ID code: '3RAX' 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' --------------------------------------------------------------------------------- 2749 C1' DG D 802 beta 2745 2750 2748 2771 C1' DT D 803 beta 2767 2772 2770 2791 C1' DT D 804 beta 2787 2792 2790 2811 C1' DG D 805 beta 2807 2812 2810 2833 C1' DG D 806 beta 2829 2834 2832 2855 C1' DA D 807 beta 2851 2856 2854 2876 C1' DT D 808 beta 2872 2877 2875 2896 C1' DG D 809 beta 2892 2897 2895 2918 C1' DG D 810 beta 2914 2919 2917 2940 C1' DT D 811 beta 2936 2941 2939 2960 C1' DA D 812 beta 2956 2961 2959 2981 C1' DG D 813 beta 2977 2982 2980 3010 C1' 2DT D 814 beta 3009 2997 3006 3020 C1' DT E 902 beta 3016 3021 3019 3040 C1' DA E 903 beta 3036 3041 3039 3061 C1' DA E 904 beta 3057 3062 3060 3082 C1' DC E 905 beta 3078 3083 3081 3101 C1' MG1 E 906 beta 3097 3102 3100 3124 C1' DC E 907 beta 3120 3125 3123 3143 C1' DT E 908 beta 3139 3144 3142 3163 C1' DA E 909 beta 3159 3164 3162 3184 C1' DC E 910 beta 3180 3185 3183 3203 C1' DC E 911 beta 3199 3204 3202 3222 C1' DA E 912 beta 3218 3223 3221 3243 C1' DT E 913 beta 3239 3244 3242 3263 C1' DC E 914 beta 3259 3264 3262 3282 C1' DC E 915 beta 3278 3283 3281 3301 C1' DA E 916 beta 3297 3302 3300 3322 C1' DA E 917 beta 3318 3323 3321 3343 C1' DC E 918 beta 3339 3344 3342 3362 C1' DC E 919 beta 3358 3363 3361 6120 C1' DG H1802 beta 6116 6121 6119 6142 C1' DT H1803 beta 6138 6143 6141 6162 C1' DT H1804 beta 6158 6163 6161 6182 C1' DG H1805 beta 6178 6183 6181 6204 C1' DG H1806 beta 6200 6205 6203 6226 C1' DA H1807 beta 6222 6227 6225 6247 C1' DT H1808 beta 6243 6248 6246 6267 C1' DG H1809 beta 6263 6268 6266 6289 C1' DG H1810 beta 6285 6290 6288 6311 C1' DT H1811 beta 6307 6312 6310 6331 C1' DA H1812 beta 6327 6332 6330 6352 C1' DG H1813 beta 6348 6353 6351 6381 C1' 2DT H1814 beta 6380 6368 6377 6391 C1' DA J1903 beta 6387 6392 6390 6412 C1' DA J1904 beta 6408 6413 6411 6433 C1' DC J1905 beta 6429 6434 6432 6452 C1' MG1 J1906 beta 6448 6453 6451 6475 C1' DC J1907 beta 6471 6476 6474 6494 C1' DT J1908 beta 6490 6495 6493 6514 C1' DA J1909 beta 6510 6515 6513 6535 C1' DC J1910 beta 6531 6536 6534 6554 C1' DC J1911 beta 6550 6555 6553 6573 C1' DA J1912 beta 6569 6574 6572 6594 C1' DT J1913 beta 6590 6595 6593 6614 C1' DC J1914 beta 6610 6615 6613 6633 C1' DC J1915 beta 6629 6634 6632 6652 C1' DA J1916 beta 6648 6653 6651 6673 C1' DA J1917 beta 6669 6674 6672 6694 C1' DC J1918 beta 6690 6695 6693 6713 C1' DC J1919 beta 6709 6714 6712 6742 C1' DGT A 414 beta 6738 6743 6741 6776 C1' DGT B1414 beta 6772 6777 6775 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2748 C2' DG D 802 2749 2746 2770 C2' DT D 803 2771 2768 2790 C2' DT D 804 2791 2788 2810 C2' DG D 805 2811 2808 2832 C2' DG D 806 2833 2830 2854 C2' DA D 807 2855 2852 2875 C2' DT D 808 2876 2873 2895 C2' DG D 809 2896 2893 2917 