ID code: '3KHH' 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 3001 C1' DOC D 814 beta 3005 2993 3002 3019 C1' DA E 904 beta 3015 3020 3018 3040 C1' DC E 905 beta 3036 3041 3039 3059 C1' DG E 906 beta 3055 3060 3058 3081 C1' DC E 907 beta 3077 3082 3080 3100 C1' DT E 908 beta 3096 3101 3099 3120 C1' DA E 909 beta 3116 3121 3119 3141 C1' DC E 910 beta 3137 3142 3140 3160 C1' DC E 911 beta 3156 3161 3159 3179 C1' DA E 912 beta 3175 3180 3178 3200 C1' DT E 913 beta 3196 3201 3199 3220 C1' DC E 914 beta 3216 3221 3219 3239 C1' DC E 915 beta 3235 3240 3238 3258 C1' DA E 916 beta 3254 3259 3257 3279 C1' DA E 917 beta 3275 3280 3278 3300 C1' DC E 918 beta 3296 3301 3299 3319 C1' DC E 919 beta 3315 3320 3318 6080 C1' DG H1802 beta 6076 6081 6079 6102 C1' DT H1803 beta 6098 6103 6101 6122 C1' DT H1804 beta 6118 6123 6121 6142 C1' DG H1805 beta 6138 6143 6141 6164 C1' DG H1806 beta 6160 6165 6163 6186 C1' DA H1807 beta 6182 6187 6185 6207 C1' DT H1808 beta 6203 6208 6206 6227 C1' DG H1809 beta 6223 6228 6226 6249 C1' DG H1810 beta 6245 6250 6248 6271 C1' DT H1811 beta 6267 6272 6270 6291 C1' DA H1812 beta 6287 6292 6290 6312 C1' DG H1813 beta 6308 6313 6311 6332 C1' DOC H1814 beta 6336 6324 6333 6350 C1' DA J1903 beta 6346 6351 6349 6371 C1' DA J1904 beta 6367 6372 6370 6392 C1' DC J1905 beta 6388 6393 6391 6411 C1' DG J1906 beta 6407 6412 6410 6433 C1' DC J1907 beta 6429 6434 6432 6452 C1' DT J1908 beta 6448 6453 6451 6472 C1' DA J1909 beta 6468 6473 6471 6493 C1' DC J1910 beta 6489 6494 6492 6512 C1' DC J1911 beta 6508 6513 6511 6531 C1' DA J1912 beta 6527 6532 6530 6552 C1' DT J1913 beta 6548 6553 6551 6572 C1' DC J1914 beta 6568 6573 6571 6591 C1' DC J1915 beta 6587 6592 6590 6610 C1' DA J1916 beta 6606 6611 6609 6631 C1' DA J1917 beta 6627 6632 6630 6652 C1' DC J1918 beta 6648 6653 6651 6671 C1' DC J1919 beta 6667 6672 6670 6700 C1' DGT A 414 beta 6696 6701 6699 6748 C1' DGT B1414 beta 6744 6749 6747 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 3002 C2' DOC D 814 3001 3003 3018 C2' DA E 904 3019 3016 3039 C2' DC E 905 3040 3037 3058 C2' DG E 906 3059 3056 3080 C2' DC E 907 3081 3078 3099 C2' DT E 908 3100 3097 3119 C2' DA E 909 3120 3117 3140 C2' DC E 910 3141 3138 3159 C2' DC E 911 3160 3157 3178 C2' DA E 912 3179 3176 3199 C2' DT E 913 3200 3197 3219 C2' DC E 914 3220 3217 3238 C2' DC E 915 3239 3236 3257 C2' DA E 916 3258 3255 3278 C2' DA E 917 3279 3276 3299 C2' DC E 918 3300 3297 3318 C2' DC E 919 3319 3316 6079 C2' DG H1802 6080 6077 6101 C2' DT H1803 6102 6099 6121 C2' DT H1804 6122 6119 6141 C2' DG H1805 6142 6139 6163 C2' DG H1806 6164 6161 6185 C2' DA H1807 6186 6183 6206 C2' DT H1808 6207 6204 6226 C2' DG H1809 6227 6224 6248 C2' DG H1810 6249 6246 6270 C2' DT H1811 6271 6268 6290 C2' DA H1812 6291 