ID code: '4IG8' 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' --------------------------------------------------------------------------------- 2751 C1' G B 1 beta 2746 2752 2749 2774 C1' G B 2 beta 2769 2775 2772 2797 C1' C B 3 beta 2792 2798 2795 2817 C1' U B 4 beta 2812 2818 2815 2837 C1' U B 5 beta 2832 2838 2835 2857 C1' U B 6 beta 2852 2858 2855 2877 C1' U B 7 beta 2872 2878 2875 2897 C1' G B 8 beta 2892 2898 2895 2920 C1' A B 9 beta 2915 2921 2918 2942 C1' C B 10 beta 2937 2943 2940 2962 C1' C B 11 beta 2957 2963 2960 2982 C1' U B 12 beta 2977 2983 2980 3002 C1' U B 13 beta 2997 3003 3000 3022 C1' U B 14 beta 3017 3023 3020 3042 C1' A B 15 beta 3037 3043 3040 3064 C1' U B 16 beta 3059 3065 3062 3084 C1' G B 17 beta 3079 3085 3082 3107 C1' C B 18 beta 3102 3108 3105 3125 C1' G C 1 beta 3120 3126 3123 3148 C1' C C 2 beta 3143 3149 3146 3168 C1' A C 3 beta 3163 3169 3166 3190 C1' U C 4 beta 3185 3191 3188 3210 C1' A C 5 beta 3205 3211 3208 3232 C1' A C 6 beta 3227 3233 3230 3254 C1' A C 7 beta 3249 3255 3252 3276 C1' G C 8 beta 3271 3277 3274 3299 C1' G C 9 beta 3294 3300 3297 3322 C1' U C 10 beta 3317 3323 3320 3342 C1' C C 11 beta 3337 3343 3340 3362 C1' A C 12 beta 3357 3363 3360 3384 C1' A C 13 beta 3379 3385 3382 3406 C1' A C 14 beta 3401 3407 3404 3428 C1' A C 15 beta 3423 3429 3426 3450 C1' G C 16 beta 3445 3451 3448 3473 C1' C C 17 beta 3468 3474 3471 3493 C1' C C 18 beta 3488 3494 3491 3524 C1' DTP A 403 beta 3520 3525 3523 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2749 C2' G B 1 OK 2751 2747 2750 2772 C2' G B 2 OK 2774 2770 2773 2795 C2' C B 3 OK 2797 2793 2796 2815 C2' U B 4 OK 2817 2813 2816 2835 C2' U B 5 OK 2837 2833 2836 2855 C2' U B 6 OK 2857 2853 2856 2875 C2' U B 7 OK 2877 2873 2876 2895 C2' G B 8 OK 2897 2893 2896 2918 C2' A B 9 OK 2920 2916 2919 2940 C2' C B 10 OK 2942 2938 2941 2960 C2' C B 11 OK 2962 2958 2961 2980 C2' U B 12 OK 2982 2978 2981 3000 C2' U B 13 OK 3002 2998 3001 3020 C2' U B 14 OK 3022 3018 3021 3040 C2' A B 15 OK 3042 3038 3041 3062 C2' U B 16 OK 3064 3060 3063 3082 C2' G B 17 OK 3084 3080 3083 3105 C2' C B 18 OK 3107 3103 3106 3123 C2' G C 1 OK 3125 3121 3124 3146 C2' C C 2 OK 3148 3144 3147 3166 C2' A C 3 OK 3168 3164 3167 3188 C2' U C 4 OK 3190 3186 3189 3208 C2' A C 5 OK 3210 3206 3209 3230 C2' A C 6 OK 3232 3228 3231 3252 C2' A C 7 OK 3254 3250 3253 3274 C2' G C 8 OK 3276 3272 3275 3297 C2' G C 9 OK 3299 3295 3298 3320 C2' U C 10 OK 3322 3318 3321 3340 C2' C C 11 OK 3342 3338 3341 3360 C2' A C 12 OK 3362 3358 3361 3382 C2' A C 13 OK 3384 3380 3383 3404 C2' A C 14 OK 3406 3402 3405 3426 C2' A C 15 OK 3428 3424 3427 3448 C2' G C 16 OK 3450 3446 3449 3471 C2' C C 17 OK 3473 3469 3472 3491 C2' C C 18 OK 3493 3489 3492 3523 C2' DTP A 403 3524 3521 