ID code: '3RAQ' 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 3037 C1' DT E 902 beta 3033 3038 3036 3057 C1' DA E 903 beta 3053 3058 3056 3078 C1' DA E 904 beta 3074 3079 3077 3099 C1' DC E 905 beta 3095 3100 3098 3118 C1' MG1 E 906 beta 3114 3119 3117 3141 C1' DC E 907 beta 3137 3142 3140 3160 C1' DT E 908 beta 3156 3161 3159 3180 C1' DA E 909 beta 3176 3181 3179 3201 C1' DC E 910 beta 3197 3202 3200 3220 C1' DC E 911 beta 3216 3221 3219 3239 C1' DA E 912 beta 3235 3240 3238 3260 C1' DT E 913 beta 3256 3261 3259 3280 C1' DC E 914 beta 3276 3281 3279 3299 C1' DC E 915 beta 3295 3300 3298 3318 C1' DA E 916 beta 3314 3319 3317 3339 C1' DA E 917 beta 3335 3340 3338 3360 C1' DC E 918 beta 3356 3361 3359 3379 C1' DC E 919 beta 3375 3380 3378 6137 C1' DG H1802 beta 6133 6138 6136 6159 C1' DT H1803 beta 6155 6160 6158 6179 C1' DT H1804 beta 6175 6180 6178 6199 C1' DG H1805 beta 6195 6200 6198 6221 C1' DG H1806 beta 6217 6222 6220 6243 C1' DA H1807 beta 6239 6244 6242 6264 C1' DT H1808 beta 6260 6265 6263 6284 C1' DG H1809 beta 6280 6285 6283 6306 C1' DG H1810 beta 6302 6307 6305 6328 C1' DT H1811 beta 6324 6329 6327 6348 C1' DA H1812 beta 6344 6349 6347 6369 C1' DG H1813 beta 6365 6370 6368 6389 C1' DOC H1814 beta 6393 6381 6390 6410 C1' DA J1903 beta 6406 6411 6409 6431 C1' DA J1904 beta 6427 6432 6430 6452 C1' DC J1905 beta 6448 6453 6451 6471 C1' MG1 J1906 beta 6467 6472 6470 6494 C1' DC J1907 beta 6490 6495 6493 6513 C1' DT J1908 beta 6509 6514 6512 6533 C1' DA J1909 beta 6529 6534 6532 6554 C1' DC J1910 beta 6550 6555 6553 6573 C1' DC J1911 beta 6569 6574 6572 6592 C1' DA J1912 beta 6588 6593 6591 6613 C1' DT J1913 beta 6609 6614 6612 6633 C1' DC J1914 beta 6629 6634 6632 6652 C1' DC J1915 beta 6648 6653 6651 6671 C1' DA J1916 beta 6667 6672 6670 6692 C1' DA J1917 beta 6688 6693 6691 6713 C1' DC J1918 beta 6709 6714 6712 6732 C1' DC J1919 beta 6728 6733 6731 6761 C1' DGT A 414 beta 6757 6762 6760 6810 C1' DGT B1414 beta 6806 6811 6809 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 3036 C2' DT E 902 3037 3034 3056 C2' DA E 903 3057 3054 3077 C2' DA E 904 3078 3075 3098 C2' DC E 905 3099 3096 3117 C2' MG1 E 906 3118 3115 3140 C2' DC E 907 3141 3138 3159 C2' DT E 908 3160 3157 3179 C2' DA E 909 3180 3177 3200 C2' DC E 910 3201 3198 3219 C2' DC E 911 3220 3217 3238 C2' DA E 912 3239 3236 3259 C2' DT E 913 3260 3257 3279 C2' DC E 914 3280 3277 3298 C2' DC E 915 3299 3296 3317 C2' DA E 916 3318 3315 3338 C2' DA E 917 3339 3336 3359 C2' DC E 918 3360 3357 3378 C2' DC E 919 3379 3376 6136 C2' DG H1802 6137 6134 6158 C2' DT H1803 6159 6156 6178 C2' DT H1804 6179 6176 6198 C2' DG H1805 6199 6196 6220 C2' DG H1806 6221 6218 6242 C2' DA H1807 6243 6240 6263 C2' DT H1808 6264 6261 6283 C2' DG H1809 6284 6281 6305 C2' DG H1810 6306 6303 6327 C2' DT H1811 6328 6325 6347 C2' DA H1812 6348 