6288 6311 C2' DG H1813 6312 6309 6333 C2' DOC H1814 6332 6334 6349 C2' DA J1903 6350 6347 6370 C2' DA J1904 6371 6368 6391 C2' DC J1905 6392 6389 6410 C2' DG J1906 6411 6408 6432 C2' DC J1907 6433 6430 6451 C2' DT J1908 6452 6449 6471 C2' DA J1909 6472 6469 6492 C2' DC J1910 6493 6490 6511 C2' DC J1911 6512 6509 6530 C2' DA J1912 6531 6528 6551 C2' DT J1913 6552 6549 6571 C2' DC J1914 6572 6569 6590 C2' DC J1915 6591 6588 6609 C2' DA J1916 6610 6607 6630 C2' DA J1917 6631 6628 6651 C2' DC J1918 6652 6649 6670 C2' DC J1919 6671 6668 6699 C2' DGT A 414 6700 6697 6747 C2' DGT B1414 6748 6745 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3003 C3' DOC D 814 3004 3002 3016 C3' DA E 904 OK 3014 3017 3018 3037 C3' DC E 905 OK 3035 3038 3039 3056 C3' DG E 906 OK 3054 3057 3058 3078 C3' DC E 907 OK 3076 3079 3080 3097 C3' DT E 908 OK 3095 3098 3099 3117 C3' DA E 909 OK 3115 3118 3119 3138 C3' DC E 910 OK 3136 3139 3140 3157 C3' DC E 911 OK 3155 3158 3159 3176 C3' DA E 912 OK 3174 3177 3178 3197 C3' DT E 913 OK 3195 3198 3199 3217 C3' DC E 914 OK 3215 3218 3219 3236 C3' DC E 915 OK 3234 3237 3238 3255 C3' DA E 916 OK 3253 3256 3257 3276 C3' DA E 917 OK 3274 3277 3278 3297 C3' DC E 918 OK 3295 3298 3299 3316 C3' DC E 919 OK 3314 3317 3318 6077 C3' DG H1802 OK 6075 6078 6079 6099 C3' DT H1803 OK 6097 6100 6101 6119 C3' DT H1804 OK 6117 6120 6121 6139 C3' DG H1805 OK 6137 6140 6141 6161 C3' DG H1806 OK 6159 6162 6163 6183 C3' DA H1807 OK 6181 6184 6185 6204 C3' DT H1808 OK 6202 6205 6206 6224 C3' DG H1809 OK 6222 6225 6226 6246 C3' DG H1810 OK 6244 6247 6248 6268 C3' DT H1811 OK 6266 6269 6270 6288 C3' DA H1812 OK 6286 6289 6290 6309 C3' DG H1813 OK 6307 6310 6311 6334 C3' DOC H1814 6335 6333 6347 C3' DA J1903 OK 6345 6348 6349 6368 C3' DA J1904 OK 6366 6369 6370 6389 C3' DC J1905 OK 6387 6390 6391 6408 C3' DG J1906 OK 6406 6409 6410 6430 C3' DC J1907 OK 6428 6431 6432 6449 C3' DT J1908 OK 6447 6450 6451 6469 C3' DA J1909 OK 6467 6470 6471 6490 C3' DC J1910 OK 6488 6491 6492 6509 C3' DC J1911 OK 6507 6510 6511 6528 C3' DA J1912 OK 6526 6529 6530 6549 C3' DT J1913 OK 6547 6550 6551 6569 C3' DC J1914 OK 6567 6570 6571 6588 C3' DC J1915 OK 6586 6589 6590 6607 C3' DA J1916 OK 6605 6608 6609 6628 C3' DA J1917 OK 6626 6629 6630 6649 C3' DC J1918 OK 6647 6650 6651 6668 C3' DC J1919 OK 6666 6669 6670 6697 C3' DGT A 414 OK 6695 6698 6699 6745 C3' DGT B1414 OK 6743 6746 6747 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3004 C4' DOC D 814 OK 3003 3006 3005 3014 C4' DA E 904 OK 3016 3013 3015 3035 C4' DC E 905 OK 3037 3034 3036 3054 C4' DG E 906 OK 3056 3053 3055 3076 C4' DC E 907 OK 3078 3075 3077 3095 C4' DT E 908 OK 3097 3094 3096 3115 C4' DA E 909 OK 3117 3114 3116 3136 C4' DC E 910 OK 3138 3135 3137 3155 C4' DC E 911 OK 