C2' DG D 810 2918 2915 2939 C2' DT D 811 2940 2937 2959 C2' DA D 812 2960 2957 2980 C2' DG D 813 2981 2978 3006 C2' 2DT D 814 3010 3011 3019 C2' DT E 902 3020 3017 3039 C2' DA E 903 3040 3037 3060 C2' DA E 904 3061 3058 3081 C2' DC E 905 3082 3079 3100 C2' MG1 E 906 3101 3098 3123 C2' DC E 907 3124 3121 3142 C2' DT E 908 3143 3140 3162 C2' DA E 909 3163 3160 3183 C2' DC E 910 3184 3181 3202 C2' DC E 911 3203 3200 3221 C2' DA E 912 3222 3219 3242 C2' DT E 913 3243 3240 3262 C2' DC E 914 3263 3260 3281 C2' DC E 915 3282 3279 3300 C2' DA E 916 3301 3298 3321 C2' DA E 917 3322 3319 3342 C2' DC E 918 3343 3340 3361 C2' DC E 919 3362 3359 6119 C2' DG H1802 6120 6117 6141 C2' DT H1803 6142 6139 6161 C2' DT H1804 6162 6159 6181 C2' DG H1805 6182 6179 6203 C2' DG H1806 6204 6201 6225 C2' DA H1807 6226 6223 6246 C2' DT H1808 6247 6244 6266 C2' DG H1809 6267 6264 6288 C2' DG H1810 6289 6286 6310 C2' DT H1811 6311 6308 6330 C2' DA H1812 6331 6328 6351 C2' DG H1813 6352 6349 6377 C2' 2DT H1814 6381 6382 6390 C2' DA J1903 6391 6388 6411 C2' DA J1904 6412 6409 6432 C2' DC J1905 6433 6430 6451 C2' MG1 J1906 6452 6449 6474 C2' DC J1907 6475 6472 6493 C2' DT J1908 6494 6491 6513 C2' DA J1909 6514 6511 6534 C2' DC J1910 6535 6532 6553 C2' DC J1911 6554 6551 6572 C2' DA J1912 6573 6570 6593 C2' DT J1913 6594 6591 6613 C2' DC J1914 6614 6611 6632 C2' DC J1915 6633 6630 6651 C2' DA J1916 6652 6649 6672 C2' DA J1917 6673 6670 6693 C2' DC J1918 6694 6691 6712 C2' DC J1919 6713 6710 6741 C2' DGT A 414 6742 6739 6775 C2' DGT B1414 6776 6773 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2746 C3' DG D 802 OK 2744 2747 2748 2768 C3' DT D 803 OK 2766 2769 2770 2788 C3' DT D 804 OK 2786 2789 2790 2808 C3' DG D 805 OK 2806 2809 2810 2830 C3' DG D 806 OK 2828 2831 2832 2852 C3' DA D 807 OK 2850 2853 2854 2873 C3' DT D 808 OK 2871 2874 2875 2893 C3' DG D 809 OK 2891 2894 2895 2915 C3' DG D 810 OK 2913 2916 2917 2937 C3' DT D 811 OK 2935 2938 2939 2957 C3' DA D 812 OK 2955 2958 2959 2978 C3' DG D 813 OK 2976 2979 2980 3011 C3' 2DT D 814 3008 3006 3017 C3' DT E 902 OK 3015 3018 3019 3037 C3' DA E 903 OK 3035 3038 3039 3058 C3' DA E 904 OK 3056 3059 3060 3079 C3' DC E 905 OK 3077 3080 3081 3098 C3' MG1 E 906 OK 3096 3099 3100 3121 C3' DC E 907 OK 3119 3122 3123 3140 C3' DT E 908 OK 3138 3141 3142 3160 C3' DA E 909 OK 3158 3161 3162 3181 C3' DC E 910 OK 3179 3182 3183 3200 C3' DC E 911 OK 3198 3201 3202 3219 C3' DA E 912 OK 3217 3220 3221 3240 C3' DT E 913 OK 3238 3241 3242 3260 C3' DC E 914 OK 3258 3261 3262 3279 C3' DC E 915 OK 3277 3280 3281 3298 C3' DA E 916 OK 3296 3299 3300 3319 C3' DA E 917 OK 3317 3320 3321 3340 C3' DC E 918 OK 3338 3341 3342 3359 C3' DC E 919 OK 3357 3360 3361 6117 C3' DG H1802 OK 6115 6118 6119 6139 C3' DT H1803 OK 6137 6140 6141 6159 C3' DT H1804 OK 6157 6160 6161 6179 C3' DG H1805 OK 