ID code: '4S3N' 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' --------------------------------------------------------------------------------- 2714 C1' G B 1 beta 2709 2715 2712 2737 C1' G B 2 beta 2732 2738 2735 2760 C1' C B 3 beta 2755 2761 2758 2780 C1' U B 4 beta 2775 2781 2778 2800 C1' U B 5 beta 2795 2801 2798 2820 C1' U B 6 beta 2815 2821 2818 2840 C1' U B 7 beta 2835 2841 2838 2860 C1' G B 8 beta 2855 2861 2858 2883 C1' A B 9 beta 2878 2884 2881 2905 C1' C B 10 beta 2900 2906 2903 2925 C1' C B 11 beta 2920 2926 2923 2945 C1' U B 12 beta 2940 2946 2943 2965 C1' U B 13 beta 2960 2966 2963 2985 C1' U B 14 beta 2980 2986 2983 3005 C1' A B 15 beta 3000 3006 3003 3027 C1' U B 16 beta 3022 3028 3025 3047 C1' G B 17 beta 3042 3048 3045 3070 C1' A B 18 beta 3065 3071 3068 3092 C1' A B 19 beta 3087 3093 3090 3112 C1' U C 1 beta 3107 3113 3110 3132 C1' U C 2 beta 3127 3133 3130 3152 C1' C C 3 beta 3147 3153 3150 3172 C1' A C 4 beta 3167 3173 3170 3194 C1' U C 5 beta 3189 3195 3192 3214 C1' A C 6 beta 3209 3215 3212 3236 C1' A C 7 beta 3231 3237 3234 3258 C1' A C 8 beta 3253 3259 3256 3280 C1' G C 9 beta 3275 3281 3278 3303 C1' G C 10 beta 3298 3304 3301 3326 C1' U C 11 beta 3321 3327 3324 3346 C1' C C 12 beta 3341 3347 3344 3366 C1' A C 13 beta 3361 3367 3364 3388 C1' A C 14 beta 3383 3389 3386 3410 C1' A C 15 beta 3405 3411 3408 3432 C1' A C 16 beta 3427 3433 3430 3454 C1' G C 17 beta 3449 3455 3452 3477 C1' C C 18 beta 3472 3478 3475 3497 C1' C C 19 beta 3492 3498 3495 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2712 C2' G B 1 OK 2714 2710 2713 2735 C2' G B 2 OK 2737 2733 2736 2758 C2' C B 3 OK 2760 2756 2759 2778 C2' U B 4 OK 2780 2776 2779 2798 C2' U B 5 OK 2800 2796 2799 2818 C2' U B 6 OK 2820 2816 2819 2838 C2' U B 7 OK 2840 2836 2839 2858 C2' G B 8 OK 2860 2856 2859 2881 C2' A B 9 OK 2883 2879 2882 2903 C2' C B 10 OK 2905 2901 2904 2923 C2' C B 11 OK 2925 2921 2924 2943 C2' U B 12 OK 2945 2941 2944 2963 C2' U B 13 OK 2965 2961 2964 2983 C2' U B 14 OK 2985 2981 2984 3003 C2' A B 15 OK 3005 3001 3004 3025 C2' U B 16 OK 3027 3023 3026 3045 C2' G B 17 OK 3047 3043 3046 3068 C2' A B 18 OK 3070 3066 3069 3090 C2' A B 19 OK 3092 3088 3091 3110 C2' U C 1 OK 3112 3108 3111 3130 C2' U C 2 OK 3132 3128 3131 3150 C2' C C 3 OK 3152 3148 3151 3170 C2' A C 4 OK 3172 3168 3171 3192 C2' U C 5 OK 3194 3190 3193 3212 C2' A C 6 OK 3214 3210 3213 3234 C2' A C 7 OK 3236 3232 3235 3256 C2' A C 8 OK 3258 3254 3257 3278 C2' G C 9 OK 3280 3276 3279 3301 C2' G C 10 OK 3303 3299 3302 3324 C2' U C 11 OK 3326 3322 3325 3344 C2' C C 12 OK 3346 3342 3345 3364 C2' A C 13 OK 3366 3362 3365 3386 C2' A C 14 OK 3388 3384 3387 3408 C2' A C 15 OK 3410 3406 3409 3430 C2' A C 16 OK 3432 3428 3431 3452 C2' G C 17 OK 3454 3450 3453 3475 C2' C C 18 OK 3477 3473 3476 3495 C2' C C 19 OK 3497 3493 3496 