ID code: '4IRK' 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' --------------------------------------------------------------------------------- 2697 C1' DT C 837 beta 2693 2698 2696 2717 C1' DC C 838 beta 2713 2718 2716 2736 C1' DT C 839 beta 2732 2737 2735 2756 C1' DA C 840 beta 2752 2757 2755 2777 C1' DG C 841 beta 2773 2778 2776 2799 C1' DG C 842 beta 2795 2800 2798 2821 C1' DG C 843 beta 2817 2822 2820 2843 C1' DT C 844 beta 2839 2844 2842 2863 C1' DC C 845 beta 2859 2864 2862 2882 C1' DC C 846 beta 2878 2883 2881 2901 C1' DT C 847 beta 2897 2902 2900 2921 C1' DA C 848 beta 2917 2922 2920 2942 C1' DG C 849 beta 2938 2943 2941 2964 C1' DG C 850 beta 2960 2965 2963 2986 C1' DA C 851 beta 2982 2987 2985 3007 C1' DC C 852 beta 3003 3008 3006 3026 C1' DC C 853 beta 3022 3027 3025 3045 C1' DC C 854 beta 3041 3046 3044 3062 C1' DG G 860 beta 3058 3063 3061 3084 C1' DG G 861 beta 3080 3085 3083 3106 C1' DG G 862 beta 3102 3107 3105 3128 C1' DT G 863 beta 3124 3129 3127 3148 C1' DC G 864 beta 3144 3149 3147 3167 C1' DC G 865 beta 3163 3168 3166 3186 C1' DT G 866 beta 3182 3187 3185 3206 C1' DA G 867 beta 3202 3207 3205 3227 C1' DG G 868 beta 3223 3228 3226 3249 C1' DG G 869 beta 3245 3250 3248 3271 C1' DA G 870 beta 3267 3272 3270 3292 C1' DC G 871 beta 3288 3293 3291 3311 C1' DC G 872 beta 3307 3312 3310 3328 C1' DOC G 873 beta 3332 3320 3329 6035 C1' DT F 837 beta 6031 6036 6034 6055 C1' DC F 838 beta 6051 6056 6054 6074 C1' DT F 839 beta 6070 6075 6073 6094 C1' DA F 840 beta 6090 6095 6093 6115 C1' DG F 841 beta 6111 6116 6114 6137 C1' DG F 842 beta 6133 6138 6136 6159 C1' DG F 843 beta 6155 6160 6158 6181 C1' DT F 844 beta 6177 6182 6180 6201 C1' DC F 845 beta 6197 6202 6200 6220 C1' DC F 846 beta 6216 6221 6219 6239 C1' DT F 847 beta 6235 6240 6238 6259 C1' DA F 848 beta 6255 6260 6258 6280 C1' DG F 849 beta 6276 6281 6279 6302 C1' DG F 850 beta 6298 6303 6301 6324 C1' DA F 851 beta 6320 6325 6323 6345 C1' DC F 852 beta 6341 6346 6344 6364 C1' DC F 853 beta 6360 6365 6363 6383 C1' DC F 854 beta 6379 6384 6382 6400 C1' DG H 860 beta 6396 6401 6399 6422 C1' DG H 861 beta 6418 6423 6421 6444 C1' DG H 862 beta 6440 6445 6443 6466 C1' DT H 863 beta 6462 6467 6465 6486 C1' DC H 864 beta 6482 6487 6485 6505 C1' DC H 865 beta 6501 6506 6504 6524 C1' DT H 866 beta 6520 6525 6523 6544 C1' DA H 867 beta 6540 6545 6543 6565 C1' DG H 868 beta 6561 6566 6564 6587 C1' DG H 869 beta 6583 6588 6586 6609 C1' DA H 870 beta 6605 6610 6608 6630 C1' DC H 871 beta 6626 6631 6629 6649 C1' DC H 872 beta 6645 6650 6648 6666 C1' DOC H 873 beta 6670 6658 6667 6685 C1' DCP B 401 beta 6689 6677 6686 6714 C1' DCP A 401 beta 6718 6706 6715 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2696 C2' DT C 837 2697 2694 2716 C2' DC C 838 2717 2714 2735 C2' DT C 839 2736 2733 2755 C2' DA C 840 2756 2753 2776 C2' DG C 841 2777 2774 2798 C2' DG C 842 2799 2796 2820 C2' DG C 843 2821 2818 2842 C2' DT C 844 2843 2840 2862 C2' DC C 845 2863 