ID code: '3GIJ' 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' --------------------------------------------------------------------------------- 2759 C1' DG D 802 beta 2755 2760 2758 2781 C1' DT D 803 beta 2777 2782 2780 2801 C1' DT D 804 beta 2797 2802 2800 2821 C1' DG D 805 beta 2817 2822 2820 2843 C1' DG D 806 beta 2839 2844 2842 2865 C1' DA D 807 beta 2861 2866 2864 2886 C1' DT D 808 beta 2882 2887 2885 2906 C1' DG D 809 beta 2902 2907 2905 2928 C1' DG D 810 beta 2924 2929 2927 2950 C1' DT D 811 beta 2946 2951 2949 2970 C1' DA D 812 beta 2966 2971 2969 2991 C1' DG D 813 beta 2987 2992 2990 3051 C1' DC E 901 beta 3047 3052 3050 3070 C1' DT E 902 beta 3066 3071 3069 3090 C1' DA E 903 beta 3086 3091 3089 3111 C1' DA E 904 beta 3107 3112 3110 3132 C1' DC E 905 beta 3128 3133 3131 3197 C1' DC E 907 beta 3193 3198 3196 3216 C1' DT E 908 beta 3212 3217 3215 3236 C1' DA E 909 beta 3232 3237 3235 3257 C1' DC E 910 beta 3253 3258 3256 3276 C1' DC E 911 beta 3272 3277 3275 3295 C1' DA E 912 beta 3291 3296 3294 3316 C1' DT E 913 beta 3312 3317 3315 3336 C1' DC E 914 beta 3332 3337 3335 3355 C1' DC E 915 beta 3351 3356 3354 3374 C1' DA E 916 beta 3370 3375 3373 3395 C1' DA E 917 beta 3391 3396 3394 3416 C1' DC E 918 beta 3412 3417 3415 6174 C1' DG H1802 beta 6170 6175 6173 6196 C1' DT H1803 beta 6192 6197 6195 6216 C1' DT H1804 beta 6212 6217 6215 6236 C1' DG H1805 beta 6232 6237 6235 6258 C1' DG H1806 beta 6254 6259 6257 6280 C1' DA H1807 beta 6276 6281 6279 6301 C1' DT H1808 beta 6297 6302 6300 6321 C1' DG H1809 beta 6317 6322 6320 6343 C1' DG H1810 beta 6339 6344 6342 6365 C1' DT H1811 beta 6361 6366 6364 6385 C1' DA H1812 beta 6381 6386 6384 6406 C1' DG H1813 beta 6402 6407 6405 6427 C1' 2DA H1814 beta 6424 6428 6426 6449 C1' DC J1905 beta 6445 6450 6448 6468 C1' 8OG J1906 beta 6464 6469 6467 6491 C1' DC J1907 beta 6487 6492 6490 6510 C1' DT J1908 beta 6506 6511 6509 6530 C1' DA J1909 beta 6526 6531 6529 6551 C1' DC J1910 beta 6547 6552 6550 6570 C1' DC J1911 beta 6566 6571 6569 6589 C1' DA J1912 beta 6585 6590 6588 6610 C1' DT J1913 beta 6606 6611 6609 6630 C1' DC J1914 beta 6626 6631 6629 6649 C1' DC J1915 beta 6645 6650 6648 6668 C1' DA J1916 beta 6664 6669 6667 6689 C1' DA J1917 beta 6685 6690 6688 6710 C1' DC J1918 beta 6706 6711 6709 6739 C1' DGT A 414 beta 6735 6740 6738 6773 C1' DGT B1414 beta 6769 6774 6772 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2758 C2' DG D 802 2759 2756 2780 C2' DT D 803 2781 2778 2800 C2' DT D 804 2801 2798 2820 C2' DG D 805 2821 2818 2842 C2' DG D 806 2843 2840 2864 C2' DA D 807 2865 2862 2885 C2' DT D 808 2886 2883 2905 C2' DG D 809 2906 2903 