3157 3154 3156 3174 C4' DA E 912 OK 3176 3173 3175 3195 C4' DT E 913 OK 3197 3194 3196 3215 C4' DC E 914 OK 3217 3214 3216 3234 C4' DC E 915 OK 3236 3233 3235 3253 C4' DA E 916 OK 3255 3252 3254 3274 C4' DA E 917 OK 3276 3273 3275 3295 C4' DC E 918 OK 3297 3294 3296 3314 C4' DC E 919 OK 3316 3313 3315 6075 C4' DG H1802 OK 6077 6074 6076 6097 C4' DT H1803 OK 6099 6096 6098 6117 C4' DT H1804 OK 6119 6116 6118 6137 C4' DG H1805 OK 6139 6136 6138 6159 C4' DG H1806 OK 6161 6158 6160 6181 C4' DA H1807 OK 6183 6180 6182 6202 C4' DT H1808 OK 6204 6201 6203 6222 C4' DG H1809 OK 6224 6221 6223 6244 C4' DG H1810 OK 6246 6243 6245 6266 C4' DT H1811 OK 6268 6265 6267 6286 C4' DA H1812 OK 6288 6285 6287 6307 C4' DG H1813 OK 6309 6306 6308 6335 C4' DOC H1814 OK 6334 6337 6336 6345 C4' DA J1903 OK 6347 6344 6346 6366 C4' DA J1904 OK 6368 6365 6367 6387 C4' DC J1905 OK 6389 6386 6388 6406 C4' DG J1906 OK 6408 6405 6407 6428 C4' DC J1907 OK 6430 6427 6429 6447 C4' DT J1908 OK 6449 6446 6448 6467 C4' DA J1909 OK 6469 6466 6468 6488 C4' DC J1910 OK 6490 6487 6489 6507 C4' DC J1911 OK 6509 6506 6508 6526 C4' DA J1912 OK 6528 6525 6527 6547 C4' DT J1913 OK 6549 6546 6548 6567 C4' DC J1914 OK 6569 6566 6568 6586 C4' DC J1915 OK 6588 6585 6587 6605 C4' DA J1916 OK 6607 6604 6606 6626 C4' DA J1917 OK 6628 6625 6627 6647 C4' DC J1918 OK 6649 6646 6648 6666 C4' DC J1919 OK 6668 6665 6667 6695 C4' DGT A 414 OK 6697 6694 6696 6743 C4' DGT B1414 OK 6745 6742 6744 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3006 C5' DOC D 814 3007 3004 3013 C5' DA E 904 3012 3014 3034 C5' DC E 905 3033 3035 3053 C5' DG E 906 3052 3054 3075 C5' DC E 907 3074 3076 3094 C5' DT E 908 3093 3095 3114 C5' DA E 909 3113 3115 3135 C5' DC E 910 3134 3136 3154 C5' DC E 911 3153 3155 3173 C5' DA E 912 3172 3174 3194 C5' DT E 913 3193 3195 3214 C5' DC E 914 3213 3215 3233 C5' DC E 915 3232 3234 3252 C5' DA E 916 3251 3253 3273 C5' DA E 917 3272 3274 3294 C5' DC E 918 3293 3295 3313 C5' DC E 919 3312 3314 6074 C5' DG H1802 6073 6075 6096 C5' DT H1803 6095 6097 6116 C5' DT H1804 6115 6117 6136 C5' DG H1805 6135 6137 6158 C5' DG H1806 6157 6159 6180 C5' DA H1807 6179 6181 6201 C5' DT H1808 6200 6202 6221 C5' DG H1809 6220 6222 6243 C5' DG H1810 6242 6244 6265 C5' DT H1811 6264 6266 6285 C5' DA H1812 6284 6286 6306 C5' DG H1813 6305 6307 6337 C5' DOC H1814 6338 6335 6344 C5' DA J1903 6343 6345 6365 C5' DA J1904 6364 6366 6386 C5' DC J1905 6385 6387 6405 C5' DG J1906 6404 6406 6427 C5' DC J1907 6426 6428 6446 C5' DT J1908 6445 6447 6466 C5' DA J1909 6465 6467 6487 C5' DC J1910 6486 6488 6506 C5' DC J1911 6505 6507 6525 C5' DA J1912 6524 6526 6546 C5' DT J1913 6545 6547 6566 C5' DC J1914 6565 6567 6585 C5' DC J1915 6584 6586 6604 C5' DA J1916 6603 6605 6625 C5' DA J1917 6624 