ID code: '4YCP' 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' --------------------------------------------------------------------------------- 2411 C1' G B 5 beta 2406 2412 2409 2434 C1' C B 6 beta 2429 2435 2432 2454 C1' G B 7 beta 2449 2455 2452 2477 C1' U B 8 beta 2472 2478 2475 2497 C1' A B 9 beta 2492 2498 2495 2519 C1' G B 10 beta 2514 2520 2517 2542 C1' U B 11 beta 2537 2543 2540 2562 C1' U B 12 beta 2557 2563 2560 2582 C1' C B 13 beta 2577 2583 2580 2602 C1' A B 14 beta 2597 2603 2600 2624 C1' A B 15 beta 2619 2625 2622 2646 C1' U B 16 beta 2641 2647 2644 2666 C1' U B 17 beta 2661 2667 2664 2686 C1' G B 18 beta 2681 2687 2684 2709 C1' G B 19 beta 2704 2710 2707 2732 C1' U B 20 beta 2727 2733 2730 2752 C1' A B 21 beta 2747 2753 2750 2774 C1' G B 22 beta 2769 2775 2772 2797 C1' A B 23 beta 2792 2798 2795 2819 C1' G B 24 beta 2814 2820 2817 2842 C1' C B 25 beta 2837 2843 2840 2862 C1' A B 26 beta 2857 2863 2860 2884 C1' C B 27 beta 2879 2885 2882 2904 C1' C B 28 beta 2899 2905 2902 2924 C1' G B 29 beta 2919 2925 2922 2947 C1' G B 30 beta 2942 2948 2945 2970 C1' U B 31 beta 2965 2971 2968 2990 C1' C B 32 beta 2985 2991 2988 3007 C1' A B 36 beta 3002 3008 3005 3029 C1' A B 37 beta 3024 3030 3027 3051 C1' A B 38 beta 3046 3052 3049 3073 C1' A B 39 beta 3068 3074 3071 3095 C1' C B 40 beta 3090 3096 3093 3115 C1' C B 41 beta 3110 3116 3113 3135 C1' G B 42 beta 3130 3136 3133 3158 C1' G B 43 beta 3153 3159 3156 3181 C1' G B 44 beta 3176 3182 3179 3209 C1' G B 46 beta 3204 3210 3207 3233 C1' U B 48 beta 3228 3234 3231 3253 C1' G B 49 beta 3248 3254 3251 3276 C1' G B 50 beta 3271 3277 3274 3299 C1' G B 51 beta 3294 3300 3297 3322 C1' A B 52 beta 3317 3323 3320 3344 C1' G B 53 beta 3339 3345 3342 3367 C1' U B 54 beta 3362 3368 3365 3387 C1' U B 55 beta 3382 3388 3385 3407 C1' C B 56 beta 3402 3408 3405 3427 C1' G B 57 beta 3422 3428 3425 3450 C1' A B 58 beta 3445 3451 3448 3472 C1' G B 59 beta 3467 3473 3470 3495 C1' U B 60 beta 3490 3496 3493 3515 C1' C B 61 beta 3510 3516 3513 3535 C1' U B 62 beta 3530 3536 3533 3555 C1' C B 63 beta 3550 3556 3553 3575 C1' U B 64 beta 3570 3576 3573 3595 C1' C B 65 beta 3590 3596 3593 3615 C1' C B 66 beta 3610 3616 3613 3635 C1' G B 67 beta 3630 3636 3633 3658 C1' C B 68 beta 3653 3659 3656 3678 C1' C B 69 beta 3673 3679 3676 3706 C1' FMN A 401 3707 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2409 C2' G B 5 OK 2411 2407 2410 2432 C2' C B 6 OK 2434 2430 2433 2452 C2' G B 7 OK 2454 2450 2453 2475 C2' U B 8 OK 2477 2473 2476 2495 C2' A B 9 OK 2497 2493 2496 2517 C2' G B 10 OK 2519 2515 2518 2540 C2' U B 11 OK 2542 2538 2541 2560 C2' U B 12 OK 2562 2558 2561 2580 C2' C B 13 OK 2582 2578 2581 2600 C2' A B 14 OK 2602 2598 2601 2622 C2' A B 15 OK 2624 2620 2623 