2860 2881 C2' DC C 846 2882 2879 2900 C2' DT C 847 2901 2898 2920 C2' DA C 848 2921 2918 2941 C2' DG C 849 2942 2939 2963 C2' DG C 850 2964 2961 2985 C2' DA C 851 2986 2983 3006 C2' DC C 852 3007 3004 3025 C2' DC C 853 3026 3023 3044 C2' DC C 854 3045 3042 3061 C2' DG G 860 3062 3059 3083 C2' DG G 861 3084 3081 3105 C2' DG G 862 3106 3103 3127 C2' DT G 863 3128 3125 3147 C2' DC G 864 3148 3145 3166 C2' DC G 865 3167 3164 3185 C2' DT G 866 3186 3183 3205 C2' DA G 867 3206 3203 3226 C2' DG G 868 3227 3224 3248 C2' DG G 869 3249 3246 3270 C2' DA G 870 3271 3268 3291 C2' DC G 871 3292 3289 3310 C2' DC G 872 3311 3308 3329 C2' DOC G 873 3328 3330 6034 C2' DT F 837 6035 6032 6054 C2' DC F 838 6055 6052 6073 C2' DT F 839 6074 6071 6093 C2' DA F 840 6094 6091 6114 C2' DG F 841 6115 6112 6136 C2' DG F 842 6137 6134 6158 C2' DG F 843 6159 6156 6180 C2' DT F 844 6181 6178 6200 C2' DC F 845 6201 6198 6219 C2' DC F 846 6220 6217 6238 C2' DT F 847 6239 6236 6258 C2' DA F 848 6259 6256 6279 C2' DG F 849 6280 6277 6301 C2' DG F 850 6302 6299 6323 C2' DA F 851 6324 6321 6344 C2' DC F 852 6345 6342 6363 C2' DC F 853 6364 6361 6382 C2' DC F 854 6383 6380 6399 C2' DG H 860 6400 6397 6421 C2' DG H 861 6422 6419 6443 C2' DG H 862 6444 6441 6465 C2' DT H 863 6466 6463 6485 C2' DC H 864 6486 6483 6504 C2' DC H 865 6505 6502 6523 C2' DT H 866 6524 6521 6543 C2' DA H 867 6544 6541 6564 C2' DG H 868 6565 6562 6586 C2' DG H 869 6587 6584 6608 C2' DA H 870 6609 6606 6629 C2' DC H 871 6630 6627 6648 C2' DC H 872 6649 6646 6667 C2' DOC H 873 6666 6668 6686 C2' DCP B 401 6685 6687 6715 C2' DCP A 401 6714 6716 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2694 C3' DT C 837 OK 2692 2695 2696 2714 C3' DC C 838 OK 2712 2715 2716 2733 C3' DT C 839 OK 2731 2734 2735 2753 C3' DA C 840 OK 2751 2754 2755 2774 C3' DG C 841 OK 2772 2775 2776 2796 C3' DG C 842 OK 2794 2797 2798 2818 C3' DG C 843 OK 2816 2819 2820 2840 C3' DT C 844 OK 2838 2841 2842 2860 C3' DC C 845 OK 2858 2861 2862 2879 C3' DC C 846 OK 2877 2880 2881 2898 C3' DT C 847 OK 2896 2899 2900 2918 C3' DA C 848 OK 2916 2919 2920 2939 C3' DG C 849 OK 2937 2940 2941 2961 C3' DG C 850 OK 2959 2962 2963 2983 C3' DA C 851 OK 2981 2984 2985 3004 C3' DC C 852 OK 3002 3005 3006 3023 C3' DC C 853 OK 3021 3024 3025 3042 C3' DC C 854 OK 3040 3043 3044 3059 C3' DG G 860 OK 3057 3060 3061 3081 C3' DG G 861 OK 3079 3082 3083 3103 C3' DG G 862 OK 3101 3104 3105 3125 C3' DT G 863 OK 3123 3126 3127 3145 C3' DC G 864 OK 3143 3146 3147 3164 C3' DC G 865 OK 3162 3165 3166 3183 C3' DT G 866 OK 3181 3184 3185 3203 C3' DA G 867 OK 3201 3204 3205 3224 C3' DG G 868 OK 3222 3225 3226 3246 C3' DG G 869 OK 3244 3247 3248 3268 C3' DA G 870 OK 3266 3269 3270 3289 C3' DC G 871 OK 3287 3290 3291 3308 C3' DC G 872 OK 3306 3309 3310 3330 C3' DOC G 873 3331 3329 6032 C3' DT F 837 OK 6030 6033 6034 6052 C3' DC F 838 OK 6050 6053 6054 6071 C3' DT F 839 OK 6069 6072 6073 6091 C3' DA F 840 OK 6089 6092 6093 6112 C3' DG F 841 