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2747 C3' G B 1 OK 2745 2748 2749 2770 C3' G B 2 OK 2768 2771 2772 2793 C3' C B 3 OK 2791 2794 2795 2813 C3' U B 4 OK 2811 2814 2815 2833 C3' U B 5 OK 2831 2834 2835 2853 C3' U B 6 OK 2851 2854 2855 2873 C3' U B 7 OK 2871 2874 2875 2893 C3' G B 8 OK 2891 2894 2895 2916 C3' A B 9 OK 2914 2917 2918 2938 C3' C B 10 OK 2936 2939 2940 2958 C3' C B 11 OK 2956 2959 2960 2978 C3' U B 12 OK 2976 2979 2980 2998 C3' U B 13 OK 2996 2999 3000 3018 C3' U B 14 OK 3016 3019 3020 3038 C3' A B 15 OK 3036 3039 3040 3060 C3' U B 16 OK 3058 3061 3062 3080 C3' G B 17 OK 3078 3081 3082 3103 C3' C B 18 OK 3101 3104 3105 3121 C3' G C 1 OK 3119 3122 3123 3144 C3' C C 2 OK 3142 3145 3146 3164 C3' A C 3 OK 3162 3165 3166 3186 C3' U C 4 OK 3184 3187 3188 3206 C3' A C 5 OK 3204 3207 3208 3228 C3' A C 6 OK 3226 3229 3230 3250 C3' A C 7 OK 3248 3251 3252 3272 C3' G C 8 OK 3270 3273 3274 3295 C3' G C 9 OK 3293 3296 3297 3318 C3' U C 10 OK 3316 3319 3320 3338 C3' C C 11 OK 3336 3339 3340 3358 C3' A C 12 OK 3356 3359 3360 3380 C3' A C 13 OK 3378 3381 3382 3402 C3' A C 14 OK 3400 3403 3404 3424 C3' A C 15 OK 3422 3425 3426 3446 C3' G C 16 OK 3444 3447 3448 3469 C3' C C 17 OK 3467 3470 3471 3489 C3' C C 18 OK 3487 3490 3491 3521 C3' DTP A 403 OK 3519 3522 3523 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2745 C4' G B 1 OK 2747 2744 2746 2768 C4' G B 2 OK 2770 2767 2769 2791 C4' C B 3 OK 2793 2790 2792 2811 C4' U B 4 OK 2813 2810 2812 2831 C4' U B 5 OK 2833 2830 2832 2851 C4' U B 6 OK 2853 2850 2852 2871 C4' U B 7 OK 2873 2870 2872 2891 C4' G B 8 OK 2893 2890 2892 2914 C4' A B 9 OK 2916 2913 2915 2936 C4' C B 10 OK 2938 2935 2937 2956 C4' C B 11 OK 2958 2955 2957 2976 C4' U B 12 OK 2978 2975 2977 2996 C4' U B 13 OK 2998 2995 2997 3016 C4' U B 14 OK 3018 3015 3017 3036 C4' A B 15 OK 3038 3035 3037 3058 C4' U B 16 OK 3060 3057 3059 3078 C4' G B 17 OK 3080 3077 3079 3101 C4' C B 18 OK 3103 3100 3102 3119 C4' G C 1 OK 3121 3118 3120 3142 C4' C C 2 OK 3144 3141 3143 3162 C4' A C 3 OK 3164 3161 3163 3184 C4' U C 4 OK 3186 3183 3185 3204 C4' A C 5 OK 3206 3203 3205 3226 C4' A C 6 OK 3228 3225 3227 3248 C4' A C 7 OK 3250 3247 3249 3270 C4' G C 8 OK 3272 3269 3271 3293 C4' G C 9 OK 3295 3292 3294 3316 C4' U C 10 OK 3318 3315 3317 3336 C4' C C 11 OK 3338 3335 3337 3356 C4' A C 12 OK 3358 3355 3357 3378 C4' A C 13 OK 3380 3377 3379 3400 C4' A C 14 OK 3402 3399 3401 3422 C4' A C 15 OK 3424 3421 3423 3444 C4' G C 16 OK 3446 3443 3445 3467 C4' C C 17 OK 3469 3466 3468 3487 C4' C C 18 OK 3489 3486 3488 3519 C4' DTP A 403 OK 3521 3518 3520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2744 C5' G B 1 2743 2745 2767 C5' G B 2 2766 2768 2790 C5' C B 3 2789 2791 2810 C5' U B 4 2809 2811 2830 C5' U B 5 2829 2831 2850 