2644 C2' U B 16 OK 2646 2642 2645 2664 C2' U B 17 OK 2666 2662 2665 2684 C2' G B 18 OK 2686 2682 2685 2707 C2' G B 19 OK 2709 2705 2708 2730 C2' U B 20 OK 2732 2728 2731 2750 C2' A B 21 OK 2752 2748 2751 2772 C2' G B 22 OK 2774 2770 2773 2795 C2' A B 23 OK 2797 2793 2796 2817 C2' G B 24 OK 2819 2815 2818 2840 C2' C B 25 OK 2842 2838 2841 2860 C2' A B 26 OK 2862 2858 2861 2882 C2' C B 27 OK 2884 2880 2883 2902 C2' C B 28 OK 2904 2900 2903 2922 C2' G B 29 OK 2924 2920 2923 2945 C2' G B 30 OK 2947 2943 2946 2968 C2' U B 31 OK 2970 2966 2969 2988 C2' C B 32 OK 2990 2986 2989 3005 C2' A B 36 OK 3007 3003 3006 3027 C2' A B 37 OK 3029 3025 3028 3049 C2' A B 38 OK 3051 3047 3050 3071 C2' A B 39 OK 3073 3069 3072 3093 C2' C B 40 OK 3095 3091 3094 3113 C2' C B 41 OK 3115 3111 3114 3133 C2' G B 42 OK 3135 3131 3134 3156 C2' G B 43 OK 3158 3154 3157 3179 C2' G B 44 OK 3181 3177 3180 3207 C2' G B 46 OK 3209 3205 3208 3231 C2' U B 48 OK 3233 3229 3232 3251 C2' G B 49 OK 3253 3249 3252 3274 C2' G B 50 OK 3276 3272 3275 3297 C2' G B 51 OK 3299 3295 3298 3320 C2' A B 52 OK 3322 3318 3321 3342 C2' G B 53 OK 3344 3340 3343 3365 C2' U B 54 OK 3367 3363 3366 3385 C2' U B 55 OK 3387 3383 3386 3405 C2' C B 56 OK 3407 3403 3406 3425 C2' G B 57 OK 3427 3423 3426 3448 C2' A B 58 OK 3450 3446 3449 3470 C2' G B 59 OK 3472 3468 3471 3493 C2' U B 60 OK 3495 3491 3494 3513 C2' C B 61 OK 3515 3511 3514 3533 C2' U B 62 OK 3535 3531 3534 3553 C2' C B 63 OK 3555 3551 3554 3573 C2' U B 64 OK 3575 3571 3574 3593 C2' C B 65 OK 3595 3591 3594 3613 C2' C B 66 OK 3615 3611 3614 3633 C2' G B 67 OK 3635 3631 3634 3656 C2' C B 68 OK 3658 3654 3657 3676 C2' C B 69 OK 3678 3674 3677 3707 C2' FMN A 401 OK 3706 3709 3708 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2407 C3' G B 5 OK 2405 2408 2409 2430 C3' C B 6 OK 2428 2431 2432 2450 C3' G B 7 OK 2448 2451 2452 2473 C3' U B 8 OK 2471 2474 2475 2493 C3' A B 9 OK 2491 2494 2495 2515 C3' G B 10 OK 2513 2516 2517 2538 C3' U B 11 OK 2536 2539 2540 2558 C3' U B 12 OK 2556 2559 2560 2578 C3' C B 13 OK 2576 2579 2580 2598 C3' A B 14 OK 2596 2599 2600 2620 C3' A B 15 OK 2618 2621 2622 2642 C3' U B 16 OK 2640 2643 2644 2662 C3' U B 17 OK 2660 2663 2664 2682 C3' G B 18 OK 2680 2683 2684 2705 C3' G B 19 OK 2703 2706 2707 2728 C3' U B 20 OK 2726 2729 2730 2748 C3' A B 21 OK 2746 2749 2750 2770 C3' G B 22 OK 2768 2771 2772 2793 C3' A B 23 OK 2791 2794 2795 2815 C3' G B 24 OK 2813 2816 2817 2838 C3' C B 25 OK 2836 2839 2840 2858 C3' A B 26 OK 2856 2859 2860 2880 C3' C B 27 OK 2878 2881 2882 2900 C3' C B 28 OK 2898 2901 2902 2920 C3' G B 29 OK 2918 2921 2922 2943 C3' G B 30 OK 2941 2944 2945 2966 C3' U B 31 OK 2964 2967 2968 2986 C3' C B 32 OK 2984 2987 2988 3003 C3' A B 36 OK 3001 3004 3005 3025 C3' A B 