6177 6180 6181 6201 C3' DG H1806 OK 6199 6202 6203 6223 C3' DA H1807 OK 6221 6224 6225 6244 C3' DT H1808 OK 6242 6245 6246 6264 C3' DG H1809 OK 6262 6265 6266 6286 C3' DG H1810 OK 6284 6287 6288 6308 C3' DT H1811 OK 6306 6309 6310 6328 C3' DA H1812 OK 6326 6329 6330 6349 C3' DG H1813 OK 6347 6350 6351 6382 C3' 2DT H1814 6379 6377 6388 C3' DA J1903 OK 6386 6389 6390 6409 C3' DA J1904 OK 6407 6410 6411 6430 C3' DC J1905 OK 6428 6431 6432 6449 C3' MG1 J1906 OK 6447 6450 6451 6472 C3' DC J1907 OK 6470 6473 6474 6491 C3' DT J1908 OK 6489 6492 6493 6511 C3' DA J1909 OK 6509 6512 6513 6532 C3' DC J1910 OK 6530 6533 6534 6551 C3' DC J1911 OK 6549 6552 6553 6570 C3' DA J1912 OK 6568 6571 6572 6591 C3' DT J1913 OK 6589 6592 6593 6611 C3' DC J1914 OK 6609 6612 6613 6630 C3' DC J1915 OK 6628 6631 6632 6649 C3' DA J1916 OK 6647 6650 6651 6670 C3' DA J1917 OK 6668 6671 6672 6691 C3' DC J1918 OK 6689 6692 6693 6710 C3' DC J1919 OK 6708 6711 6712 6739 C3' DGT A 414 OK 6737 6740 6741 6773 C3' DGT B1414 OK 6771 6774 6775 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2744 C4' DG D 802 OK 2746 2743 2745 2766 C4' DT D 803 OK 2768 2765 2767 2786 C4' DT D 804 OK 2788 2785 2787 2806 C4' DG D 805 OK 2808 2805 2807 2828 C4' DG D 806 OK 2830 2827 2829 2850 C4' DA D 807 OK 2852 2849 2851 2871 C4' DT D 808 OK 2873 2870 2872 2891 C4' DG D 809 OK 2893 2890 2892 2913 C4' DG D 810 OK 2915 2912 2914 2935 C4' DT D 811 OK 2937 2934 2936 2955 C4' DA D 812 OK 2957 2954 2956 2976 C4' DG D 813 OK 2978 2975 2977 3008 C4' 2DT D 814 OK 3011 3007 3009 3015 C4' DT E 902 OK 3017 3014 3016 3035 C4' DA E 903 OK 3037 3034 3036 3056 C4' DA E 904 OK 3058 3055 3057 3077 C4' DC E 905 OK 3079 3076 3078 3096 C4' MG1 E 906 OK 3098 3095 3097 3119 C4' DC E 907 OK 3121 3118 3120 3138 C4' DT E 908 OK 3140 3137 3139 3158 C4' DA E 909 OK 3160 3157 3159 3179 C4' DC E 910 OK 3181 3178 3180 3198 C4' DC E 911 OK 3200 3197 3199 3217 C4' DA E 912 OK 3219 3216 3218 3238 C4' DT E 913 OK 3240 3237 3239 3258 C4' DC E 914 OK 3260 3257 3259 3277 C4' DC E 915 OK 3279 3276 3278 3296 C4' DA E 916 OK 3298 3295 3297 3317 C4' DA E 917 OK 3319 3316 3318 3338 C4' DC E 918 OK 3340 3337 3339 3357 C4' DC E 919 OK 3359 3356 3358 6115 C4' DG H1802 OK 6117 6114 6116 6137 C4' DT H1803 OK 6139 6136 6138 6157 C4' DT H1804 OK 6159 6156 6158 6177 C4' DG H1805 OK 6179 6176 6178 6199 C4' DG H1806 OK 6201 6198 6200 6221 C4' DA H1807 OK 6223 6220 6222 6242 C4' DT H1808 OK 6244 6241 6243 6262 C4' DG H1809 OK 6264 6261 6263 6284 C4' DG H1810 OK 6286 6283 6285 6306 C4' DT H1811 OK 6308 6305 6307 6326 C4' DA H1812 OK 6328 6325 6327 6347 C4' DG H1813 OK 6349 6346 6348 6379 C4' 2DT H1814 OK 6382 6378 6380 6386 C4' DA J1903 OK 6388 6385 6387 6407 C4' DA J1904 OK 6409 6406 6408 6428 C4' DC J1905 OK 6430 6427 6429 6447 C4' MG1 J1906 OK 6449 6446 6448 6470 C4' DC J1907 OK 6472 