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2710 C3' G B 1 OK 2708 2711 2712 2733 C3' G B 2 OK 2731 2734 2735 2756 C3' C B 3 OK 2754 2757 2758 2776 C3' U B 4 OK 2774 2777 2778 2796 C3' U B 5 OK 2794 2797 2798 2816 C3' U B 6 OK 2814 2817 2818 2836 C3' U B 7 OK 2834 2837 2838 2856 C3' G B 8 OK 2854 2857 2858 2879 C3' A B 9 OK 2877 2880 2881 2901 C3' C B 10 OK 2899 2902 2903 2921 C3' C B 11 OK 2919 2922 2923 2941 C3' U B 12 OK 2939 2942 2943 2961 C3' U B 13 OK 2959 2962 2963 2981 C3' U B 14 OK 2979 2982 2983 3001 C3' A B 15 OK 2999 3002 3003 3023 C3' U B 16 OK 3021 3024 3025 3043 C3' G B 17 OK 3041 3044 3045 3066 C3' A B 18 OK 3064 3067 3068 3088 C3' A B 19 OK 3086 3089 3090 3108 C3' U C 1 OK 3106 3109 3110 3128 C3' U C 2 OK 3126 3129 3130 3148 C3' C C 3 OK 3146 3149 3150 3168 C3' A C 4 OK 3166 3169 3170 3190 C3' U C 5 OK 3188 3191 3192 3210 C3' A C 6 OK 3208 3211 3212 3232 C3' A C 7 OK 3230 3233 3234 3254 C3' A C 8 OK 3252 3255 3256 3276 C3' G C 9 OK 3274 3277 3278 3299 C3' G C 10 OK 3297 3300 3301 3322 C3' U C 11 OK 3320 3323 3324 3342 C3' C C 12 OK 3340 3343 3344 3362 C3' A C 13 OK 3360 3363 3364 3384 C3' A C 14 OK 3382 3385 3386 3406 C3' A C 15 OK 3404 3407 3408 3428 C3' A C 16 OK 3426 3429 3430 3450 C3' G C 17 OK 3448 3451 3452 3473 C3' C C 18 OK 3471 3474 3475 3493 C3' C C 19 OK 3491 3494 3495 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2708 C4' G B 1 OK 2710 2707 2709 2731 C4' G B 2 OK 2733 2730 2732 2754 C4' C B 3 OK 2756 2753 2755 2774 C4' U B 4 OK 2776 2773 2775 2794 C4' U B 5 OK 2796 2793 2795 2814 C4' U B 6 OK 2816 2813 2815 2834 C4' U B 7 OK 2836 2833 2835 2854 C4' G B 8 OK 2856 2853 2855 2877 C4' A B 9 OK 2879 2876 2878 2899 C4' C B 10 OK 2901 2898 2900 2919 C4' C B 11 OK 2921 2918 2920 2939 C4' U B 12 OK 2941 2938 2940 2959 C4' U B 13 OK 2961 2958 2960 2979 C4' U B 14 OK 2981 2978 2980 2999 C4' A B 15 OK 3001 2998 3000 3021 C4' U B 16 OK 3023 3020 3022 3041 C4' G B 17 OK 3043 3040 3042 3064 C4' A B 18 OK 3066 3063 3065 3086 C4' A B 19 OK 3088 3085 3087 3106 C4' U C 1 OK 3108 3105 3107 3126 C4' U C 2 OK 3128 3125 3127 3146 C4' C C 3 OK 3148 3145 3147 3166 C4' A C 4 OK 3168 3165 3167 3188 C4' U C 5 OK 3190 3187 3189 3208 C4' A C 6 OK 3210 3207 3209 3230 C4' A C 7 OK 3232 3229 3231 3252 C4' A C 8 OK 3254 3251 3253 3274 C4' G C 9 OK 3276 3273 3275 3297 C4' G C 10 OK 3299 3296 3298 3320 C4' U C 11 OK 3322 3319 3321 3340 C4' C C 12 OK 3342 3339 3341 3360 C4' A C 13 OK 3362 3359 3361 3382 C4' A C 14 OK 3384 3381 3383 3404 C4' A C 15 OK 3406 3403 3405 3426 C4' A C 16 OK 3428 3425 3427 3448 C4' G C 17 OK 3450 3447 3449 3471 C4' C C 18 OK 3473 3470 3472 3491 C4' C C 19 OK 3493 3490 3492 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2707 C5' G B 1 2706 2708 2730 C5' G B 2 2729 2731 2753 C5' C B 3 2752 2754 2773 C5' U B 4 2772 2774 2793 C5' U B 5 2792 2794 2813 C5' U B 6 2812 2814 2833 C5' U B 7 2832 2834 