37 OK 3023 3026 3027 3047 C3' A B 38 OK 3045 3048 3049 3069 C3' A B 39 OK 3067 3070 3071 3091 C3' C B 40 OK 3089 3092 3093 3111 C3' C B 41 OK 3109 3112 3113 3131 C3' G B 42 OK 3129 3132 3133 3154 C3' G B 43 OK 3152 3155 3156 3177 C3' G B 44 OK 3175 3178 3179 3205 C3' G B 46 OK 3203 3206 3207 3229 C3' U B 48 OK 3227 3230 3231 3249 C3' G B 49 OK 3247 3250 3251 3272 C3' G B 50 OK 3270 3273 3274 3295 C3' G B 51 OK 3293 3296 3297 3318 C3' A B 52 OK 3316 3319 3320 3340 C3' G B 53 OK 3338 3341 3342 3363 C3' U B 54 OK 3361 3364 3365 3383 C3' U B 55 OK 3381 3384 3385 3403 C3' C B 56 OK 3401 3404 3405 3423 C3' G B 57 OK 3421 3424 3425 3446 C3' A B 58 OK 3444 3447 3448 3468 C3' G B 59 OK 3466 3469 3470 3491 C3' U B 60 OK 3489 3492 3493 3511 C3' C B 61 OK 3509 3512 3513 3531 C3' U B 62 OK 3529 3532 3533 3551 C3' C B 63 OK 3549 3552 3553 3571 C3' U B 64 OK 3569 3572 3573 3591 C3' C B 65 OK 3589 3592 3593 3611 C3' C B 66 OK 3609 3612 3613 3631 C3' G B 67 OK 3629 3632 3633 3654 C3' C B 68 OK 3652 3655 3656 3674 C3' C B 69 OK 3672 3675 3676 3709 C3' FMN A 401 OK 3711 3710 3707 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2405 C4' G B 5 OK 2407 2404 2406 2428 C4' C B 6 OK 2430 2427 2429 2448 C4' G B 7 OK 2450 2447 2449 2471 C4' U B 8 OK 2473 2470 2472 2491 C4' A B 9 OK 2493 2490 2492 2513 C4' G B 10 OK 2515 2512 2514 2536 C4' U B 11 OK 2538 2535 2537 2556 C4' U B 12 OK 2558 2555 2557 2576 C4' C B 13 OK 2578 2575 2577 2596 C4' A B 14 OK 2598 2595 2597 2618 C4' A B 15 OK 2620 2617 2619 2640 C4' U B 16 OK 2642 2639 2641 2660 C4' U B 17 OK 2662 2659 2661 2680 C4' G B 18 OK 2682 2679 2681 2703 C4' G B 19 OK 2705 2702 2704 2726 C4' U B 20 OK 2728 2725 2727 2746 C4' A B 21 OK 2748 2745 2747 2768 C4' G B 22 OK 2770 2767 2769 2791 C4' A B 23 OK 2793 2790 2792 2813 C4' G B 24 OK 2815 2812 2814 2836 C4' C B 25 OK 2838 2835 2837 2856 C4' A B 26 OK 2858 2855 2857 2878 C4' C B 27 OK 2880 2877 2879 2898 C4' C B 28 OK 2900 2897 2899 2918 C4' G B 29 OK 2920 2917 2919 2941 C4' G B 30 OK 2943 2940 2942 2964 C4' U B 31 OK 2966 2963 2965 2984 C4' C B 32 OK 2986 2983 2985 3001 C4' A B 36 OK 3003 3000 3002 3023 C4' A B 37 OK 3025 3022 3024 3045 C4' A B 38 OK 3047 3044 3046 3067 C4' A B 39 OK 3069 3066 3068 3089 C4' C B 40 OK 3091 3088 3090 3109 C4' C B 41 OK 3111 3108 3110 3129 C4' G B 42 OK 3131 3128 3130 3152 C4' G B 43 OK 3154 3151 3153 3175 C4' G B 44 OK 3177 3174 3176 3203 C4' G B 46 OK 3205 3202 3204 3227 C4' U B 48 OK 3229 3226 3228 3247 C4' G B 49 OK 3249 3246 3248 3270 C4' G B 50 OK 3272 3269 3271 3293 C4' G B 51 OK 3295 3292 3294 3316 C4' A B 52 OK 3318 3315 3317 3338 C4' G B 53 OK 3340 3337 3339 3361 C4' U B 54 OK 3363 3360 3362 3381 C4' U B 55 OK 3383 3380 3382 3401 C4' C B 56 OK 3403 3400 3402 3421 C4' G B 57 OK 3423 3420 