ID code: '4QWC' 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' --------------------------------------------------------------------------------- 2761 C1' DG B 1 beta 2757 2762 2760 2783 C1' DG B 2 beta 2779 2784 2782 2805 C1' DC B 3 beta 2801 2806 2804 2824 C1' DT B 4 beta 2820 2825 2823 2844 C1' DA B 5 beta 2840 2845 2843 2865 C1' DC B 6 beta 2861 2866 2864 2884 C1' DA B 7 beta 2880 2885 2883 2905 C1' DG B 8 beta 2901 2906 2904 2927 C1' DG B 9 beta 2923 2928 2926 2949 C1' DA B 10 beta 2945 2950 2948 2970 C1' DC B 11 beta 2966 2971 2969 2989 C1' DT B 12 beta 2985 2990 2988 3010 C1' DA C 4 beta 3006 3011 3009 3031 C1' DG C 5 beta 3027 3032 3030 3053 C1' DG C 6 beta 3049 3054 3052 3075 C1' DA C 7 beta 3071 3076 3074 3096 C1' DG C 8 beta 3092 3097 3095 3118 C1' DT C 9 beta 3114 3119 3117 3138 C1' DC C 10 beta 3134 3139 3137 3157 C1' DC C 11 beta 3153 3158 3156 3176 C1' DT C 12 beta 3172 3177 3175 3196 C1' DG C 13 beta 3192 3197 3195 3218 C1' DT C 14 beta 3214 3219 3217 3238 C1' DA C 15 beta 3234 3239 3237 3259 C1' DG C 16 beta 3255 3260 3258 3281 C1' DC C 17 beta 3277 3282 3280 3300 C1' DC C 18 beta 3296 3301 3299 6070 C1' DG E 1 beta 6066 6071 6069 6092 C1' DG E 2 beta 6088 6093 6091 6114 C1' DC E 3 beta 6110 6115 6113 6133 C1' DT E 4 beta 6129 6134 6132 6153 C1' DA E 5 beta 6149 6154 6152 6174 C1' DC E 6 beta 6170 6175 6173 6193 C1' DA E 7 beta 6189 6194 6192 6214 C1' DG E 8 beta 6210 6215 6213 6236 C1' DG E 9 beta 6232 6237 6235 6258 C1' DA E 10 beta 6254 6259 6257 6279 C1' DC E 11 beta 6275 6280 6278 6298 C1' DT E 12 beta 6294 6299 6297 6319 C1' DA F 4 beta 6315 6320 6318 6340 C1' DG F 5 beta 6336 6341 6339 6362 C1' DG F 6 beta 6358 6363 6361 6384 C1' DA F 7 beta 6380 6385 6383 6405 C1' DG F 8 beta 6401 6406 6404 6427 C1' DT F 9 beta 6423 6428 6426 6447 C1' DC F 10 beta 6443 6448 6446 6466 C1' DC F 11 beta 6462 6467 6465 6485 C1' DT F 12 beta 6481 6486 6484 6505 C1' DG F 13 beta 6501 6506 6504 6527 C1' DT F 14 beta 6523 6528 6526 6547 C1' DA F 15 beta 6543 6548 6546 6568 C1' DG F 16 beta 6564 6569 6567 6590 C1' DC F 17 beta 6586 6591 6589 6609 C1' DC F 18 beta 6605 6610 6608 6692 C1' DOC B 101 beta 6696 6684 6693 6790 C1' DOC E 101 beta 6794 6782 6791 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2760 C2' DG B 1 2761 2758 2782 C2' DG B 2 2783 2780 2804 C2' DC B 3 2805 2802 2823 C2' DT B 4 2824 2821 2843 C2' DA B 5 2844 2841 2864 C2' DC B 6 2865 2862 2883 C2' DA B 7 2884 2881 2904 C2' DG B 8 2905 2902 2926 C2' DG B 9 2927 2924 2948 C2' DA B 10 2949 2946 2969 C2' DC B 11 2970 2967 2988 C2' DT B 12 2989 2986 3009 C2' DA C 4 3010 3007 3030 C2' DG C 5 3031 3028 3052 C2' DG C 6 3053 3050 3074 C2' DA C 7 3075 3072 3095 C2' DG C 8 3096 3093 3117 C2' DT C 9 3118 3115 3137 C2' DC C 10 3138 3135 3156 C2' DC C 11 3157 3154 3175 C2' DT C 12 3176 3173 3195 C2' DG C 13 3196 3193 3217 C2' DT C 14 3218 3215 3237 C2' DA C 15 3238 3235 3258 C2' DG C 16 3259 3256 3280 C2' DC C 17 3281 3278 3299 C2' DC C 18 3300 3297 6069 C2' DG E 1 6070 6067 6091 C2' DG E 2 6092 6089 6113 C2' DC E 3 6114 6111 6132 C2' DT E 4 6133 6130 6152 