OK 6110 6113 6114 6134 C3' DG F 842 OK 6132 6135 6136 6156 C3' DG F 843 OK 6154 6157 6158 6178 C3' DT F 844 OK 6176 6179 6180 6198 C3' DC F 845 OK 6196 6199 6200 6217 C3' DC F 846 OK 6215 6218 6219 6236 C3' DT F 847 OK 6234 6237 6238 6256 C3' DA F 848 OK 6254 6257 6258 6277 C3' DG F 849 OK 6275 6278 6279 6299 C3' DG F 850 OK 6297 6300 6301 6321 C3' DA F 851 OK 6319 6322 6323 6342 C3' DC F 852 OK 6340 6343 6344 6361 C3' DC F 853 OK 6359 6362 6363 6380 C3' DC F 854 OK 6378 6381 6382 6397 C3' DG H 860 OK 6395 6398 6399 6419 C3' DG H 861 OK 6417 6420 6421 6441 C3' DG H 862 OK 6439 6442 6443 6463 C3' DT H 863 OK 6461 6464 6465 6483 C3' DC H 864 OK 6481 6484 6485 6502 C3' DC H 865 OK 6500 6503 6504 6521 C3' DT H 866 OK 6519 6522 6523 6541 C3' DA H 867 OK 6539 6542 6543 6562 C3' DG H 868 OK 6560 6563 6564 6584 C3' DG H 869 OK 6582 6585 6586 6606 C3' DA H 870 OK 6604 6607 6608 6627 C3' DC H 871 OK 6625 6628 6629 6646 C3' DC H 872 OK 6644 6647 6648 6668 C3' DOC H 873 6669 6667 6687 C3' DCP B 401 OK 6688 6690 6686 6716 C3' DCP A 401 OK 6717 6719 6715 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2692 C4' DT C 837 OK 2694 2691 2693 2712 C4' DC C 838 OK 2714 2711 2713 2731 C4' DT C 839 OK 2733 2730 2732 2751 C4' DA C 840 OK 2753 2750 2752 2772 C4' DG C 841 OK 2774 2771 2773 2794 C4' DG C 842 OK 2796 2793 2795 2816 C4' DG C 843 OK 2818 2815 2817 2838 C4' DT C 844 OK 2840 2837 2839 2858 C4' DC C 845 OK 2860 2857 2859 2877 C4' DC C 846 OK 2879 2876 2878 2896 C4' DT C 847 OK 2898 2895 2897 2916 C4' DA C 848 OK 2918 2915 2917 2937 C4' DG C 849 OK 2939 2936 2938 2959 C4' DG C 850 OK 2961 2958 2960 2981 C4' DA C 851 OK 2983 2980 2982 3002 C4' DC C 852 OK 3004 3001 3003 3021 C4' DC C 853 OK 3023 3020 3022 3040 C4' DC C 854 OK 3042 3039 3041 3057 C4' DG G 860 OK 3059 3056 3058 3079 C4' DG G 861 OK 3081 3078 3080 3101 C4' DG G 862 OK 3103 3100 3102 3123 C4' DT G 863 OK 3125 3122 3124 3143 C4' DC G 864 OK 3145 3142 3144 3162 C4' DC G 865 OK 3164 3161 3163 3181 C4' DT G 866 OK 3183 3180 3182 3201 C4' DA G 867 OK 3203 3200 3202 3222 C4' DG G 868 OK 3224 3221 3223 3244 C4' DG G 869 OK 3246 3243 3245 3266 C4' DA G 870 OK 3268 3265 3267 3287 C4' DC G 871 OK 3289 3286 3288 3306 C4' DC G 872 OK 3308 3305 3307 3331 C4' DOC G 873 OK 3330 3333 3332 6030 C4' DT F 837 OK 6032 6029 6031 6050 C4' DC F 838 OK 6052 6049 6051 6069 C4' DT F 839 OK 6071 6068 6070 6089 C4' DA F 840 OK 6091 6088 6090 6110 C4' DG F 841 OK 6112 6109 6111 6132 C4' DG F 842 OK 6134 6131 6133 6154 C4' DG F 843 OK 6156 6153 6155 6176 C4' DT F 844 OK 6178 6175 6177 6196 C4' DC F 845 OK 6198 6195 6197 6215 C4' DC F 846 OK 6217 6214 6216 6234 C4' DT F 847 OK 6236 6233 6235 6254 C4' DA F 848 OK 6256 6253 6255 6275 C4' DG F 849 OK 6277 6274 6276 6297 C4' DG F 850 OK 6299 6296 6298 6319 C4' DA F 851 OK 6321 6318 6320 6340 C4' DC F 852 OK 6342 6339 6341 6359 C4' DC F 853 OK 6361 6358 6360 6378 C4' DC F 854 OK 6380 6377 6379 6395 C4' DG H 860 OK 6397 6394 6396 6417 C4' DG H 