3422 3444 C4' A B 58 OK 3446 3443 3445 3466 C4' G B 59 OK 3468 3465 3467 3489 C4' U B 60 OK 3491 3488 3490 3509 C4' C B 61 OK 3511 3508 3510 3529 C4' U B 62 OK 3531 3528 3530 3549 C4' C B 63 OK 3551 3548 3550 3569 C4' U B 64 OK 3571 3568 3570 3589 C4' C B 65 OK 3591 3588 3590 3609 C4' C B 66 OK 3611 3608 3610 3629 C4' G B 67 OK 3631 3628 3630 3652 C4' C B 68 OK 3654 3651 3653 3672 C4' C B 69 OK 3674 3671 3673 3711 C4' FMN A 401 OK 3709 3713 3712 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2404 C5' G B 5 2403 2405 2427 C5' C B 6 2426 2428 2447 C5' G B 7 2446 2448 2470 C5' U B 8 2469 2471 2490 C5' A B 9 2489 2491 2512 C5' G B 10 2511 2513 2535 C5' U B 11 2534 2536 2555 C5' U B 12 2554 2556 2575 C5' C B 13 2574 2576 2595 C5' A B 14 2594 2596 2617 C5' A B 15 2616 2618 2639 C5' U B 16 2638 2640 2659 C5' U B 17 2658 2660 2679 C5' G B 18 2678 2680 2702 C5' G B 19 2701 2703 2725 C5' U B 20 2724 2726 2745 C5' A B 21 2744 2746 2767 C5' G B 22 2766 2768 2790 C5' A B 23 2789 2791 2812 C5' G B 24 2811 2813 2835 C5' C B 25 2834 2836 2855 C5' A B 26 2854 2856 2877 C5' C B 27 2876 2878 2897 C5' C B 28 2896 2898 2917 C5' G B 29 2916 2918 2940 C5' G B 30 2939 2941 2963 C5' U B 31 2962 2964 2983 C5' C B 32 2982 2984 3000 C5' A B 36 2999 3001 3022 C5' A B 37 3021 3023 3044 C5' A B 38 3043 3045 3066 C5' A B 39 3065 3067 3088 C5' C B 40 3087 3089 3108 C5' C B 41 3107 3109 3128 C5' G B 42 3127 3129 3151 C5' G B 43 3150 3152 3174 C5' G B 44 3173 3175 3202 C5' G B 46 3201 3203 3226 C5' U B 48 3225 3227 3246 C5' G B 49 3245 3247 3269 C5' G B 50 3268 3270 3292 C5' G B 51 3291 3293 3315 C5' A B 52 3314 3316 3337 C5' G B 53 3336 3338 3360 C5' U B 54 3359 3361 3380 C5' U B 55 3379 3381 3400 C5' C B 56 3399 3401 3420 C5' G B 57 3419 3421 3443 C5' A B 58 3442 3444 3465 C5' G B 59 3464 3466 3488 C5' U B 60 3487 3489 3508 C5' C B 61 3507 3509 3528 C5' U B 62 3527 3529 3548 C5' C B 63 3547 3549 3568 C5' U B 64 3567 3569 3588 C5' C B 65 3587 3589 3608 C5' C B 66 3607 3609 3628 C5' G B 67 3627 3629 3651 C5' C B 68 3650 3652 3671 C5' C B 69 3670 3672 3713 C5' FMN A 401 3714 3711 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2400 P G B 5 distorted distorted 2401 2402 2403 2423 P C B 6 distorted distorted 2408 2424 2425 2426 2443 P G B 7 distorted distorted 2431 2444 2445 2446 2466 P U B 8 distorted distorted 2451 2467 2468 2469 2486 P A B 9 distorted distorted 2474 2487 2488 2489 2508 P G B 10 distorted distorted 2494 2509 2510 2511 2531 P U B 11 distorted distorted 2516 2532 2533 2534 2551 P U B 12 distorted distorted 2539 2552 2553 2554 2571 P C B 13 distorted distorted 2559 2572 2573 2574 2591 P A B 14 distorted distorted 2579 2592 2593 2594 2613 P A B 15 distorted distorted 2599 2614 2615 2616 2635 P U B 16 distorted