2927 C2' DG D 810 2928 2925 2949 C2' DT D 811 2950 2947 2969 C2' DA D 812 2970 2967 2990 C2' DG D 813 2991 2988 3050 C2' DC E 901 3051 3048 3069 C2' DT E 902 3070 3067 3089 C2' DA E 903 3090 3087 3110 C2' DA E 904 3111 3108 3131 C2' DC E 905 3132 3129 3196 C2' DC E 907 3197 3194 3215 C2' DT E 908 3216 3213 3235 C2' DA E 909 3236 3233 3256 C2' DC E 910 3257 3254 3275 C2' DC E 911 3276 3273 3294 C2' DA E 912 3295 3292 3315 C2' DT E 913 3316 3313 3335 C2' DC E 914 3336 3333 3354 C2' DC E 915 3355 3352 3373 C2' DA E 916 3374 3371 3394 C2' DA E 917 3395 3392 3415 C2' DC E 918 3416 3413 6173 C2' DG H1802 6174 6171 6195 C2' DT H1803 6196 6193 6215 C2' DT H1804 6216 6213 6235 C2' DG H1805 6236 6233 6257 C2' DG H1806 6258 6255 6279 C2' DA H1807 6280 6277 6300 C2' DT H1808 6301 6298 6320 C2' DG H1809 6321 6318 6342 C2' DG H1810 6343 6340 6364 C2' DT H1811 6365 6362 6384 C2' DA H1812 6385 6382 6405 C2' DG H1813 6406 6403 6426 C2' 2DA H1814 6427 6425 6448 C2' DC J1905 6449 6446 6467 C2' 8OG J1906 6468 6465 6490 C2' DC J1907 6491 6488 6509 C2' DT J1908 6510 6507 6529 C2' DA J1909 6530 6527 6550 C2' DC J1910 6551 6548 6569 C2' DC J1911 6570 6567 6588 C2' DA J1912 6589 6586 6609 C2' DT J1913 6610 6607 6629 C2' DC J1914 6630 6627 6648 C2' DC J1915 6649 6646 6667 C2' DA J1916 6668 6665 6688 C2' DA J1917 6689 6686 6709 C2' DC J1918 6710 6707 6738 C2' DGT A 414 6739 6736 6772 C2' DGT B1414 6773 6770 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2756 C3' DG D 802 OK 2754 2757 2758 2778 C3' DT D 803 OK 2776 2779 2780 2798 C3' DT D 804 OK 2796 2799 2800 2818 C3' DG D 805 OK 2816 2819 2820 2840 C3' DG D 806 OK 2838 2841 2842 2862 C3' DA D 807 OK 2860 2863 2864 2883 C3' DT D 808 OK 2881 2884 2885 2903 C3' DG D 809 OK 2901 2904 2905 2925 C3' DG D 810 OK 2923 2926 2927 2947 C3' DT D 811 OK 2945 2948 2949 2967 C3' DA D 812 OK 2965 2968 2969 2988 C3' DG D 813 OK 2986 2989 2990 3048 C3' DC E 901 OK 3046 3049 3050 3067 C3' DT E 902 OK 3065 3068 3069 3087 C3' DA E 903 OK 3085 3088 3089 3108 C3' DA E 904 OK 3106 3109 3110 3129 C3' DC E 905 OK 3127 3130 3131 3194 C3' DC E 907 OK 3192 3195 3196 3213 C3' DT E 908 OK 3211 3214 3215 3233 C3' DA E 909 OK 3231 3234 3235 3254 C3' DC E 910 OK 3252 3255 3256 3273 C3' DC E 911 OK 3271 3274 3275 3292 C3' DA E 912 OK 3290 3293 3294 3313 C3' DT E 913 OK 3311 3314 3315 3333 C3' DC E 914 OK 3331 3334 3335 3352 C3' DC E 915 OK 3350 3353 3354 3371 C3' DA E 916 OK 3369 3372 3373 3392 C3' DA E 917 OK 3390 3393 3394 3413 C3' DC E 918 OK 3411 3414 3415 6171 C3' DG H1802 OK 6169 6172 6173 6193 C3' DT H1803 OK 6191 6194 6195 6213 C3' DT H1804 OK 6211 6214 6215 6233 C3' DG H1805 OK 6231 