ID code: '4GCW' 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' --------------------------------------------------------------------------------- 2414 C1' G B 1 beta 2409 2415 2412 2437 C1' C B 2 beta 2432 2438 2435 2457 C1' U B 3 beta 2452 2458 2455 2477 C1' U B 4 beta 2472 2478 2475 2497 C1' C B 5 beta 2492 2498 2495 2517 C1' C B 6 beta 2512 2518 2515 2537 C1' A B 7 beta 2532 2538 2535 2559 C1' U B 8 beta 2554 2560 2557 2579 C1' A B 9 beta 2574 2580 2577 2601 C1' G B 10 beta 2596 2602 2599 2624 C1' C B 11 beta 2619 2625 2622 2644 C1' U B 12 beta 2639 2645 2642 2664 C1' C B 13 beta 2659 2665 2662 2684 C1' A B 14 beta 2679 2685 2682 2706 C1' G B 15 beta 2701 2707 2704 2729 C1' C B 16 beta 2724 2730 2727 2749 C1' A B 17 beta 2744 2750 2747 2771 C1' G B 18 beta 2766 2772 2769 2794 C1' G B 19 beta 2789 2795 2792 2817 C1' U B 20 beta 2812 2818 2815 2837 C1' A B 21 beta 2832 2838 2835 2859 C1' G B 22 beta 2854 2860 2857 2882 C1' A B 23 beta 2877 2883 2880 2904 C1' G B 24 beta 2899 2905 2902 2927 C1' C B 25 beta 2922 2928 2925 2947 C1' A B 26 beta 2942 2948 2945 2965 C1' G B 46 beta 2960 2966 2963 2988 C1' U B 47 beta 2983 2989 2986 3008 C1' C B 48 beta 3003 3009 3006 3028 C1' A B 49 beta 3023 3029 3026 3050 C1' G B 50 beta 3045 3051 3048 3073 C1' C B 51 beta 3068 3074 3071 3093 C1' G B 52 beta 3088 3094 3091 3116 C1' G B 53 beta 3111 3117 3114 3139 C1' U B 54 beta 3134 3140 3137 3159 C1' U B 55 beta 3154 3160 3157 3179 C1' C B 56 beta 3174 3180 3177 3199 C1' G B 57 beta 3194 3200 3197 3222 C1' A B 58 beta 3217 3223 3220 3244 C1' G B 59 beta 3239 3245 3242 3267 C1' C B 60 beta 3262 3268 3265 3287 C1' C B 61 beta 3282 3288 3285 3307 C1' C B 62 beta 3302 3308 3305 3327 C1' G B 63 beta 3322 3328 3325 3350 C1' C B 64 beta 3345 3351 3348 3370 C1' U B 65 beta 3365 3371 3368 3390 C1' U B 66 beta 3385 3391 3388 3410 C1' G B 67 beta 3405 3411 3408 3433 C1' G B 68 beta 3428 3434 3431 3456 C1' A B 69 beta 3451 3457 3454 3478 C1' A B 70 beta 3473 3479 3476 3500 C1' G B 71 beta 3495 3501 3498 3523 C1' C B 72 beta 3518 3524 3521 3540 C1' OMU B 73 beta 3547 3532 3541 3561 C1' OMU B 74 beta 3568 3553 3562 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2412 C2' G B 1 OK 2414 2410 2413 2435 C2' C B 2 OK 2437 2433 2436 2455 C2' U B 3 OK 2457 2453 2456 2475 C2' U B 4 OK 2477 2473 2476 2495 C2' C B 5 OK 2497 2493 2496 2515 C2' C B 6 OK 2517 2513 2516 2535 C2' A B 7 OK 2537 2533 2536 2557 C2' U B 8 OK 2559 2555 2558 2577 C2' A B 9 OK 2579 2575 2578 2599 C2' G B 10 OK 2601 2597 2600 2622 C2' C B 11 OK 2624 2620 2623 2642 C2' U B 12 OK 2644 2640 2643 2662 C2' C B 13 OK 2664 2660 2663 2682 C2' A B 14 OK 2684 2680 2683 2704 C2' G B 15 OK 2706 2702 2705 2727 C2' C B 16 OK 2729 2725 2728 2747 C2' A B 17 OK 2749 2745 2748 2769 C2' G B 18 OK 2771 2767 2770 2792 C2' G B 19 OK 2794 2790 2793 2815 C2' U B 20 OK 2817 2813 2816 2835 C2' A B 21 OK 2837 2833 2836 2857 C2' G B 22 OK 2859 2855 2858 2880 C2' A B 23 OK 2882 2878 2881 2902 C2' G B 24 OK 2904 2900 2903 2925 C2' C B 25 OK 2927 2923 2926 2945 C2' A B 26 OK 2947 2943 2946 2963 C2' G B 46 OK 2965 2961 2964 