861 OK 6419 6416 6418 6439 C4' DG H 862 OK 6441 6438 6440 6461 C4' DT H 863 OK 6463 6460 6462 6481 C4' DC H 864 OK 6483 6480 6482 6500 C4' DC H 865 OK 6502 6499 6501 6519 C4' DT H 866 OK 6521 6518 6520 6539 C4' DA H 867 OK 6541 6538 6540 6560 C4' DG H 868 OK 6562 6559 6561 6582 C4' DG H 869 OK 6584 6581 6583 6604 C4' DA H 870 OK 6606 6603 6605 6625 C4' DC H 871 OK 6627 6624 6626 6644 C4' DC H 872 OK 6646 6643 6645 6669 C4' DOC H 873 OK 6668 6671 6670 6688 C4' DCP B 401 OK 6687 6691 6689 6717 C4' DCP A 401 OK 6716 6720 6718 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2691 C5' DT C 837 2690 2692 2711 C5' DC C 838 2710 2712 2730 C5' DT C 839 2729 2731 2750 C5' DA C 840 2749 2751 2771 C5' DG C 841 2770 2772 2793 C5' DG C 842 2792 2794 2815 C5' DG C 843 2814 2816 2837 C5' DT C 844 2836 2838 2857 C5' DC C 845 2856 2858 2876 C5' DC C 846 2875 2877 2895 C5' DT C 847 2894 2896 2915 C5' DA C 848 2914 2916 2936 C5' DG C 849 2935 2937 2958 C5' DG C 850 2957 2959 2980 C5' DA C 851 2979 2981 3001 C5' DC C 852 3000 3002 3020 C5' DC C 853 3019 3021 3039 C5' DC C 854 3038 3040 3056 C5' DG G 860 3055 3057 3078 C5' DG G 861 3077 3079 3100 C5' DG G 862 3099 3101 3122 C5' DT G 863 3121 3123 3142 C5' DC G 864 3141 3143 3161 C5' DC G 865 3160 3162 3180 C5' DT G 866 3179 3181 3200 C5' DA G 867 3199 3201 3221 C5' DG G 868 3220 3222 3243 C5' DG G 869 3242 3244 3265 C5' DA G 870 3264 3266 3286 C5' DC G 871 3285 3287 3305 C5' DC G 872 3304 3306 3333 C5' DOC G 873 3334 3331 6029 C5' DT F 837 6028 6030 6049 C5' DC F 838 6048 6050 6068 C5' DT F 839 6067 6069 6088 C5' DA F 840 6087 6089 6109 C5' DG F 841 6108 6110 6131 C5' DG F 842 6130 6132 6153 C5' DG F 843 6152 6154 6175 C5' DT F 844 6174 6176 6195 C5' DC F 845 6194 6196 6214 C5' DC F 846 6213 6215 6233 C5' DT F 847 6232 6234 6253 C5' DA F 848 6252 6254 6274 C5' DG F 849 6273 6275 6296 C5' DG F 850 6295 6297 6318 C5' DA F 851 6317 6319 6339 C5' DC F 852 6338 6340 6358 C5' DC F 853 6357 6359 6377 C5' DC F 854 6376 6378 6394 C5' DG H 860 6393 6395 6416 C5' DG H 861 6415 6417 6438 C5' DG H 862 6437 6439 6460 C5' DT H 863 6459 6461 6480 C5' DC H 864 6479 6481 6499 C5' DC H 865 6498 6500 6518 C5' DT H 866 6517 6519 6538 C5' DA H 867 6537 6539 6559 C5' DG H 868 6558 6560 6581 C5' DG H 869 6580 6582 6603 C5' DA H 870 6602 6604 6624 C5' DC H 871 6623 6625 6643 C5' DC H 872 6642 6644 6671 C5' DOC H 873 6672 6669 6691 C5' DCP B 401 6692 6688 6720 C5' DCP A 401 6721 6717 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2707 P DC C 838 distorted distorted 2695 2708 2709 2710 2726 P DT C 839 distorted distorted 2715 2727 2728 2729 2746 P DA C 840 distorted distorted 2734 2747 2748 2749 2767 P DG C 841 distorted distorted 2754 2768 2769 2770 2789 P DG C 842 distorted distorted 2775 2790 2791 2792 2811 P DG C 843 distorted distorted 2797 2812 2813 2814 2833 P DT C 844 distorted distorted 2819 2834 2835 2836 2853 P DC C 845 distorted distorted 2841 2854 2855 2856 2872 P DC C 846 distorted