ID code: '3WBM' 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' --------------------------------------------------------------------------------- 2677 C1' G X 1 beta 2672 2678 2675 2700 C1' G X 2 beta 2695 2701 2698 2723 C1' U X 3 beta 2718 2724 2721 2743 C1' A X 4 beta 2738 2744 2741 2765 C1' A X 5 beta 2760 2766 2763 2787 C1' G X 6 beta 2782 2788 2785 2810 C1' A X 7 beta 2805 2811 2808 2832 C1' G X 8 beta 2827 2833 2830 2855 C1' C X 9 beta 2850 2856 2853 2875 C1' A X 10 beta 2870 2876 2873 2897 C1' C X 11 beta 2892 2898 2895 2917 C1' C X 12 beta 2912 2918 2915 2937 C1' C X 13 beta 2932 2938 2935 2957 C1' G X 14 beta 2952 2958 2955 2980 C1' A X 15 beta 2975 2981 2978 3002 C1' C X 16 beta 2997 3003 3000 3022 C1' U X 17 beta 3017 3023 3020 3042 C1' G X 18 beta 3037 3043 3040 3065 C1' C X 19 beta 3060 3066 3063 3085 C1' U X 20 beta 3080 3086 3083 3105 C1' C X 21 beta 3100 3106 3103 3125 C1' U X 22 beta 3120 3126 3123 3145 C1' U X 23 beta 3140 3146 3143 3165 C1' C X 24 beta 3160 3166 3163 3185 C1' C X 25 beta 3180 3186 3183 3203 C1' G Y 1 beta 3198 3204 3201 3226 C1' G Y 2 beta 3221 3227 3224 3249 C1' U Y 3 beta 3244 3250 3247 3269 C1' A Y 4 beta 3264 3270 3267 3291 C1' A Y 5 beta 3286 3292 3289 3313 C1' G Y 6 beta 3308 3314 3311 3336 C1' A Y 7 beta 3331 3337 3334 3358 C1' G Y 8 beta 3353 3359 3356 3381 C1' C Y 9 beta 3376 3382 3379 3401 C1' A Y 10 beta 3396 3402 3399 3423 C1' C Y 11 beta 3418 3424 3421 3443 C1' C Y 12 beta 3438 3444 3441 3463 C1' C Y 13 beta 3458 3464 3461 3483 C1' G Y 14 beta 3478 3484 3481 3506 C1' A Y 15 beta 3501 3507 3504 3528 C1' C Y 16 beta 3523 3529 3526 3548 C1' U Y 17 beta 3543 3549 3546 3568 C1' G Y 18 beta 3563 3569 3566 3591 C1' C Y 19 beta 3586 3592 3589 3611 C1' U Y 20 beta 3606 3612 3609 3631 C1' C Y 21 beta 3626 3632 3629 3651 C1' U Y 22 beta 3646 3652 3649 3671 C1' U Y 23 beta 3666 3672 3669 3691 C1' C Y 24 beta 3686 3692 3689 3711 C1' C Y 25 beta 3706 3712 3709 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2675 C2' G X 1 OK 2677 2673 2676 2698 C2' G X 2 OK 2700 2696 2699 2721 C2' U X 3 OK 2723 2719 2722 2741 C2' A X 4 OK 2743 2739 2742 2763 C2' A X 5 OK 2765 2761 2764 2785 C2' G X 6 OK 2787 2783 2786 2808 C2' A X 7 OK 2810 2806 2809 2830 C2' G X 8 OK 2832 2828 2831 2853 C2' C X 9 OK 2855 2851 2854 2873 C2' A X 10 OK 2875 2871 2874 2895 C2' C X 11 OK 2897 2893 2896 2915 C2' C X 12 OK 2917 2913 2916 2935 C2' C X 13 OK 2937 2933 2936 2955 C2' G X 14 OK 2957 2953 2956 2978 C2' A X 15 OK 2980 2976 2979 3000 C2' C X 16 OK 3002 2998 3001 3020 C2' U X 17 OK 3022 3018 3021 3040 C2' G X 18 OK 3042 3038 3041 3063 C2' C X 19 OK 3065 3061 3064 3083 C2' U X 20 OK 3085 3081 3084 3103 C2' C X 21 OK 3105 3101 3104 3123 C2' U X 22 OK 3125 3121 3124 3143 C2' U X 23 OK 3145 3141 3144 3163 C2' C X 24 OK 3165 3161 3164 