2986 C2' U B 47 OK 2988 2984 2987 3006 C2' C B 48 OK 3008 3004 3007 3026 C2' A B 49 OK 3028 3024 3027 3048 C2' G B 50 OK 3050 3046 3049 3071 C2' C B 51 OK 3073 3069 3072 3091 C2' G B 52 OK 3093 3089 3092 3114 C2' G B 53 OK 3116 3112 3115 3137 C2' U B 54 OK 3139 3135 3138 3157 C2' U B 55 OK 3159 3155 3158 3177 C2' C B 56 OK 3179 3175 3178 3197 C2' G B 57 OK 3199 3195 3198 3220 C2' A B 58 OK 3222 3218 3221 3242 C2' G B 59 OK 3244 3240 3243 3265 C2' C B 60 OK 3267 3263 3266 3285 C2' C B 61 OK 3287 3283 3286 3305 C2' C B 62 OK 3307 3303 3306 3325 C2' G B 63 OK 3327 3323 3326 3348 C2' C B 64 OK 3350 3346 3349 3368 C2' U B 65 OK 3370 3366 3369 3388 C2' U B 66 OK 3390 3386 3389 3408 C2' G B 67 OK 3410 3406 3409 3431 C2' G B 68 OK 3433 3429 3432 3454 C2' A B 69 OK 3456 3452 3455 3476 C2' A B 70 OK 3478 3474 3477 3498 C2' G B 71 OK 3500 3496 3499 3521 C2' C B 72 OK 3523 3519 3522 3541 C2' OMU B 73 OK 3540 3544 3542 3562 C2' OMU B 74 OK 3561 3565 3563 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2410 C3' G B 1 OK 2408 2411 2412 2433 C3' C B 2 OK 2431 2434 2435 2453 C3' U B 3 OK 2451 2454 2455 2473 C3' U B 4 OK 2471 2474 2475 2493 C3' C B 5 OK 2491 2494 2495 2513 C3' C B 6 OK 2511 2514 2515 2533 C3' A B 7 OK 2531 2534 2535 2555 C3' U B 8 OK 2553 2556 2557 2575 C3' A B 9 OK 2573 2576 2577 2597 C3' G B 10 OK 2595 2598 2599 2620 C3' C B 11 OK 2618 2621 2622 2640 C3' U B 12 OK 2638 2641 2642 2660 C3' C B 13 OK 2658 2661 2662 2680 C3' A B 14 OK 2678 2681 2682 2702 C3' G B 15 OK 2700 2703 2704 2725 C3' C B 16 OK 2723 2726 2727 2745 C3' A B 17 OK 2743 2746 2747 2767 C3' G B 18 OK 2765 2768 2769 2790 C3' G B 19 OK 2788 2791 2792 2813 C3' U B 20 OK 2811 2814 2815 2833 C3' A B 21 OK 2831 2834 2835 2855 C3' G B 22 OK 2853 2856 2857 2878 C3' A B 23 OK 2876 2879 2880 2900 C3' G B 24 OK 2898 2901 2902 2923 C3' C B 25 OK 2921 2924 2925 2943 C3' A B 26 OK 2941 2944 2945 2961 C3' G B 46 OK 2959 2962 2963 2984 C3' U B 47 OK 2982 2985 2986 3004 C3' C B 48 OK 3002 3005 3006 3024 C3' A B 49 OK 3022 3025 3026 3046 C3' G B 50 OK 3044 3047 3048 3069 C3' C B 51 OK 3067 3070 3071 3089 C3' G B 52 OK 3087 3090 3091 3112 C3' G B 53 OK 3110 3113 3114 3135 C3' U B 54 OK 3133 3136 3137 3155 C3' U B 55 OK 3153 3156 3157 3175 C3' C B 56 OK 3173 3176 3177 3195 C3' G B 57 OK 3193 3196 3197 3218 C3' A B 58 OK 3216 3219 3220 3240 C3' G B 59 OK 3238 3241 3242 3263 C3' C B 60 OK 3261 3264 3265 3283 C3' C B 61 OK 3281 3284 3285 3303 C3' C B 62 OK 3301 3304 3305 3323 C3' G B 63 OK 3321 3324 3325 3346 C3' C B 64 OK 3344 3347 3348 3366 C3' U B 65 OK 3364 3367 3368 3386 C3' U B 66 OK 3384 3387 3388 3406 C3' G B 67 OK 3404 3407 3408 3429 C3' G B 68 OK 3427 3430 3431 3452 C3' A B 69 OK 3450 3453 3454 3474 C3' A B 70 OK 3472 3475 3476 3496 C3' G B 71 OK 3494 3497 3498 3519 C3' C B 72 OK 3517 3520 3521 3544 C3' OMU B 73 OK 3545 3546 3541 3565 C3' OMU B 74 OK 3566 3567 3562 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2408 C4' G B 1 OK 2410 2407 2409 2431 C4' C B 2 OK 2433 2430 2432 2451 C4' U B 3 OK 2453 2450 2452 2471 C4' U B 4 OK 2473 2470 2472 2491 C4' C B 5 OK 2493 2490 2492 