6345 6368 C2' DG H1813 6369 6366 6390 C2' DOC H1814 6389 6391 6409 C2' DA J1903 6410 6407 6430 C2' DA J1904 6431 6428 6451 C2' DC J1905 6452 6449 6470 C2' MG1 J1906 6471 6468 6493 C2' DC J1907 6494 6491 6512 C2' DT J1908 6513 6510 6532 C2' DA J1909 6533 6530 6553 C2' DC J1910 6554 6551 6572 C2' DC J1911 6573 6570 6591 C2' DA J1912 6592 6589 6612 C2' DT J1913 6613 6610 6632 C2' DC J1914 6633 6630 6651 C2' DC J1915 6652 6649 6670 C2' DA J1916 6671 6668 6691 C2' DA J1917 6692 6689 6712 C2' DC J1918 6713 6710 6731 C2' DC J1919 6732 6729 6760 C2' DGT A 414 6761 6758 6809 C2' DGT B1414 6810 6807 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3034 C3' DT E 902 OK 3032 3035 3036 3054 C3' DA E 903 OK 3052 3055 3056 3075 C3' DA E 904 OK 3073 3076 3077 3096 C3' DC E 905 OK 3094 3097 3098 3115 C3' MG1 E 906 OK 3113 3116 3117 3138 C3' DC E 907 OK 3136 3139 3140 3157 C3' DT E 908 OK 3155 3158 3159 3177 C3' DA E 909 OK 3175 3178 3179 3198 C3' DC E 910 OK 3196 3199 3200 3217 C3' DC E 911 OK 3215 3218 3219 3236 C3' DA E 912 OK 3234 3237 3238 3257 C3' DT E 913 OK 3255 3258 3259 3277 C3' DC E 914 OK 3275 3278 3279 3296 C3' DC E 915 OK 3294 3297 3298 3315 C3' DA E 916 OK 3313 3316 3317 3336 C3' DA E 917 OK 3334 3337 3338 3357 C3' DC E 918 OK 3355 3358 3359 3376 C3' DC E 919 OK 3374 3377 3378 6134 C3' DG H1802 OK 6132 6135 6136 6156 C3' DT H1803 OK 6154 6157 6158 6176 C3' DT H1804 OK 6174 6177 6178 6196 C3' DG H1805 OK 6194 6197 6198 6218 C3' DG H1806 OK 6216 6219 6220 6240 C3' DA H1807 OK 6238 6241 6242 6261 C3' DT H1808 OK 6259 6262 6263 6281 C3' DG H1809 OK 6279 6282 6283 6303 C3' DG H1810 OK 6301 6304 6305 6325 C3' DT H1811 OK 6323 6326 6327 6345 C3' DA H1812 OK 6343 6346 6347 6366 C3' DG H1813 OK 6364 6367 6368 6391 C3' DOC H1814 6392 6390 6407 C3' DA J1903 OK 6405 6408 6409 6428 C3' DA J1904 OK 6426 6429 6430 6449 C3' DC J1905 OK 6447 6450 6451 6468 C3' MG1 J1906 OK 6466 6469 6470 6491 C3' DC J1907 OK 6489 6492 6493 6510 C3' DT J1908 OK 6508 6511 6512 6530 C3' DA J1909 OK 6528 6531 6532 6551 C3' DC J1910 OK 6549 6552 6553 6570 C3' DC J1911 OK 6568 6571 6572 6589 C3' DA J1912 OK 6587 6590 6591 6610 C3' DT J1913 OK 6608 6611 6612 6630 C3' DC J1914 OK 6628 6631 6632 6649 C3' DC J1915 OK 6647 6650 6651 6668 C3' DA J1916 OK 6666 6669 6670 6689 C3' DA J1917 OK 6687 6690 6691 6710 C3' DC J1918 OK 6708 6711 6712 6729 C3' DC J1919 OK 6727 6730 6731 6758 C3' DGT A 414 OK 6756 6759 6760 6807 C3' DGT B1414 OK 6805 6808 6809 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3032 C4' DT E 902 OK 3034 3031 3033 3052 C4' DA E 903 OK 3054 3051 3053 3073 C4' DA E 904 OK 3075 3072 3074 3094 C4' DC E 905 OK 3096 3093 3095 3113 C4' MG1 E 906 OK 3115 3112 3114 3136 C4' DC E 907 OK 3138 3135 3137 3155 C4' DT E 908 OK 3157 3154 3156 3175 C4' DA E 909 OK 3177 3174 3176 3196 C4' DC E 910 OK 3198 3195 3197 3215 C4' DC E 