6234 6235 6255 C3' DG H1806 OK 6253 6256 6257 6277 C3' DA H1807 OK 6275 6278 6279 6298 C3' DT H1808 OK 6296 6299 6300 6318 C3' DG H1809 OK 6316 6319 6320 6340 C3' DG H1810 OK 6338 6341 6342 6362 C3' DT H1811 OK 6360 6363 6364 6382 C3' DA H1812 OK 6380 6383 6384 6403 C3' DG H1813 OK 6401 6404 6405 6425 C3' 2DA H1814 6423 6426 6446 C3' DC J1905 OK 6444 6447 6448 6465 C3' 8OG J1906 OK 6463 6466 6467 6488 C3' DC J1907 OK 6486 6489 6490 6507 C3' DT J1908 OK 6505 6508 6509 6527 C3' DA J1909 OK 6525 6528 6529 6548 C3' DC J1910 OK 6546 6549 6550 6567 C3' DC J1911 OK 6565 6568 6569 6586 C3' DA J1912 OK 6584 6587 6588 6607 C3' DT J1913 OK 6605 6608 6609 6627 C3' DC J1914 OK 6625 6628 6629 6646 C3' DC J1915 OK 6644 6647 6648 6665 C3' DA J1916 OK 6663 6666 6667 6686 C3' DA J1917 OK 6684 6687 6688 6707 C3' DC J1918 OK 6705 6708 6709 6736 C3' DGT A 414 OK 6734 6737 6738 6770 C3' DGT B1414 OK 6768 6771 6772 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2754 C4' DG D 802 OK 2756 2753 2755 2776 C4' DT D 803 OK 2778 2775 2777 2796 C4' DT D 804 OK 2798 2795 2797 2816 C4' DG D 805 OK 2818 2815 2817 2838 C4' DG D 806 OK 2840 2837 2839 2860 C4' DA D 807 OK 2862 2859 2861 2881 C4' DT D 808 OK 2883 2880 2882 2901 C4' DG D 809 OK 2903 2900 2902 2923 C4' DG D 810 OK 2925 2922 2924 2945 C4' DT D 811 OK 2947 2944 2946 2965 C4' DA D 812 OK 2967 2964 2966 2986 C4' DG D 813 OK 2988 2985 2987 3046 C4' DC E 901 OK 3048 3045 3047 3065 C4' DT E 902 OK 3067 3064 3066 3085 C4' DA E 903 OK 3087 3084 3086 3106 C4' DA E 904 OK 3108 3105 3107 3127 C4' DC E 905 OK 3129 3126 3128 3192 C4' DC E 907 OK 3194 3191 3193 3211 C4' DT E 908 OK 3213 3210 3212 3231 C4' DA E 909 OK 3233 3230 3232 3252 C4' DC E 910 OK 3254 3251 3253 3271 C4' DC E 911 OK 3273 3270 3272 3290 C4' DA E 912 OK 3292 3289 3291 3311 C4' DT E 913 OK 3313 3310 3312 3331 C4' DC E 914 OK 3333 3330 3332 3350 C4' DC E 915 OK 3352 3349 3351 3369 C4' DA E 916 OK 3371 3368 3370 3390 C4' DA E 917 OK 3392 3389 3391 3411 C4' DC E 918 OK 3413 3410 3412 6169 C4' DG H1802 OK 6171 6168 6170 6191 C4' DT H1803 OK 6193 6190 6192 6211 C4' DT H1804 OK 6213 6210 6212 6231 C4' DG H1805 OK 6233 6230 6232 6253 C4' DG H1806 OK 6255 6252 6254 6275 C4' DA H1807 OK 6277 6274 6276 6296 C4' DT H1808 OK 6298 6295 6297 6316 C4' DG H1809 OK 6318 6315 6317 6338 C4' DG H1810 OK 6340 6337 6339 6360 C4' DT H1811 OK 6362 6359 6361 6380 C4' DA H1812 OK 6382 6379 6381 6401 C4' DG H1813 OK 6403 6400 6402 6423 C4' 2DA H1814 OK 6425 6422 6424 6444 C4' DC J1905 OK 6446 6443 6445 6463 C4' 8OG J1906 OK 6465 6462 6464 6486 C4' DC J1907 OK 6488 6485 6487 6505 C4' DT J1908 OK 6507 6504 6506 6525 C4' DA J1909 OK 