distorted 2861 2873 2874 2875 2891 P DT C 847 distorted distorted 2880 2892 2893 2894 2911 P DA C 848 distorted distorted 2899 2912 2913 2914 2932 P DG C 849 distorted distorted 2919 2933 2934 2935 2954 P DG C 850 distorted distorted 2940 2955 2956 2957 2976 P DA C 851 distorted distorted 2962 2977 2978 2979 2997 P DC C 852 distorted distorted 2984 2998 2999 3000 3016 P DC C 853 distorted distorted 3005 3017 3018 3019 3035 P DC C 854 distorted distorted 3024 3036 3037 3038 3074 P DG G 861 distorted distorted 3060 3075 3076 3077 3096 P DG G 862 distorted distorted 3082 3097 3098 3099 3118 P DT G 863 distorted distorted 3104 3119 3120 3121 3138 P DC G 864 distorted distorted 3126 3139 3140 3141 3157 P DC G 865 distorted distorted 3146 3158 3159 3160 3176 P DT G 866 distorted distorted 3165 3177 3178 3179 3196 P DA G 867 distorted distorted 3184 3197 3198 3199 3217 P DG G 868 distorted distorted 3204 3218 3219 3220 3239 P DG G 869 distorted distorted 3225 3240 3241 3242 3261 P DA G 870 distorted distorted 3247 3262 3263 3264 3282 P DC G 871 distorted distorted 3269 3283 3284 3285 3301 P DC G 872 distorted distorted 3290 3302 3303 3304 3335 P DOC G 873 distorted distorted 3309 3336 3337 3334 6045 P DC F 838 distorted distorted 6033 6046 6047 6048 6064 P DT F 839 distorted distorted 6053 6065 6066 6067 6084 P DA F 840 distorted distorted 6072 6085 6086 6087 6105 P DG F 841 distorted distorted 6092 6106 6107 6108 6127 P DG F 842 distorted distorted 6113 6128 6129 6130 6149 P DG F 843 distorted distorted 6135 6150 6151 6152 6171 P DT F 844 distorted distorted 6157 6172 6173 6174 6191 P DC F 845 distorted distorted 6179 6192 6193 6194 6210 P DC F 846 distorted distorted 6199 6211 6212 6213 6229 P DT F 847 distorted distorted 6218 6230 6231 6232 6249 P DA F 848 distorted distorted 6237 6250 6251 6252 6270 P DG F 849 distorted distorted 6257 6271 6272 6273 6292 P DG F 850 distorted distorted 6278 6293 6294 6295 6314 P DA F 851 distorted distorted 6300 6315 6316 6317 6335 P DC F 852 distorted distorted 6322 6336 6337 6338 6354 P DC F 853 distorted distorted 6343 6355 6356 6357 6373 P DC F 854 distorted distorted 6362 6374 6375 6376 6412 P DG H 861 distorted distorted 6398 6413 6414 6415 6434 P DG H 862 distorted distorted 6420 6435 6436 6437 6456 P DT H 863 distorted distorted 6442 6457 6458 6459 6476 P DC H 864 distorted distorted 6464 6477 6478 6479 6495 P DC H 865 distorted distorted 6484 6496 6497 6498 6514 P DT H 866 distorted distorted 6503 6515 6516 6517 6534 P DA H 867 distorted distorted 6522 6535 6536 6537 6555 P DG H 868 distorted distorted 6542 6556 6557 6558 6577 P DG H 869 distorted distorted 6563 6578 6579 6580 6599 P DA H 870 distorted distorted 6585 6600 6601 6602 6620 P DC H 871 distorted distorted 6607 6621 6622 6623 6639 P DC H 872 distorted distorted 6628 6640 6641 6642 6673 P DOC H 873 distorted distorted 6647 6674 6675 6672 ---------------------------------------------------------------------------------