C2' DA E 5 6153 6150 6173 C2' DC E 6 6174 6171 6192 C2' DA E 7 6193 6190 6213 C2' DG E 8 6214 6211 6235 C2' DG E 9 6236 6233 6257 C2' DA E 10 6258 6255 6278 C2' DC E 11 6279 6276 6297 C2' DT E 12 6298 6295 6318 C2' DA F 4 6319 6316 6339 C2' DG F 5 6340 6337 6361 C2' DG F 6 6362 6359 6383 C2' DA F 7 6384 6381 6404 C2' DG F 8 6405 6402 6426 C2' DT F 9 6427 6424 6446 C2' DC F 10 6447 6444 6465 C2' DC F 11 6466 6463 6484 C2' DT F 12 6485 6482 6504 C2' DG F 13 6505 6502 6526 C2' DT F 14 6527 6524 6546 C2' DA F 15 6547 6544 6567 C2' DG F 16 6568 6565 6589 C2' DC F 17 6590 6587 6608 C2' DC F 18 6609 6606 6693 C2' DOC B 101 6692 6694 6791 C2' DOC E 101 6790 6792 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2758 C3' DG B 1 OK 2756 2759 2760 2780 C3' DG B 2 OK 2778 2781 2782 2802 C3' DC B 3 OK 2800 2803 2804 2821 C3' DT B 4 OK 2819 2822 2823 2841 C3' DA B 5 OK 2839 2842 2843 2862 C3' DC B 6 OK 2860 2863 2864 2881 C3' DA B 7 OK 2879 2882 2883 2902 C3' DG B 8 OK 2900 2903 2904 2924 C3' DG B 9 OK 2922 2925 2926 2946 C3' DA B 10 OK 2944 2947 2948 2967 C3' DC B 11 OK 2965 2968 2969 2986 C3' DT B 12 OK 2984 2987 2988 3007 C3' DA C 4 OK 3005 3008 3009 3028 C3' DG C 5 OK 3026 3029 3030 3050 C3' DG C 6 OK 3048 3051 3052 3072 C3' DA C 7 OK 3070 3073 3074 3093 C3' DG C 8 OK 3091 3094 3095 3115 C3' DT C 9 OK 3113 3116 3117 3135 C3' DC C 10 OK 3133 3136 3137 3154 C3' DC C 11 OK 3152 3155 3156 3173 C3' DT C 12 OK 3171 3174 3175 3193 C3' DG C 13 OK 3191 3194 3195 3215 C3' DT C 14 OK 3213 3216 3217 3235 C3' DA C 15 OK 3233 3236 3237 3256 C3' DG C 16 OK 3254 3257 3258 3278 C3' DC C 17 OK 3276 3279 3280 3297 C3' DC C 18 OK 3295 3298 3299 6067 C3' DG E 1 OK 6065 6068 6069 6089 C3' DG E 2 OK 6087 6090 6091 6111 C3' DC E 3 OK 6109 6112 6113 6130 C3' DT E 4 OK 6128 6131 6132 6150 C3' DA E 5 OK 6148 6151 6152 6171 C3' DC E 6 OK 6169 6172 6173 6190 C3' DA E 7 OK 6188 6191 6192 6211 C3' DG E 8 OK 6209 6212 6213 6233 C3' DG E 9 OK 6231 6234 6235 6255 C3' DA E 10 OK 6253 6256 6257 6276 C3' DC E 11 OK 6274 6277 6278 6295 C3' DT E 12 OK 6293 6296 6297 6316 C3' DA F 4 OK 6314 6317 6318 6337 C3' DG F 5 OK 6335 6338 6339 6359 C3' DG F 6 OK 6357 6360 6361 6381 C3' DA F 7 OK 6379 6382 6383 6402 C3' DG F 8 OK 6400 6403 6404 6424 C3' DT F 9 OK 6422 6425 6426 6444 C3' DC F 10 OK 6442 6445 6446 6463 C3' DC F 11 OK 6461 6464 6465 6482 C3' DT F 12 OK 6480 6483 6484 6502 C3' DG F 13 OK 6500 6503 6504 6524 C3' DT F 14 OK 6522 6525 6526 6544 C3' DA F 15 OK 6542 6545 6546 6565 C3' DG F 16 OK 6563 6566 6567 6587 C3' DC F 17 OK 6585 6588 6589 6606 C3' DC F 18 OK 6604 6607 6608 6694 C3' DOC B 101 6695 6693 6792 C3' DOC E 101 6793 6791 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2756 C4' DG B 1 OK 2758 2755 2757 2778 C4' DG B 2 OK 2780 2777 2779 2800 C4' DC B 3 OK 2802 2799 2801 2819 C4' DT B 4 OK 2821 2818 2820 2839 C4' DA B 5 OK 2841 2838 2840 2860 C4' DC B 6 OK 2862 2859 2861 2879 C4' DA B 7 OK 2881 2878 2880 2900 C4' DG B 8 OK 2902 2899 2901 2922 C4' DG B 9 OK 2924 2921 2923 2944 C4' DA B 10 OK 2946 2943 2945 2965 C4' DC B 11 OK 2967 2964 2966 2984 