6626 6646 C5' DC J1918 6645 6647 6665 C5' DC J1919 6664 6666 6694 C5' DGT A 414 6693 6695 6742 C5' DGT B1414 6741 6743 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3008 P DOC D 814 distorted distorted 2979 3009 3010 3007 3030 P DC E 905 distorted distorted 3017 3031 3032 3033 3049 P DG E 906 distorted distorted 3038 3050 3051 3052 3071 P DC E 907 distorted distorted 3057 3072 3073 3074 3090 P DT E 908 distorted distorted 3079 3091 3092 3093 3110 P DA E 909 distorted distorted 3098 3111 3112 3113 3131 P DC E 910 distorted distorted 3118 3132 3133 3134 3150 P DC E 911 distorted distorted 3139 3151 3152 3153 3169 P DA E 912 distorted distorted 3158 3170 3171 3172 3190 P DT E 913 distorted distorted 3177 3191 3192 3193 3210 P DC E 914 distorted distorted 3198 3211 3212 3213 3229 P DC E 915 distorted distorted 3218 3230 3231 3232 3248 P DA E 916 distorted distorted 3237 3249 3250 3251 3269 P DA E 917 distorted distorted 3256 3270 3271 3272 3290 P DC E 918 distorted distorted 3277 3291 3292 3293 3309 P DC E 919 distorted distorted 3298 3310 3311 3312 6070 P DG H1802 distorted distorted 6071 6072 6073 6092 P DT H1803 distorted distorted 6078 6093 6094 6095 6112 P DT H1804 distorted distorted 6100 6113 6114 6115 6132 P DG H1805 distorted distorted 6120 6133 6134 6135 6154 P DG H1806 distorted distorted 6140 6155 6156 6157 6176 P DA H1807 distorted distorted 6162 6177 6178 6179 6197 P DT H1808 distorted distorted 6184 6198 6199 6200 6217 P DG H1809 distorted distorted 6205 6218 6219 6220 6239 P DG H1810 distorted distorted 6225 6240 6241 6242 6261 P DT H1811 distorted distorted 6247 6262 6263 6264 6281 P DA H1812 distorted distorted 6269 6282 6283 6284 6302 P DG H1813 distorted distorted 6289 6303 6304 6305 6339 P DOC H1814 distorted distorted 6310 6340 6341 6338 6361 P DA J1904 distorted distorted 6348 6362 6363 6364 6382 P DC J1905 distorted distorted 6369 6383 6384 6385 6401 P DG J1906 distorted distorted 6390 6402 6403 6404 6423 P DC J1907 distorted distorted 6409 6424 6425 6426 6442 P DT J1908 distorted distorted 6431 6443 6444 6445 6462 P DA J1909 distorted distorted 6450 6463 6464 6465 6483 P DC J1910 distorted distorted 6470 6484 6485 6486 6502 P DC J1911 distorted distorted 6491 6503 6504 6505 6521 P DA J1912 distorted distorted 6510 6522 6523 6524 6542 P DT J1913 distorted distorted 6529 6543 6544 6545 6562 P DC J1914 distorted distorted 6550 6563 6564 6565 6581 P DC J1915 distorted distorted 6570 6582 6583 6584 6600 P DA J1916 distorted distorted 6589 6601 6602 6603 6621 P DA J1917 distorted distorted 6608 6622 6623 6624 6642 P DC J1918 distorted distorted 6629 6643 6644 6645 6661 P DC J1919 distorted distorted 6650 6662 6663 6664 ---------------------------------------------------------------------------------