6469 6471 6489 C4' DT J1908 OK 6491 6488 6490 6509 C4' DA J1909 OK 6511 6508 6510 6530 C4' DC J1910 OK 6532 6529 6531 6549 C4' DC J1911 OK 6551 6548 6550 6568 C4' DA J1912 OK 6570 6567 6569 6589 C4' DT J1913 OK 6591 6588 6590 6609 C4' DC J1914 OK 6611 6608 6610 6628 C4' DC J1915 OK 6630 6627 6629 6647 C4' DA J1916 OK 6649 6646 6648 6668 C4' DA J1917 OK 6670 6667 6669 6689 C4' DC J1918 OK 6691 6688 6690 6708 C4' DC J1919 OK 6710 6707 6709 6737 C4' DGT A 414 OK 6739 6736 6738 6771 C4' DGT B1414 OK 6773 6770 6772 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2743 C5' DG D 802 2742 2744 2765 C5' DT D 803 2764 2766 2785 C5' DT D 804 2784 2786 2805 C5' DG D 805 2804 2806 2827 C5' DG D 806 2826 2828 2849 C5' DA D 807 2848 2850 2870 C5' DT D 808 2869 2871 2890 C5' DG D 809 2889 2891 2912 C5' DG D 810 2911 2913 2934 C5' DT D 811 2933 2935 2954 C5' DA D 812 2953 2955 2975 C5' DG D 813 2974 2976 3007 C5' 2DT D 814 2996 3008 3014 C5' DT E 902 3013 3015 3034 C5' DA E 903 3033 3035 3055 C5' DA E 904 3054 3056 3076 C5' DC E 905 3075 3077 3095 C5' MG1 E 906 3094 3096 3118 C5' DC E 907 3117 3119 3137 C5' DT E 908 3136 3138 3157 C5' DA E 909 3156 3158 3178 C5' DC E 910 3177 3179 3197 C5' DC E 911 3196 3198 3216 C5' DA E 912 3215 3217 3237 C5' DT E 913 3236 3238 3257 C5' DC E 914 3256 3258 3276 C5' DC E 915 3275 3277 3295 C5' DA E 916 3294 3296 3316 C5' DA E 917 3315 3317 3337 C5' DC E 918 3336 3338 3356 C5' DC E 919 3355 3357 6114 C5' DG H1802 6113 6115 6136 C5' DT H1803 6135 6137 6156 C5' DT H1804 6155 6157 6176 C5' DG H1805 6175 6177 6198 C5' DG H1806 6197 6199 6220 C5' DA H1807 6219 6221 6241 C5' DT H1808 6240 6242 6261 C5' DG H1809 6260 6262 6283 C5' DG H1810 6282 6284 6305 C5' DT H1811 6304 6306 6325 C5' DA H1812 6324 6326 6346 C5' DG H1813 6345 6347 6378 C5' 2DT H1814 6367 6379 6385 C5' DA J1903 6384 6386 6406 C5' DA J1904 6405 6407 6427 C5' DC J1905 6426 6428 6446 C5' MG1 J1906 6445 6447 6469 C5' DC J1907 6468 6470 6488 C5' DT J1908 6487 6489 6508 C5' DA J1909 6507 6509 6529 C5' DC J1910 6528 6530 6548 C5' DC J1911 6547 6549 6567 C5' DA J1912 6566 6568 6588 C5' DT J1913 6587 6589 6608 C5' DC J1914 6607 6609 6627 C5' DC J1915 6626 6628 6646 C5' DA J1916 6645 6647 6667 C5' DA J1917 6666 6668 6688 C5' DC J1918 6687 6689 6707 C5' DC J1919 6706 6708 6736 C5' DGT A 414 6735 6737 6770 C5' DGT B1414 6769 6771 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2761 P DT D 803 distorted distorted 2747 2762 2763 2764 2781 P DT D 804 distorted distorted 2769 2782 2783 2784 2801 P DG D 805 distorted distorted 2789 2802 2803 2804 2823 P DG D 806 distorted distorted 2809 2824 2825 2826 2845 P DA D 807 distorted distorted 2831 2846 2847 2848 2866 P DT D 808 distorted distorted 2853 2867 2868 2869 2886 P DG D 809 distorted distorted 2874 2887 2888 2889 2908 P DG D 810 distorted distorted 2894 2909 2910 