911 OK 3217 3214 3216 3234 C4' DA E 912 OK 3236 3233 3235 3255 C4' DT E 913 OK 3257 3254 3256 3275 C4' DC E 914 OK 3277 3274 3276 3294 C4' DC E 915 OK 3296 3293 3295 3313 C4' DA E 916 OK 3315 3312 3314 3334 C4' DA E 917 OK 3336 3333 3335 3355 C4' DC E 918 OK 3357 3354 3356 3374 C4' DC E 919 OK 3376 3373 3375 6132 C4' DG H1802 OK 6134 6131 6133 6154 C4' DT H1803 OK 6156 6153 6155 6174 C4' DT H1804 OK 6176 6173 6175 6194 C4' DG H1805 OK 6196 6193 6195 6216 C4' DG H1806 OK 6218 6215 6217 6238 C4' DA H1807 OK 6240 6237 6239 6259 C4' DT H1808 OK 6261 6258 6260 6279 C4' DG H1809 OK 6281 6278 6280 6301 C4' DG H1810 OK 6303 6300 6302 6323 C4' DT H1811 OK 6325 6322 6324 6343 C4' DA H1812 OK 6345 6342 6344 6364 C4' DG H1813 OK 6366 6363 6365 6392 C4' DOC H1814 OK 6391 6394 6393 6405 C4' DA J1903 OK 6407 6404 6406 6426 C4' DA J1904 OK 6428 6425 6427 6447 C4' DC J1905 OK 6449 6446 6448 6466 C4' MG1 J1906 OK 6468 6465 6467 6489 C4' DC J1907 OK 6491 6488 6490 6508 C4' DT J1908 OK 6510 6507 6509 6528 C4' DA J1909 OK 6530 6527 6529 6549 C4' DC J1910 OK 6551 6548 6550 6568 C4' DC J1911 OK 6570 6567 6569 6587 C4' DA J1912 OK 6589 6586 6588 6608 C4' DT J1913 OK 6610 6607 6609 6628 C4' DC J1914 OK 6630 6627 6629 6647 C4' DC J1915 OK 6649 6646 6648 6666 C4' DA J1916 OK 6668 6665 6667 6687 C4' DA J1917 OK 6689 6686 6688 6708 C4' DC J1918 OK 6710 6707 6709 6727 C4' DC J1919 OK 6729 6726 6728 6756 C4' DGT A 414 OK 6758 6755 6757 6805 C4' DGT B1414 OK 6807 6804 6806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3031 C5' DT E 902 3030 3032 3051 C5' DA E 903 3050 3052 3072 C5' DA E 904 3071 3073 3093 C5' DC E 905 3092 3094 3112 C5' MG1 E 906 3111 3113 3135 C5' DC E 907 3134 3136 3154 C5' DT E 908 3153 3155 3174 C5' DA E 909 3173 3175 3195 C5' DC E 910 3194 3196 3214 C5' DC E 911 3213 3215 3233 C5' DA E 912 3232 3234 3254 C5' DT E 913 3253 3255 3274 C5' DC E 914 3273 3275 3293 C5' DC E 915 3292 3294 3312 C5' DA E 916 3311 3313 3333 C5' DA E 917 3332 3334 3354 C5' DC E 918 3353 3355 3373 C5' DC E 919 3372 3374 6131 C5' DG H1802 6130 6132 6153 C5' DT H1803 6152 6154 6173 C5' DT H1804 6172 6174 6193 C5' DG H1805 6192 6194 6215 C5' DG H1806 6214 6216 6237 C5' DA H1807 6236 6238 6258 C5' DT H1808 6257 6259 6278 C5' DG H1809 6277 6279 6300 C5' DG H1810 6299 6301 6322 C5' DT H1811 6321 6323 6342 C5' DA H1812 6341 6343 6363 C5' DG H1813 6362 6364 6394 C5' DOC H1814 6395 6392 6404 C5' DA J1903 6403 6405 6425 C5' DA J1904 6424 6426 6446 C5' DC J1905 6445 6447 6465 C5' MG1 J1906 6464 6466 6488 C5' DC J1907 6487 6489 6507 C5' DT J1908 6506 6508 6527 C5' DA J1909 6526 6528 6548 C5' DC J1910 6547 6549 6567 C5' DC J1911 6566 6568 6586 C5' DA J1912 6585 6587 6607 C5' DT J1913 6606 6608 6627 C5' DC J1914 6626 6628 6646 C5' DC J1915 6645 6647 6665 C5' DA J1916 6664 6666 6686 C5' DA J1917 6685 6687 6707 C5' DC J1918 6706 6708 