3183 C2' C X 25 OK 3185 3181 3184 3201 C2' G Y 1 OK 3203 3199 3202 3224 C2' G Y 2 OK 3226 3222 3225 3247 C2' U Y 3 OK 3249 3245 3248 3267 C2' A Y 4 OK 3269 3265 3268 3289 C2' A Y 5 OK 3291 3287 3290 3311 C2' G Y 6 OK 3313 3309 3312 3334 C2' A Y 7 OK 3336 3332 3335 3356 C2' G Y 8 OK 3358 3354 3357 3379 C2' C Y 9 OK 3381 3377 3380 3399 C2' A Y 10 OK 3401 3397 3400 3421 C2' C Y 11 OK 3423 3419 3422 3441 C2' C Y 12 OK 3443 3439 3442 3461 C2' C Y 13 OK 3463 3459 3462 3481 C2' G Y 14 OK 3483 3479 3482 3504 C2' A Y 15 OK 3506 3502 3505 3526 C2' C Y 16 OK 3528 3524 3527 3546 C2' U Y 17 OK 3548 3544 3547 3566 C2' G Y 18 OK 3568 3564 3567 3589 C2' C Y 19 OK 3591 3587 3590 3609 C2' U Y 20 OK 3611 3607 3610 3629 C2' C Y 21 OK 3631 3627 3630 3649 C2' U Y 22 OK 3651 3647 3650 3669 C2' U Y 23 OK 3671 3667 3670 3689 C2' C Y 24 OK 3691 3687 3690 3709 C2' C Y 25 OK 3711 3707 3710 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2673 C3' G X 1 OK 2671 2674 2675 2696 C3' G X 2 OK 2694 2697 2698 2719 C3' U X 3 OK 2717 2720 2721 2739 C3' A X 4 OK 2737 2740 2741 2761 C3' A X 5 OK 2759 2762 2763 2783 C3' G X 6 OK 2781 2784 2785 2806 C3' A X 7 OK 2804 2807 2808 2828 C3' G X 8 OK 2826 2829 2830 2851 C3' C X 9 OK 2849 2852 2853 2871 C3' A X 10 OK 2869 2872 2873 2893 C3' C X 11 OK 2891 2894 2895 2913 C3' C X 12 OK 2911 2914 2915 2933 C3' C X 13 OK 2931 2934 2935 2953 C3' G X 14 OK 2951 2954 2955 2976 C3' A X 15 OK 2974 2977 2978 2998 C3' C X 16 OK 2996 2999 3000 3018 C3' U X 17 OK 3016 3019 3020 3038 C3' G X 18 OK 3036 3039 3040 3061 C3' C X 19 OK 3059 3062 3063 3081 C3' U X 20 OK 3079 3082 3083 3101 C3' C X 21 OK 3099 3102 3103 3121 C3' U X 22 OK 3119 3122 3123 3141 C3' U X 23 OK 3139 3142 3143 3161 C3' C X 24 OK 3159 3162 3163 3181 C3' C X 25 OK 3179 3182 3183 3199 C3' G Y 1 OK 3197 3200 3201 3222 C3' G Y 2 OK 3220 3223 3224 3245 C3' U Y 3 OK 3243 3246 3247 3265 C3' A Y 4 OK 3263 3266 3267 3287 C3' A Y 5 OK 3285 3288 3289 3309 C3' G Y 6 OK 3307 3310 3311 3332 C3' A Y 7 OK 3330 3333 3334 3354 C3' G Y 8 OK 3352 3355 3356 3377 C3' C Y 9 OK 3375 3378 3379 3397 C3' A Y 10 OK 3395 3398 3399 3419 C3' C Y 11 OK 3417 3420 3421 3439 C3' C Y 12 OK 3437 3440 3441 3459 C3' C Y 13 OK 3457 3460 3461 3479 C3' G Y 14 OK 3477 3480 3481 3502 C3' A Y 15 OK 3500 3503 3504 3524 C3' C Y 16 OK 3522 3525 3526 3544 C3' U Y 17 OK 3542 3545 3546 3564 C3' G Y 18 OK 3562 3565 3566 3587 C3' C Y 19 OK 3585 3588 3589 3607 C3' U Y 20 OK 3605 3608 3609 3627 C3' C Y 21 OK 3625 3628 3629 3647 C3' U Y 22 OK 3645 3648 3649 3667 C3' U Y 23 OK 3665 3668 3669 3687 C3' C Y 24 OK 3685 3688 3689 3707 C3' C Y 25 OK 3705 3708 3709 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2671 C4' G X 1 OK 2673 2670 2672 2694 C4' G X 2 OK 2696 2693 2695 2717 C4' U X 3 OK 2719 2716 2718 2737 C4' A X 4 OK 2739 2736 2738 