C4' DT B 12 OK 2986 2983 2985 3005 C4' DA C 4 OK 3007 3004 3006 3026 C4' DG C 5 OK 3028 3025 3027 3048 C4' DG C 6 OK 3050 3047 3049 3070 C4' DA C 7 OK 3072 3069 3071 3091 C4' DG C 8 OK 3093 3090 3092 3113 C4' DT C 9 OK 3115 3112 3114 3133 C4' DC C 10 OK 3135 3132 3134 3152 C4' DC C 11 OK 3154 3151 3153 3171 C4' DT C 12 OK 3173 3170 3172 3191 C4' DG C 13 OK 3193 3190 3192 3213 C4' DT C 14 OK 3215 3212 3214 3233 C4' DA C 15 OK 3235 3232 3234 3254 C4' DG C 16 OK 3256 3253 3255 3276 C4' DC C 17 OK 3278 3275 3277 3295 C4' DC C 18 OK 3297 3294 3296 6065 C4' DG E 1 OK 6067 6064 6066 6087 C4' DG E 2 OK 6089 6086 6088 6109 C4' DC E 3 OK 6111 6108 6110 6128 C4' DT E 4 OK 6130 6127 6129 6148 C4' DA E 5 OK 6150 6147 6149 6169 C4' DC E 6 OK 6171 6168 6170 6188 C4' DA E 7 OK 6190 6187 6189 6209 C4' DG E 8 OK 6211 6208 6210 6231 C4' DG E 9 OK 6233 6230 6232 6253 C4' DA E 10 OK 6255 6252 6254 6274 C4' DC E 11 OK 6276 6273 6275 6293 C4' DT E 12 OK 6295 6292 6294 6314 C4' DA F 4 OK 6316 6313 6315 6335 C4' DG F 5 OK 6337 6334 6336 6357 C4' DG F 6 OK 6359 6356 6358 6379 C4' DA F 7 OK 6381 6378 6380 6400 C4' DG F 8 OK 6402 6399 6401 6422 C4' DT F 9 OK 6424 6421 6423 6442 C4' DC F 10 OK 6444 6441 6443 6461 C4' DC F 11 OK 6463 6460 6462 6480 C4' DT F 12 OK 6482 6479 6481 6500 C4' DG F 13 OK 6502 6499 6501 6522 C4' DT F 14 OK 6524 6521 6523 6542 C4' DA F 15 OK 6544 6541 6543 6563 C4' DG F 16 OK 6565 6562 6564 6585 C4' DC F 17 OK 6587 6584 6586 6604 C4' DC F 18 OK 6606 6603 6605 6695 C4' DOC B 101 OK 6694 6697 6696 6793 C4' DOC E 101 OK 6792 6795 6794 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2755 C5' DG B 1 2754 2756 2777 C5' DG B 2 2776 2778 2799 C5' DC B 3 2798 2800 2818 C5' DT B 4 2817 2819 2838 C5' DA B 5 2837 2839 2859 C5' DC B 6 2858 2860 2878 C5' DA B 7 2877 2879 2899 C5' DG B 8 2898 2900 2921 C5' DG B 9 2920 2922 2943 C5' DA B 10 2942 2944 2964 C5' DC B 11 2963 2965 2983 C5' DT B 12 2982 2984 3004 C5' DA C 4 3003 3005 3025 C5' DG C 5 3024 3026 3047 C5' DG C 6 3046 3048 3069 C5' DA C 7 3068 3070 3090 C5' DG C 8 3089 3091 3112 C5' DT C 9 3111 3113 3132 C5' DC C 10 3131 3133 3151 C5' DC C 11 3150 3152 3170 C5' DT C 12 3169 3171 3190 C5' DG C 13 3189 3191 3212 C5' DT C 14 3211 3213 3232 C5' DA C 15 3231 3233 3253 C5' DG C 16 3252 3254 3275 C5' DC C 17 3274 3276 3294 C5' DC C 18 3293 3295 6064 C5' DG E 1 6063 6065 6086 C5' DG E 2 6085 6087 6108 C5' DC E 3 6107 6109 6127 C5' DT E 4 6126 6128 6147 C5' DA E 5 6146 6148 6168 C5' DC E 6 6167 6169 6187 C5' DA E 7 6186 6188 6208 C5' DG E 8 6207 6209 6230 C5' DG E 9 6229 6231 6252 C5' DA E 10 6251 6253 6273 C5' DC E 11 6272 6274 6292 C5' DT E 12 6291 6293 6313 C5' DA F 4 6312 6314 6334 C5' DG F 5 6333 6335 6356 C5' DG F 6 6355 6357 6378 C5' DA F 7 6377 6379 6399 C5' DG F 8 6398 6400 6421 C5' DT F 9 6420 6422 6441 C5' DC F 10 6440 6442 6460 C5' DC F 11 6459 6461 6479 C5' DT F 12 6478 6480 6499 C5' DG F 13 6498 6500 6521 C5' DT F 14 6520 6522 6541 C5' DA F 15 6540 6542 6562 C5' DG F 16 6561 6563 6584 C5' DC F 17 6583 6585 6603 C5' DC F 18 6602 6604 6697 C5' DOC B 101 6698 6695 6795 C5' DOC