distorted 2621 2636 2637 2638 2655 P U B 17 distorted distorted 2643 2656 2657 2658 2675 P G B 18 distorted distorted 2663 2676 2677 2678 2698 P G B 19 distorted distorted 2683 2699 2700 2701 2721 P U B 20 distorted distorted 2706 2722 2723 2724 2741 P A B 21 distorted distorted 2729 2742 2743 2744 2763 P G B 22 distorted distorted 2749 2764 2765 2766 2786 P A B 23 distorted distorted 2771 2787 2788 2789 2808 P G B 24 distorted distorted 2794 2809 2810 2811 2831 P C B 25 distorted distorted 2816 2832 2833 2834 2851 P A B 26 distorted distorted 2839 2852 2853 2854 2873 P C B 27 distorted distorted 2859 2874 2875 2876 2893 P C B 28 distorted distorted 2881 2894 2895 2896 2913 P G B 29 distorted distorted 2901 2914 2915 2916 2936 P G B 30 distorted distorted 2921 2937 2938 2939 2959 P U B 31 distorted distorted 2944 2960 2961 2962 2979 P C B 32 distorted distorted 2967 2980 2981 2982 3018 P A B 37 distorted distorted 3004 3019 3020 3021 3040 P A B 38 distorted distorted 3026 3041 3042 3043 3062 P A B 39 distorted distorted 3048 3063 3064 3065 3084 P C B 40 distorted distorted 3070 3085 3086 3087 3104 P C B 41 distorted distorted 3092 3105 3106 3107 3124 P G B 42 distorted distorted 3112 3125 3126 3127 3147 P G B 43 distorted distorted 3132 3148 3149 3150 3170 P G B 44 distorted distorted 3155 3171 3172 3173 3193 P U B 45 distorted distorted 3178 3194 3195 3196 3198 P G B 46 distorted distorted 3197 3199 3200 3201 3222 P U B 48 distorted distorted 3221 3223 3224 3225 3242 P G B 49 distorted distorted 3230 3243 3244 3245 3265 P G B 50 distorted distorted 3250 3266 3267 3268 3288 P G B 51 distorted distorted 3273 3289 3290 3291 3311 P A B 52 distorted distorted 3296 3312 3313 3314 3333 P G B 53 distorted distorted 3319 3334 3335 3336 3356 P U B 54 distorted distorted 3341 3357 3358 3359 3376 P U B 55 distorted distorted 3364 3377 3378 3379 3396 P C B 56 distorted distorted 3384 3397 3398 3399 3416 P G B 57 distorted distorted 3404 3417 3418 3419 3439 P A B 58 distorted distorted 3424 3440 3441 3442 3461 P G B 59 distorted distorted 3447 3462 3463 3464 3484 P U B 60 distorted distorted 3469 3485 3486 3487 3504 P C B 61 distorted distorted 3492 3505 3506 3507 3524 P U B 62 distorted distorted 3512 3525 3526 3527 3544 P C B 63 distorted distorted 3532 3545 3546 3547 3564 P U B 64 distorted distorted 3552 3565 3566 3567 3584 P C B 65 distorted distorted 3572 3585 3586 3587 3604 P C B 66 distorted distorted 3592 3605 3606 3607 3624 P G B 67 distorted distorted 3612 3625 3626 3627 3647 P C B 68 distorted distorted 3632 3648 3649 3650 3667 P C B 69 distorted distorted 3655 3668 3669 3670 3715 P FMN A 401 distorted distorted 3716 3717 3714 ---------------------------------------------------------------------------------