2911 2930 P DT D 811 distorted distorted 2916 2931 2932 2933 2950 P DA D 812 distorted distorted 2938 2951 2952 2953 2971 P DG D 813 distorted distorted 2958 2972 2973 2974 2993 P 2DT D 814 distorted distorted 2979 2994 2995 2996 3030 P DA E 903 distorted distorted 3018 3031 3032 3033 3051 P DA E 904 distorted distorted 3038 3052 3053 3054 3072 P DC E 905 distorted distorted 3059 3073 3074 3075 3091 P MG1 E 906 distorted distorted 3080 3092 3093 3094 3114 P DC E 907 distorted distorted 3099 3115 3116 3117 3133 P DT E 908 distorted distorted 3122 3134 3135 3136 3153 P DA E 909 distorted distorted 3141 3154 3155 3156 3174 P DC E 910 distorted distorted 3161 3175 3176 3177 3193 P DC E 911 distorted distorted 3182 3194 3195 3196 3212 P DA E 912 distorted distorted 3201 3213 3214 3215 3233 P DT E 913 distorted distorted 3220 3234 3235 3236 3253 P DC E 914 distorted distorted 3241 3254 3255 3256 3272 P DC E 915 distorted distorted 3261 3273 3274 3275 3291 P DA E 916 distorted distorted 3280 3292 3293 3294 3312 P DA E 917 distorted distorted 3299 3313 3314 3315 3333 P DC E 918 distorted distorted 3320 3334 3335 3336 3352 P DC E 919 distorted distorted 3341 3353 3354 3355 6132 P DT H1803 distorted distorted 6118 6133 6134 6135 6152 P DT H1804 distorted distorted 6140 6153 6154 6155 6172 P DG H1805 distorted distorted 6160 6173 6174 6175 6194 P DG H1806 distorted distorted 6180 6195 6196 6197 6216 P DA H1807 distorted distorted 6202 6217 6218 6219 6237 P DT H1808 distorted distorted 6224 6238 6239 6240 6257 P DG H1809 distorted distorted 6245 6258 6259 6260 6279 P DG H1810 distorted distorted 6265 6280 6281 6282 6301 P DT H1811 distorted distorted 6287 6302 6303 6304 6321 P DA H1812 distorted distorted 6309 6322 6323 6324 6342 P DG H1813 distorted distorted 6329 6343 6344 6345 6364 P 2DT H1814 distorted distorted 6350 6365 6366 6367 6402 P DA J1904 distorted distorted 6389 6403 6404 6405 6423 P DC J1905 distorted distorted 6410 6424 6425 6426 6442 P MG1 J1906 distorted distorted 6431 6443 6444 6445 6465 P DC J1907 distorted distorted 6450 6466 6467 6468 6484 P DT J1908 distorted distorted 6473 6485 6486 6487 6504 P DA J1909 distorted distorted 6492 6505 6506 6507 6525 P DC J1910 distorted distorted 6512 6526 6527 6528 6544 P DC J1911 distorted distorted 6533 6545 6546 6547 6563 P DA J1912 distorted distorted 6552 6564 6565 6566 6584 P DT J1913 distorted distorted 6571 6585 6586 6587 6604 P DC J1914 distorted distorted 6592 6605 6606 6607 6623 P DC J1915 distorted distorted 6612 6624 6625 6626 6642 P DA J1916 distorted distorted 6631 6643 6644 6645 6663 P DA J1917 distorted distorted 6650 6664 6665 6666 6684 P DC J1918 distorted distorted 6671 6685 6686 6687 6703 P DC J1919 distorted distorted 6692 6704 6705 6706 ---------------------------------------------------------------------------------