E 101 6796 6793 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2773 P DG B 2 distorted distorted 2759 2774 2775 2776 2795 P DC B 3 distorted distorted 2781 2796 2797 2798 2814 P DT B 4 distorted distorted 2803 2815 2816 2817 2834 P DA B 5 distorted distorted 2822 2835 2836 2837 2855 P DC B 6 distorted distorted 2842 2856 2857 2858 2874 P DA B 7 distorted distorted 2863 2875 2876 2877 2895 P DG B 8 distorted distorted 2882 2896 2897 2898 2917 P DG B 9 distorted distorted 2903 2918 2919 2920 2939 P DA B 10 distorted distorted 2925 2940 2941 2942 2960 P DC B 11 distorted distorted 2947 2961 2962 2963 2979 P DT B 12 distorted distorted 2968 2980 2981 2982 3000 P DA C 4 OK OK 3001 3002 3003 3021 P DG C 5 distorted distorted 3008 3022 3023 3024 3043 P DG C 6 distorted distorted 3029 3044 3045 3046 3065 P DA C 7 distorted distorted 3051 3066 3067 3068 3086 P DG C 8 distorted distorted 3073 3087 3088 3089 3108 P DT C 9 distorted distorted 3094 3109 3110 3111 3128 P DC C 10 distorted distorted 3116 3129 3130 3131 3147 P DC C 11 distorted distorted 3136 3148 3149 3150 3166 P DT C 12 distorted distorted 3155 3167 3168 3169 3186 P DG C 13 distorted distorted 3174 3187 3188 3189 3208 P DT C 14 distorted distorted 3194 3209 3210 3211 3228 P DA C 15 distorted distorted 3216 3229 3230 3231 3249 P DG C 16 distorted distorted 3236 3250 3251 3252 3271 P DC C 17 distorted distorted 3257 3272 3273 3274 3290 P DC C 18 distorted distorted 3279 3291 3292 3293 6082 P DG E 2 distorted distorted 6068 6083 6084 6085 6104 P DC E 3 distorted distorted 6090 6105 6106 6107 6123 P DT E 4 distorted distorted 6112 6124 6125 6126 6143 P DA E 5 distorted distorted 6131 6144 6145 6146 6164 P DC E 6 distorted distorted 6151 6165 6166 6167 6183 P DA E 7 distorted distorted 6172 6184 6185 6186 6204 P DG E 8 distorted distorted 6191 6205 6206 6207 6226 P DG E 9 distorted distorted 6212 6227 6228 6229 6248 P DA E 10 distorted distorted 6234 6249 6250 6251 6269 P DC E 11 distorted distorted 6256 6270 6271 6272 6288 P DT E 12 distorted distorted 6277 6289 6290 6291 6309 P DA F 4 distorted distorted 6310 6311 6312 6330 P DG F 5 distorted distorted 6317 6331 6332 6333 6352 P DG F 6 distorted distorted 6338 6353 6354 6355 6374 P DA F 7 distorted distorted 6360 6375 6376 6377 6395 P DG F 8 distorted distorted 6382 6396 6397 6398 6417 P DT F 9 distorted distorted 6403 6418 6419 6420 6437 P DC F 10 distorted distorted 6425 6438 6439 6440 6456 P DC F 11 distorted distorted 6445 6457 6458 6459 6475 P DT F 12 distorted distorted 6464 6476 6477 6478 6495 P DG F 13 distorted distorted 6483 6496 6497 6498 6517 P DT F 14 distorted distorted 6503 6518 6519 6520 6537 P DA F 15 distorted distorted 6525 6538 6539 6540 6558 P DG F 16 distorted distorted 6545 6559 6560 6561 6580 P DC F 17 distorted distorted 6566 6581 6582 6583 6599 P DC F 18 distorted distorted 6588 6600 6601 6602 6699 P DOC B 101 distorted distorted 2987 6700 6701 6698 6797 P DOC E 101 distorted distorted 6296 6798 6799 6796 ---------------------------------------------------------------------------------