6726 C5' DC J1919 6725 6727 6755 C5' DGT A 414 6754 6756 6804 C5' DGT B1414 6803 6805 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3023 P DOC D 814 2979 3024 P DOC D 814 2979 3047 P DA E 903 distorted distorted 3035 3048 3049 3050 3068 P DA E 904 distorted distorted 3055 3069 3070 3071 3089 P DC E 905 distorted distorted 3076 3090 3091 3092 3108 P MG1 E 906 distorted distorted 3097 3109 3110 3111 3131 P DC E 907 distorted distorted 3116 3132 3133 3134 3150 P DT E 908 distorted distorted 3139 3151 3152 3153 3170 P DA E 909 distorted distorted 3158 3171 3172 3173 3191 P DC E 910 distorted distorted 3178 3192 3193 3194 3210 P DC E 911 distorted distorted 3199 3211 3212 3213 3229 P DA E 912 distorted distorted 3218 3230 3231 3232 3250 P DT E 913 distorted distorted 3237 3251 3252 3253 3270 P DC E 914 distorted distorted 3258 3271 3272 3273 3289 P DC E 915 distorted distorted 3278 3290 3291 3292 3308 P DA E 916 distorted distorted 3297 3309 3310 3311 3329 P DA E 917 distorted distorted 3316 3330 3331 3332 3350 P DC E 918 distorted distorted 3337 3351 3352 3353 3369 P DC E 919 distorted distorted 3358 3370 3371 3372 6149 P DT H1803 distorted distorted 6135 6150 6151 6152 6169 P DT H1804 distorted distorted 6157 6170 6171 6172 6189 P DG H1805 distorted distorted 6177 6190 6191 6192 6211 P DG H1806 distorted distorted 6197 6212 6213 6214 6233 P DA H1807 distorted distorted 6219 6234 6235 6236 6254 P DT H1808 distorted distorted 6241 6255 6256 6257 6274 P DG H1809 distorted distorted 6262 6275 6276 6277 6296 P DG H1810 distorted distorted 6282 6297 6298 6299 6318 P DT H1811 distorted distorted 6304 6319 6320 6321 6338 P DA H1812 distorted distorted 6326 6339 6340 6341 6359 P DG H1813 distorted distorted 6346 6360 6361 6362 6396 P DOC H1814 distorted distorted 6367 6397 6398 6395 6400 P DA J1903 distorted distorted 6401 6402 6403 6421 P DA J1904 distorted distorted 6408 6422 6423 6424 6442 P DC J1905 distorted distorted 6429 6443 6444 6445 6461 P MG1 J1906 distorted distorted 6450 6462 6463 6464 6484 P DC J1907 distorted distorted 6469 6485 6486 6487 6503 P DT J1908 distorted distorted 6492 6504 6505 6506 6523 P DA J1909 distorted distorted 6511 6524 6525 6526 6544 P DC J1910 distorted distorted 6531 6545 6546 6547 6563 P DC J1911 distorted distorted 6552 6564 6565 6566 6582 P DA J1912 distorted distorted 6571 6583 6584 6585 6603 P DT J1913 distorted distorted 6590 6604 6605 6606 6623 P DC J1914 distorted distorted 6611 6624 6625 6626 6642 P DC J1915 distorted distorted 6631 6643 6644 6645 6661 P DA J1916 distorted distorted 6650 6662 6663 6664 6682 P DA J1917 distorted distorted 6669 6683 6684 6685 6703 P DC J1918 distorted distorted 6690 6704 6705 6706 6722 P DC J1919 distorted distorted 6711 6723 6724 6725 ---------------------------------------------------------------------------------