2759 C4' A X 5 OK 2761 2758 2760 2781 C4' G X 6 OK 2783 2780 2782 2804 C4' A X 7 OK 2806 2803 2805 2826 C4' G X 8 OK 2828 2825 2827 2849 C4' C X 9 OK 2851 2848 2850 2869 C4' A X 10 OK 2871 2868 2870 2891 C4' C X 11 OK 2893 2890 2892 2911 C4' C X 12 OK 2913 2910 2912 2931 C4' C X 13 OK 2933 2930 2932 2951 C4' G X 14 OK 2953 2950 2952 2974 C4' A X 15 OK 2976 2973 2975 2996 C4' C X 16 OK 2998 2995 2997 3016 C4' U X 17 OK 3018 3015 3017 3036 C4' G X 18 OK 3038 3035 3037 3059 C4' C X 19 OK 3061 3058 3060 3079 C4' U X 20 OK 3081 3078 3080 3099 C4' C X 21 OK 3101 3098 3100 3119 C4' U X 22 OK 3121 3118 3120 3139 C4' U X 23 OK 3141 3138 3140 3159 C4' C X 24 OK 3161 3158 3160 3179 C4' C X 25 OK 3181 3178 3180 3197 C4' G Y 1 OK 3199 3196 3198 3220 C4' G Y 2 OK 3222 3219 3221 3243 C4' U Y 3 OK 3245 3242 3244 3263 C4' A Y 4 OK 3265 3262 3264 3285 C4' A Y 5 OK 3287 3284 3286 3307 C4' G Y 6 OK 3309 3306 3308 3330 C4' A Y 7 OK 3332 3329 3331 3352 C4' G Y 8 OK 3354 3351 3353 3375 C4' C Y 9 OK 3377 3374 3376 3395 C4' A Y 10 OK 3397 3394 3396 3417 C4' C Y 11 OK 3419 3416 3418 3437 C4' C Y 12 OK 3439 3436 3438 3457 C4' C Y 13 OK 3459 3456 3458 3477 C4' G Y 14 OK 3479 3476 3478 3500 C4' A Y 15 OK 3502 3499 3501 3522 C4' C Y 16 OK 3524 3521 3523 3542 C4' U Y 17 OK 3544 3541 3543 3562 C4' G Y 18 OK 3564 3561 3563 3585 C4' C Y 19 OK 3587 3584 3586 3605 C4' U Y 20 OK 3607 3604 3606 3625 C4' C Y 21 OK 3627 3624 3626 3645 C4' U Y 22 OK 3647 3644 3646 3665 C4' U Y 23 OK 3667 3664 3666 3685 C4' C Y 24 OK 3687 3684 3686 3705 C4' C Y 25 OK 3707 3704 3706 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2670 C5' G X 1 2669 2671 2693 C5' G X 2 2692 2694 2716 C5' U X 3 2715 2717 2736 C5' A X 4 2735 2737 2758 C5' A X 5 2757 2759 2780 C5' G X 6 2779 2781 2803 C5' A X 7 2802 2804 2825 C5' G X 8 2824 2826 2848 C5' C X 9 2847 2849 2868 C5' A X 10 2867 2869 2890 C5' C X 11 2889 2891 2910 C5' C X 12 2909 2911 2930 C5' C X 13 2929 2931 2950 C5' G X 14 2949 2951 2973 C5' A X 15 2972 2974 2995 C5' C X 16 2994 2996 3015 C5' U X 17 3014 3016 3035 C5' G X 18 3034 3036 3058 C5' C X 19 3057 3059 3078 C5' U X 20 3077 3079 3098 C5' C X 21 3097 3099 3118 C5' U X 22 3117 3119 3138 C5' U X 23 3137 3139 3158 C5' C X 24 3157 3159 3178 C5' C X 25 3177 3179 3196 C5' G Y 1 3195 3197 3219 C5' G Y 2 3218 3220 3242 C5' U Y 3 3241 3243 3262 C5' A Y 4 3261 3263 3284 C5' A Y 5 3283 3285 3306 C5' G Y 6 3305 3307 3329 C5' A Y 7 3328 3330 3351 C5' G Y 8 3350 3352 3374 C5' C Y 9 3373 3375 3394 C5' A Y 10 3393 3395 3416 C5' C Y 11 3415 3417 3436 C5' C Y 12 3435 3437 3456 C5' C Y 13 3455 3457 3476 C5' G Y 14 3475 3477 3499 C5' A Y 15 3498 3500 3521 C5' C Y 16 3520 3522 3541 C5' U Y 17 3540 3542 3561 C5' G Y 18 3560 3562 3584 C5' C Y 19 3583 3585 3604 C5' U Y 20 3603 3605 3624 C5' C Y 21 3623 3625 3644 C5' U Y 22 