2511 C4' C B 6 OK 2513 2510 2512 2531 C4' A B 7 OK 2533 2530 2532 2553 C4' U B 8 OK 2555 2552 2554 2573 C4' A B 9 OK 2575 2572 2574 2595 C4' G B 10 OK 2597 2594 2596 2618 C4' C B 11 OK 2620 2617 2619 2638 C4' U B 12 OK 2640 2637 2639 2658 C4' C B 13 OK 2660 2657 2659 2678 C4' A B 14 OK 2680 2677 2679 2700 C4' G B 15 OK 2702 2699 2701 2723 C4' C B 16 OK 2725 2722 2724 2743 C4' A B 17 OK 2745 2742 2744 2765 C4' G B 18 OK 2767 2764 2766 2788 C4' G B 19 OK 2790 2787 2789 2811 C4' U B 20 OK 2813 2810 2812 2831 C4' A B 21 OK 2833 2830 2832 2853 C4' G B 22 OK 2855 2852 2854 2876 C4' A B 23 OK 2878 2875 2877 2898 C4' G B 24 OK 2900 2897 2899 2921 C4' C B 25 OK 2923 2920 2922 2941 C4' A B 26 OK 2943 2940 2942 2959 C4' G B 46 OK 2961 2958 2960 2982 C4' U B 47 OK 2984 2981 2983 3002 C4' C B 48 OK 3004 3001 3003 3022 C4' A B 49 OK 3024 3021 3023 3044 C4' G B 50 OK 3046 3043 3045 3067 C4' C B 51 OK 3069 3066 3068 3087 C4' G B 52 OK 3089 3086 3088 3110 C4' G B 53 OK 3112 3109 3111 3133 C4' U B 54 OK 3135 3132 3134 3153 C4' U B 55 OK 3155 3152 3154 3173 C4' C B 56 OK 3175 3172 3174 3193 C4' G B 57 OK 3195 3192 3194 3216 C4' A B 58 OK 3218 3215 3217 3238 C4' G B 59 OK 3240 3237 3239 3261 C4' C B 60 OK 3263 3260 3262 3281 C4' C B 61 OK 3283 3280 3282 3301 C4' C B 62 OK 3303 3300 3302 3321 C4' G B 63 OK 3323 3320 3322 3344 C4' C B 64 OK 3346 3343 3345 3364 C4' U B 65 OK 3366 3363 3365 3384 C4' U B 66 OK 3386 3383 3385 3404 C4' G B 67 OK 3406 3403 3405 3427 C4' G B 68 OK 3429 3426 3428 3450 C4' A B 69 OK 3452 3449 3451 3472 C4' A B 70 OK 3474 3471 3473 3494 C4' G B 71 OK 3496 3493 3495 3517 C4' C B 72 OK 3519 3516 3518 3545 C4' OMU B 73 OK 3544 3548 3547 3566 C4' OMU B 74 OK 3565 3569 3568 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2407 C5' G B 1 2406 2408 2430 C5' C B 2 2429 2431 2450 C5' U B 3 2449 2451 2470 C5' U B 4 2469 2471 2490 C5' C B 5 2489 2491 2510 C5' C B 6 2509 2511 2530 C5' A B 7 2529 2531 2552 C5' U B 8 2551 2553 2572 C5' A B 9 2571 2573 2594 C5' G B 10 2593 2595 2617 C5' C B 11 2616 2618 2637 C5' U B 12 2636 2638 2657 C5' C B 13 2656 2658 2677 C5' A B 14 2676 2678 2699 C5' G B 15 2698 2700 2722 C5' C B 16 2721 2723 2742 C5' A B 17 2741 2743 2764 C5' G B 18 2763 2765 2787 C5' G B 19 2786 2788 2810 C5' U B 20 2809 2811 2830 C5' A B 21 2829 2831 2852 C5' G B 22 2851 2853 2875 C5' A B 23 2874 2876 2897 C5' G B 24 2896 2898 2920 C5' C B 25 2919 2921 2940 C5' A B 26 2939 2941 2958 C5' G B 46 2959 2981 C5' U B 47 2980 2982 3001 C5' C B 48 3000 3002 3021 C5' A B 49 3020 3022 3043 C5' G B 50 3042 3044 3066 C5' C B 51 3065 3067 3086 C5' G B 52 3085 3087 3109 C5' G B 53 3108 3110 3132 C5' U B 54 3131 3133 3152 C5' U B 55 3151 3153 3172 C5' C B 56 3171 3173 3192 C5' G B 57 3191 3193 3215 C5' A B 58 3214 3216 3237 C5' G B 59 3236 3238 3260 C5' C B 60 3259 3261 3280 C5' C B 61 3279 3281 3300 C5' C B 62 3299 3301 3320 C5' G B 63 3319 3321 3343 C5' C B 64 3342 3344 3363 C5' U B 65 3362 3364 3383 C5' U B 66 3382 3384 3403 C5' G B 67 3402 3404 3426 C5' G B 68 3425 3427 3449 C5' A B 69 3448 3450 3471 C5' A B 70 3470 3472 3493 C5' G B 71 3492 3494 