D 12 OK OK 3011 3029 3008 3010 5370 C4' A G 3 OK OK 5372 5389 5369 5371 5403 C4' A G 4 OK OK 5405 5422 5402 5404 5436 C4' A G 5 OK OK 5438 5455 5435 5437 5469 C4' A G 6 OK OK 5471 5488 5468 5470 5502 C4' A G 7 OK OK 5504 5521 5501 5503 5601 C4' A G 9 OK OK 5603 5620 5600 5602 5634 C4' A G 10 OK OK 5636 5653 5633 5635 5667 C4' A G 11 OK OK 5669 5686 5666 5668 5700 C4' G G 12 OK OK 5702 5720 5699 5701 5736 C4' A H 3 OK OK 5738 5755 5735 5737 5769 C4' A H 4 OK OK 5771 5788 5768 5770 5802 C4' A H 5 OK OK 5804 5821 5801 5803 5835 C4' A H 6 OK OK 5837 5854 5834 5836 5868 C4' A H 7 OK OK 5870 5887 5867 5869 5967 C4' A H 9 OK OK 5969 5986 5966 5968 6000 C4' A H 10 OK OK 6002 6019 5999 6001 6033 C4' A H 11 OK OK 6035 6052 6032 6034 6066 C4' G H 12 OK OK 6068 6086 6065 6067 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2312 C5' A C 3 OK OK 2311 2330 2331 2313 2345 C5' A C 4 OK OK 2344 2363 2364 2346 2378 C5' A C 5 OK OK 2377 2396 2397 2379 2411 C5' A C 6 OK OK 2410 2429 2430 2412 2444 C5' A C 7 OK OK 2443 2462 2463 2445 2477 C5' A C 8 OK OK 2476 2495 2496 2478 2510 C5' A C 9 OK OK 2509 2528 2529 2511 2543 C5' A C 10 OK OK 2542 2561 2562 2544 2576 C5' A C 11 OK OK 2575 2594 2595 2577 2609 C5' G C 12 OK OK 2608 2628 2629 2610 2645 C5' A D 2 OK OK 2644 2663 2664 2646 2678 C5' A D 3 OK OK 2677 2696 2697 2679 2711 C5' A D 4 OK OK 2710 2729 2730 2712 2744 C5' A D 5 OK OK 2743 2762 2763 2745 2777 C5' A D 6 OK OK 2776 2795 2796 2778 2810 C5' A D 7 OK OK 2809 2828 2829 2811 2909 C5' A D 9 OK OK 2908 2927 2928 2910 2942 C5' A D 10 OK OK 2941 2960 2961 2943 2975 C5' A D 11 OK OK 2974 2993 2994 2976 3008 C5' G D 12 OK OK 3007 3027 3028 3009 5369 C5' A G 3 OK OK 5368 5387 5388 5370 5402 C5' A G 4 OK OK 5401 5420 5421 5403 5435 C5' A G 5 OK OK 5434 5453 5454 5436 5468 C5' A G 6 OK OK 5467 5486 5487 5469 5501 C5' A G 7 OK OK 5500 5519 5520 5502 5600 C5' A G 9 OK OK 5599 5618 5619 5601 5633 C5' A G 10 OK OK 5632 5651 5652 5634 5666 C5' A G 11 OK OK 5665 5684 5685 5667 5699 C5' G G 12 OK OK 5698 5718 5719 5700 5735 C5' A H 3 OK OK 5734 5753 5754 5736 5768 C5' A H 4 OK OK 5767 5786 5787 5769 5801 C5' A H 5 OK OK 5800 5819 5820 5802 5834 C5' A H 6 OK OK 5833 5852 5853 5835 5867 C5' A H 7 OK OK 5866 5885 5886 5868 5966 C5' A H 9 OK OK 5965 5984 5985 5967 5999 C5' A H 10 OK OK 5998 6017 6018 6000 6032 C5' A H 11 OK OK 6031 6050 6051 6033 6065 C5' G H 12 OK OK 6064 6084 6085 6066 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2308 P A C 3 distorted distorted 2309 2310 2311 2341 P A C 4 distorted distorted 2316 2342 2343 2344 2374 P A C 5 distorted distorted 2349 2375 2376 2377 2407 P A C 6 distorted distorted 2382 2408 2409 2410 2440 P A C 7 distorted distorted 2415 2441 2442 2443 2473 P A C 8 distorted distorted 2448 2474 2475 2476 2506 P A C 9 distorted distorted 2481 2507 2508 2509 2539 P A C 10 distorted distorted 2514 2540 2541 2542 2572 P A C 11 distorted distorted 2547 2573 2574 2575 2605 P G C 12 distorted distorted 2580 2606 2607 2608 2641 P A D 2 OK OK 2642 2643 2644 2674 P A D 3 distorted distorted 2649 2675 2676 2677 2707 P A D 4 distorted distorted 2682 2708 2709 2710 2740 P A D 5 distorted distorted 2715 2741 2742 2743 2773 P A D 6 distorted distorted 2748 2774 2775 2776 2806 P A D 7 distorted distorted 2781 2807 2808 2809 2839 P A D 8 2814 2840 P A D 8 2814 2905 P A D 9 distorted distorted 2906 2907 2908 2938 P A D 10 distorted distorted 2913 2939 2940 2941 2971 P A D 11 distorted distorted 2946 2972 2973 2974 3004 P G D 12 distorted distorted 2979 3005 3006 3007 5365 P A G 3 distorted distorted 5366 5367 5368 5398 P A G 4 distorted distorted 5373 5399 5400 5401 5431 P A G 5 distorted distorted 5406 5432 5433 5434 5464 P A G 6 distorted distorted 5439 5465 5466 5467 5497 P A G 7 distorted distorted 5472 5498 5499 5500 5530 P A G 8 5505 5531 P A G 8 5505 5596 P A G 9 distorted distorted 5597 5598 5599 5629 P A G 10 distorted distorted 5604 5630 5631 5632 5662 P A G 11 distorted distorted 5637 5663 5664 5665 5695 P G G 12 distorted distorted 5670 5696 5697 5698 5731 P A H 3 OK OK 5732 5733 5734 5764 P A H 4 distorted distorted 5739 5765 5766 5767 5797 P A H 5 distorted distorted 5772 5798 5799 5800 5830 P A H 6 distorted distorted 5805 5831 5832 5833 5863 P A H 7 distorted distorted 5838 5864 5865 5866 5896 P A H 8 5871 5897 P A H 8 5871 5962 P A H 9 distorted distorted 5963 5964 5965 5995 P A H 10 distorted distorted 5970 5996 5997 5998 6028 P A H 11 distorted distorted 6003 6029 6030 6031 6061 P G H 12 distorted distorted 6036 6062 6063 6064 ---------------------------------------------------------------------------------