2853 C5' G B 8 2852 2854 2876 C5' A B 9 2875 2877 2898 C5' C B 10 2897 2899 2918 C5' C B 11 2917 2919 2938 C5' U B 12 2937 2939 2958 C5' U B 13 2957 2959 2978 C5' U B 14 2977 2979 2998 C5' A B 15 2997 2999 3020 C5' U B 16 3019 3021 3040 C5' G B 17 3039 3041 3063 C5' A B 18 3062 3064 3085 C5' A B 19 3084 3086 3105 C5' U C 1 3104 3106 3125 C5' U C 2 3124 3126 3145 C5' C C 3 3144 3146 3165 C5' A C 4 3164 3166 3187 C5' U C 5 3186 3188 3207 C5' A C 6 3206 3208 3229 C5' A C 7 3228 3230 3251 C5' A C 8 3250 3252 3273 C5' G C 9 3272 3274 3296 C5' G C 10 3295 3297 3319 C5' U C 11 3318 3320 3339 C5' C C 12 3338 3340 3359 C5' A C 13 3358 3360 3381 C5' A C 14 3380 3382 3403 C5' A C 15 3402 3404 3425 C5' A C 16 3424 3426 3447 C5' G C 17 3446 3448 3470 C5' C C 18 3469 3471 3490 C5' C C 19 3489 3491 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2726 P G B 2 distorted distorted 2711 2727 2728 2729 2749 P C B 3 distorted distorted 2734 2750 2751 2752 2769 P U B 4 distorted distorted 2757 2770 2771 2772 2789 P U B 5 distorted distorted 2777 2790 2791 2792 2809 P U B 6 distorted distorted 2797 2810 2811 2812 2829 P U B 7 distorted distorted 2817 2830 2831 2832 2849 P G B 8 distorted distorted 2837 2850 2851 2852 2872 P A B 9 distorted distorted 2857 2873 2874 2875 2894 P C B 10 distorted distorted 2880 2895 2896 2897 2914 P C B 11 distorted distorted 2902 2915 2916 2917 2934 P U B 12 distorted distorted 2922 2935 2936 2937 2954 P U B 13 distorted distorted 2942 2955 2956 2957 2974 P U B 14 distorted distorted 2962 2975 2976 2977 2994 P A B 15 distorted distorted 2982 2995 2996 2997 3016 P U B 16 distorted distorted 3002 3017 3018 3019 3036 P G B 17 distorted distorted 3024 3037 3038 3039 3059 P A B 18 distorted distorted 3044 3060 3061 3062 3081 P A B 19 distorted distorted 3067 3082 3083 3084 3121 P U C 2 distorted distorted 3109 3122 3123 3124 3141 P C C 3 distorted distorted 3129 3142 3143 3144 3161 P A C 4 distorted distorted 3149 3162 3163 3164 3183 P U C 5 distorted distorted 3169 3184 3185 3186 3203 P A C 6 distorted distorted 3191 3204 3205 3206 3225 P A C 7 distorted distorted 3211 3226 3227 3228 3247 P A C 8 distorted distorted 3233 3248 3249 3250 3269 P G C 9 distorted distorted 3255 3270 3271 3272 3292 P G C 10 distorted distorted 3277 3293 3294 3295 3315 P U C 11 distorted distorted 3300 3316 3317 3318 3335 P C C 12 distorted distorted 3323 3336 3337 3338 3355 P A C 13 distorted distorted 3343 3356 3357 3358 3377 P A C 14 distorted distorted 3363 3378 3379 3380 3399 P A C 15 distorted distorted 3385 3400 3401 3402 3421 P A C 16 distorted distorted 3407 3422 3423 3424 3443 P G C 17 distorted distorted 3429 3444 3445 3446 3466 P C C 18 distorted distorted 3451 3467 3468 3469 3486 P C C 19 distorted distorted 3474 3487 3488 3489 ---------------------------------------------------------------------------------