6527 6524 6526 6546 C4' DC J1910 OK 6548 6545 6547 6565 C4' DC J1911 OK 6567 6564 6566 6584 C4' DA J1912 OK 6586 6583 6585 6605 C4' DT J1913 OK 6607 6604 6606 6625 C4' DC J1914 OK 6627 6624 6626 6644 C4' DC J1915 OK 6646 6643 6645 6663 C4' DA J1916 OK 6665 6662 6664 6684 C4' DA J1917 OK 6686 6683 6685 6705 C4' DC J1918 OK 6707 6704 6706 6734 C4' DGT A 414 OK 6736 6733 6735 6768 C4' DGT B1414 OK 6770 6767 6769 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2753 C5' DG D 802 2752 2754 2775 C5' DT D 803 2774 2776 2795 C5' DT D 804 2794 2796 2815 C5' DG D 805 2814 2816 2837 C5' DG D 806 2836 2838 2859 C5' DA D 807 2858 2860 2880 C5' DT D 808 2879 2881 2900 C5' DG D 809 2899 2901 2922 C5' DG D 810 2921 2923 2944 C5' DT D 811 2943 2945 2964 C5' DA D 812 2963 2965 2985 C5' DG D 813 2984 2986 3045 C5' DC E 901 3044 3046 3064 C5' DT E 902 3063 3065 3084 C5' DA E 903 3083 3085 3105 C5' DA E 904 3104 3106 3126 C5' DC E 905 3125 3127 3191 C5' DC E 907 3190 3192 3210 C5' DT E 908 3209 3211 3230 C5' DA E 909 3229 3231 3251 C5' DC E 910 3250 3252 3270 C5' DC E 911 3269 3271 3289 C5' DA E 912 3288 3290 3310 C5' DT E 913 3309 3311 3330 C5' DC E 914 3329 3331 3349 C5' DC E 915 3348 3350 3368 C5' DA E 916 3367 3369 3389 C5' DA E 917 3388 3390 3410 C5' DC E 918 3409 3411 6168 C5' DG H1802 6167 6169 6190 C5' DT H1803 6189 6191 6210 C5' DT H1804 6209 6211 6230 C5' DG H1805 6229 6231 6252 C5' DG H1806 6251 6253 6274 C5' DA H1807 6273 6275 6295 C5' DT H1808 6294 6296 6315 C5' DG H1809 6314 6316 6337 C5' DG H1810 6336 6338 6359 C5' DT H1811 6358 6360 6379 C5' DA H1812 6378 6380 6400 C5' DG H1813 6399 6401 6422 C5' 2DA H1814 6421 6423 6443 C5' DC J1905 6442 6444 6462 C5' 8OG J1906 6461 6463 6485 C5' DC J1907 6484 6486 6504 C5' DT J1908 6503 6505 6524 C5' DA J1909 6523 6525 6545 C5' DC J1910 6544 6546 6564 C5' DC J1911 6563 6565 6583 C5' DA J1912 6582 6584 6604 C5' DT J1913 6603 6605 6624 C5' DC J1914 6623 6625 6643 C5' DC J1915 6642 6644 6662 C5' DA J1916 6661 6663 6683 C5' DA J1917 6682 6684 6704 C5' DC J1918 6703 6705 6733 C5' DGT A 414 6732 6734 6767 C5' DGT B1414 6766 6768 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2771 P DT D 803 distorted distorted 2757 2772 2773 2774 2791 P DT D 804 distorted distorted 2779 2792 2793 2794 2811 P DG D 805 distorted distorted 2799 2812 2813 2814 2833 P DG D 806 distorted distorted 2819 2834 2835 2836 2855 P DA D 807 distorted distorted 2841 2856 2857 2858 2876 P DT D 808 distorted distorted 2863 2877 2878 2879 2896 P DG D 809 distorted distorted 2884 2897 2898 2899 2918 P DG D 810 distorted distorted 2904 2919 2920 2921 2940 P DT D 811 distorted distorted 2926 2941 