3516 C5' C B 72 3515 3517 3548 C5' OMU B 73 3549 3545 3569 C5' OMU B 74 3570 3566 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2403 P G B 1 distorted distorted 2404 2405 2406 2426 P C B 2 distorted distorted 2411 2427 2428 2429 2446 P U B 3 distorted distorted 2434 2447 2448 2449 2466 P U B 4 distorted distorted 2454 2467 2468 2469 2486 P C B 5 distorted distorted 2474 2487 2488 2489 2506 P C B 6 distorted distorted 2494 2507 2508 2509 2526 P A B 7 distorted distorted 2514 2527 2528 2529 2548 P U B 8 distorted distorted 2534 2549 2550 2551 2568 P A B 9 distorted distorted 2556 2569 2570 2571 2590 P G B 10 distorted distorted 2576 2591 2592 2593 2613 P C B 11 distorted distorted 2598 2614 2615 2616 2633 P U B 12 distorted distorted 2621 2634 2635 2636 2653 P C B 13 distorted distorted 2641 2654 2655 2656 2673 P A B 14 distorted distorted 2661 2674 2675 2676 2695 P G B 15 distorted distorted 2681 2696 2697 2698 2718 P C B 16 distorted distorted 2703 2719 2720 2721 2738 P A B 17 distorted distorted 2726 2739 2740 2741 2760 P G B 18 distorted distorted 2746 2761 2762 2763 2783 P G B 19 distorted distorted 2768 2784 2785 2786 2806 P U B 20 distorted distorted 2791 2807 2808 2809 2826 P A B 21 distorted distorted 2814 2827 2828 2829 2848 P G B 22 distorted distorted 2834 2849 2850 2851 2871 P A B 23 distorted distorted 2856 2872 2873 2874 2893 P G B 24 distorted distorted 2879 2894 2895 2896 2916 P C B 25 distorted distorted 2901 2917 2918 2919 2936 P A B 26 distorted distorted 2924 2937 2938 2939 2977 P U B 47 distorted distorted 2962 2978 2979 2980 2997 P C B 48 distorted distorted 2985 2998 2999 3000 3017 P A B 49 distorted distorted 3005 3018 3019 3020 3039 P G B 50 distorted distorted 3025 3040 3041 3042 3062 P C B 51 distorted distorted 3047 3063 3064 3065 3082 P G B 52 distorted distorted 3070 3083 3084 3085 3105 P G B 53 distorted distorted 3090 3106 3107 3108 3128 P U B 54 distorted distorted 3113 3129 3130 3131 3148 P U B 55 distorted distorted 3136 3149 3150 3151 3168 P C B 56 distorted distorted 3156 3169 3170 3171 3188 P G B 57 distorted distorted 3176 3189 3190 3191 3211 P A B 58 distorted distorted 3196 3212 3213 3214 3233 P G B 59 distorted distorted 3219 3234 3235 3236 3256 P C B 60 distorted distorted 3241 3257 3258 3259 3276 P C B 61 distorted distorted 3264 3277 3278 3279 3296 P C B 62 distorted distorted 3284 3297 3298 3299 3316 P G B 63 distorted distorted 3304 3317 3318 3319 3339 P C B 64 distorted distorted 3324 3340 3341 3342 3359 P U B 65 distorted distorted 3347 3360 3361 3362 3379 P U B 66 distorted distorted 3367 3380 3381 3382 3399 P G B 67 distorted distorted 3387 3400 3401 3402 3422 P G B 68 distorted distorted 3407 3423 3424 3425 3445 P A B 69 distorted distorted 3430 3446 3447 3448 3467 P A B 70 distorted distorted 3453 3468 3469 3470 3489 P G B 71 distorted distorted 3475 3490 3491 3492 3512 P C B 72 distorted distorted 3497 3513 3514 3515 3550 P OMU B 73 OK OK 3520 3551 3552 3549 3571 P OMU B 74 OK OK 3546 3572 3573 3570 ---------------------------------------------------------------------------------