3643 3645 3664 C5' U Y 23 3663 3665 3684 C5' C Y 24 3683 3685 3704 C5' C Y 25 3703 3705 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2689 P G X 2 distorted distorted 2674 2690 2691 2692 2712 P U X 3 distorted distorted 2697 2713 2714 2715 2732 P A X 4 distorted distorted 2720 2733 2734 2735 2754 P A X 5 distorted distorted 2740 2755 2756 2757 2776 P G X 6 distorted distorted 2762 2777 2778 2779 2799 P A X 7 distorted distorted 2784 2800 2801 2802 2821 P G X 8 distorted distorted 2807 2822 2823 2824 2844 P C X 9 distorted distorted 2829 2845 2846 2847 2864 P A X 10 distorted distorted 2852 2865 2866 2867 2886 P C X 11 distorted distorted 2872 2887 2888 2889 2906 P C X 12 distorted distorted 2894 2907 2908 2909 2926 P C X 13 distorted distorted 2914 2927 2928 2929 2946 P G X 14 distorted distorted 2934 2947 2948 2949 2969 P A X 15 distorted distorted 2954 2970 2971 2972 2991 P C X 16 distorted distorted 2977 2992 2993 2994 3011 P U X 17 distorted distorted 2999 3012 3013 3014 3031 P G X 18 distorted distorted 3019 3032 3033 3034 3054 P C X 19 distorted distorted 3039 3055 3056 3057 3074 P U X 20 distorted distorted 3062 3075 3076 3077 3094 P C X 21 distorted distorted 3082 3095 3096 3097 3114 P U X 22 distorted distorted 3102 3115 3116 3117 3134 P U X 23 distorted distorted 3122 3135 3136 3137 3154 P C X 24 distorted distorted 3142 3155 3156 3157 3174 P C X 25 distorted distorted 3162 3175 3176 3177 3215 P G Y 2 distorted distorted 3200 3216 3217 3218 3238 P U Y 3 distorted distorted 3223 3239 3240 3241 3258 P A Y 4 distorted distorted 3246 3259 3260 3261 3280 P A Y 5 distorted distorted 3266 3281 3282 3283 3302 P G Y 6 distorted distorted 3288 3303 3304 3305 3325 P A Y 7 distorted distorted 3310 3326 3327 3328 3347 P G Y 8 distorted distorted 3333 3348 3349 3350 3370 P C Y 9 distorted distorted 3355 3371 3372 3373 3390 P A Y 10 distorted distorted 3378 3391 3392 3393 3412 P C Y 11 distorted distorted 3398 3413 3414 3415 3432 P C Y 12 distorted distorted 3420 3433 3434 3435 3452 P C Y 13 distorted distorted 3440 3453 3454 3455 3472 P G Y 14 distorted distorted 3460 3473 3474 3475 3495 P A Y 15 distorted distorted 3480 3496 3497 3498 3517 P C Y 16 distorted distorted 3503 3518 3519 3520 3537 P U Y 17 distorted distorted 3525 3538 3539 3540 3557 P G Y 18 distorted distorted 3545 3558 3559 3560 3580 P C Y 19 distorted distorted 3565 3581 3582 3583 3600 P U Y 20 distorted distorted 3588 3601 3602 3603 3620 P C Y 21 distorted distorted 3608 3621 3622 3623 3640 P U Y 22 distorted distorted 3628 3641 3642 3643 3660 P U Y 23 distorted distorted 3648 3661 3662 3663 3680 P C Y 24 distorted distorted 3668 3681 3682 3683 3700 P C Y 25 distorted distorted 3688 3701 3702 3703 ---------------------------------------------------------------------------------