2942 2943 2960 P DA D 812 distorted distorted 2948 2961 2962 2963 2981 P DG D 813 distorted distorted 2968 2982 2983 2984 3003 P 2DA D 814 2989 3004 P 2DA D 814 2989 3060 P DT E 902 distorted distorted 3049 3061 3062 3063 3080 P DA E 903 distorted distorted 3068 3081 3082 3083 3101 P DA E 904 distorted distorted 3088 3102 3103 3104 3122 P DC E 905 distorted distorted 3109 3123 3124 3125 3141 P 8OG E 906 3130 3142 P 8OG E 906 3130 3187 P DC E 907 distorted distorted 3188 3189 3190 3206 P DT E 908 distorted distorted 3195 3207 3208 3209 3226 P DA E 909 distorted distorted 3214 3227 3228 3229 3247 P DC E 910 distorted distorted 3234 3248 3249 3250 3266 P DC E 911 distorted distorted 3255 3267 3268 3269 3285 P DA E 912 distorted distorted 3274 3286 3287 3288 3306 P DT E 913 distorted distorted 3293 3307 3308 3309 3326 P DC E 914 distorted distorted 3314 3327 3328 3329 3345 P DC E 915 distorted distorted 3334 3346 3347 3348 3364 P DA E 916 distorted distorted 3353 3365 3366 3367 3385 P DA E 917 distorted distorted 3372 3386 3387 3388 3406 P DC E 918 distorted distorted 3393 3407 3408 3409 6186 P DT H1803 distorted distorted 6172 6187 6188 6189 6206 P DT H1804 distorted distorted 6194 6207 6208 6209 6226 P DG H1805 distorted distorted 6214 6227 6228 6229 6248 P DG H1806 distorted distorted 6234 6249 6250 6251 6270 P DA H1807 distorted distorted 6256 6271 6272 6273 6291 P DT H1808 distorted distorted 6278 6292 6293 6294 6311 P DG H1809 distorted distorted 6299 6312 6313 6314 6333 P DG H1810 distorted distorted 6319 6334 6335 6336 6355 P DT H1811 distorted distorted 6341 6356 6357 6358 6375 P DA H1812 distorted distorted 6363 6376 6377 6378 6396 P DG H1813 distorted distorted 6383 6397 6398 6399 6418 P 2DA H1814 distorted distorted 6404 6419 6420 6421 6439 P DC J1905 distorted distorted 6440 6441 6442 6458 P 8OG J1906 distorted distorted 6447 6459 6460 6461 6481 P DC J1907 distorted distorted 6466 6482 6483 6484 6500 P DT J1908 distorted distorted 6489 6501 6502 6503 6520 P DA J1909 distorted distorted 6508 6521 6522 6523 6541 P DC J1910 distorted distorted 6528 6542 6543 6544 6560 P DC J1911 distorted distorted 6549 6561 6562 6563 6579 P DA J1912 distorted distorted 6568 6580 6581 6582 6600 P DT J1913 distorted distorted 6587 6601 6602 6603 6620 P DC J1914 distorted distorted 6608 6621 6622 6623 6639 P DC J1915 distorted distorted 6628 6640 6641 6642 6658 P DA J1916 distorted distorted 6647 6659 6660 6661 6679 P DA J1917 distorted distorted 6666 6680 6681 6682 6700 P DC J1918 distorted distorted 6687 6701 6702 6703 ---------------------------------------------------------------------------------