C5' U B 6 2849 2851 2870 C5' U B 7 2869 2871 2890 C5' G B 8 2889 2891 2913 C5' A B 9 2912 2914 2935 C5' C B 10 2934 2936 2955 C5' C B 11 2954 2956 2975 C5' U B 12 2974 2976 2995 C5' U B 13 2994 2996 3015 C5' U B 14 3014 3016 3035 C5' A B 15 3034 3036 3057 C5' U B 16 3056 3058 3077 C5' G B 17 3076 3078 3100 C5' C B 18 3099 3101 3118 C5' G C 1 3117 3119 3141 C5' C C 2 3140 3142 3161 C5' A C 3 3160 3162 3183 C5' U C 4 3182 3184 3203 C5' A C 5 3202 3204 3225 C5' A C 6 3224 3226 3247 C5' A C 7 3246 3248 3269 C5' G C 8 3268 3270 3292 C5' G C 9 3291 3293 3315 C5' U C 10 3314 3316 3335 C5' C C 11 3334 3336 3355 C5' A C 12 3354 3356 3377 C5' A C 13 3376 3378 3399 C5' A C 14 3398 3400 3421 C5' A C 15 3420 3422 3443 C5' G C 16 3442 3444 3466 C5' C C 17 3465 3467 3486 C5' C C 18 3485 3487 3518 C5' DTP A 403 3517 3519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2763 P G B 2 distorted distorted 2748 2764 2765 2766 2786 P C B 3 distorted distorted 2771 2787 2788 2789 2806 P U B 4 distorted distorted 2794 2807 2808 2809 2826 P U B 5 distorted distorted 2814 2827 2828 2829 2846 P U B 6 distorted distorted 2834 2847 2848 2849 2866 P U B 7 distorted distorted 2854 2867 2868 2869 2886 P G B 8 distorted distorted 2874 2887 2888 2889 2909 P A B 9 distorted distorted 2894 2910 2911 2912 2931 P C B 10 distorted distorted 2917 2932 2933 2934 2951 P C B 11 distorted distorted 2939 2952 2953 2954 2971 P U B 12 distorted distorted 2959 2972 2973 2974 2991 P U B 13 distorted distorted 2979 2992 2993 2994 3011 P U B 14 distorted distorted 2999 3012 3013 3014 3031 P A B 15 distorted distorted 3019 3032 3033 3034 3053 P U B 16 distorted distorted 3039 3054 3055 3056 3073 P G B 17 distorted distorted 3061 3074 3075 3076 3096 P C B 18 distorted distorted 3081 3097 3098 3099 3137 P C C 2 distorted distorted 3122 3138 3139 3140 3157 P A C 3 distorted distorted 3145 3158 3159 3160 3179 P U C 4 distorted distorted 3165 3180 3181 3182 3199 P A C 5 distorted distorted 3187 3200 3201 3202 3221 P A C 6 distorted distorted 3207 3222 3223 3224 3243 P A C 7 distorted distorted 3229 3244 3245 3246 3265 P G C 8 distorted distorted 3251 3266 3267 3268 3288 P G C 9 distorted distorted 3273 3289 3290 3291 3311 P U C 10 distorted distorted 3296 3312 3313 3314 3331 P C C 11 distorted distorted 3319 3332 3333 3334 3351 P A C 12 distorted distorted 3339 3352 3353 3354 3373 P A C 13 distorted distorted 3359 3374 3375 3376 3395 P A C 14 distorted distorted 3381 3396 3397 3398 3417 P A C 15 distorted distorted 3403 3418 3419 3420 3439 P G C 16 distorted distorted 3425 3440 3441 3442 3462 P C C 17 distorted distorted 3447 3463 3464 3465 3482 P C C 18 distorted distorted 3470 3483 3484 3485 ---------------------------------------------------------------------------------