ID code: '1IHF' 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' --------------------------------------------------------------------------------- 1925 C1' G C -49 beta 1921 1926 1924 1950 C1' G C -48 beta 1946 1951 1949 1975 C1' T C -47 beta 1971 1976 1974 1996 C1' G C -46 beta 1992 1997 1995 2021 C1' C C -45 beta 2017 2022 2020 2042 C1' A C -44 beta 2038 2043 2041 2065 C1' A C -43 beta 2061 2066 2064 2088 C1' C C -42 beta 2084 2089 2087 2109 C1' A C -41 beta 2105 2110 2108 2132 C1' A C -40 beta 2128 2133 2131 2155 C1' A C -39 beta 2151 2156 2154 2178 C1' T C -38 beta 2174 2179 2177 2199 C1' T C -37 beta 2195 2200 2198 2220 C1' G C -36 beta 2216 2221 2219 2245 C1' A C -35 beta 2241 2246 2244 2268 C1' T C -34 beta 2264 2269 2267 2289 C1' A C -33 beta 2285 2290 2288 2312 C1' A C -32 beta 2308 2313 2311 2335 C1' G C -31 beta 2331 2336 2334 2360 C1' C C -30 beta 2356 2361 2359 2381 C1' A C -29 beta 2377 2382 2380 2404 C1' A C -28 beta 2400 2405 2403 2427 C1' T C -27 beta 2423 2428 2426 2448 C1' G C -26 beta 2444 2449 2447 2473 C1' C C -25 beta 2469 2474 2472 2494 C1' T C -24 beta 2490 2495 2493 2515 C1' T C -23 beta 2511 2516 2514 2536 C1' T C -22 beta 2532 2537 2535 2557 C1' T C -21 beta 2553 2558 2556 2578 C1' T C -20 beta 2574 2579 2577 2599 C1' T C -19 beta 2595 2600 2598 2620 C1' G C -18 beta 2616 2621 2619 2645 C1' G C -17 beta 2641 2646 2644 2670 C1' C C -16 beta 2666 2671 2669 2716 C1' G D 16 beta 2712 2717 2715 2741 C1' C D 17 beta 2737 2742 2740 2762 C1' C D 18 beta 2758 2763 2761 2783 C1' A D 19 beta 2779 2784 2782 2806 C1' A D 20 beta 2802 2807 2805 2829 C1' A D 21 beta 2825 2830 2828 2852 C1' A D 22 beta 2848 2853 2851 2875 C1' A D 23 beta 2871 2876 2874 2898 C1' A D 24 beta 2894 2899 2897 2921 C1' G D 25 beta 2917 2922 2920 2946 C1' C D 26 beta 2942 2947 2945 2967 C1' A D 27 beta 2963 2968 2966 2990 C1' T D 28 beta 2986 2991 2989 3011 C1' T D 29 beta 3007 3012 3010 3031 C1' G E 30 beta 3027 3032 3030 3057 C1' C E 31 beta 3053 3058 3056 3078 C1' T E 32 beta 3074 3079 3077 3099 C1' T E 33 beta 3095 3100 3098 3120 C1' A E 34 beta 3116 3121 3119 3143 C1' T E 35 beta 3139 3144 3142 3164 C1' C E 36 beta 3160 3165 3163 3185 C1' A E 37 beta 3181 3186 3184 3208 C1' A E 38 beta 3204 3209 3207 3231 C1' T E 39 beta 3227 3232 3230 3252 C1' T E 40 beta 3248 3253 3251 3273 C1' T E 41 beta 3269 3274 3272 3294 C1' G E 42 beta 3290 3295 3293 3319 C1' T E 43 beta 3315 3320 3318 3340 C1' T E 44 beta 3336 3341 3339 3361 C1' G E 45 beta 3357 3362 3360 3386 C1' C E 46 beta 3382 3387 3385 3407 C1' A E 47 beta 3403 3408 3406 3430 C1' C E 48 beta 3426 3431 3429 3451 C1' C E 49 beta 3447 3452 3450 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1924 C2' G C -49 1925 1922 1949 C2' G C -48 1950 1947 1974 C2' T C -47 1975 1972 1995 C2' G C -46 1996 1993 2020 C2' C C -45 2021 2018 2041 C2' A C -44 2042 2039 2064 C2' A C -43 2065 2062 2087 C2' C C -42 2088 2085 2108 C2' A C -41 2109 2106 2131 C2' A C -40 2132 2129 2154 C2' A C -39 2155 2152 2177 C2' T C -38 2178 2175 2198 C2' T C -37 2199 2196 2219 C2' G C -36 2220 2217 2244 C2' A C -35 2245 2242 2267 C2' T C -34 2268 2265 2288 C2' A C -33 2289 2286 2311 C2' A C -32 2312 2309 2334 C2' G C -31 2335 2332 2359 C2' C C -30 2360 2357 2380 C2' A C -29 2381 2378 2403 C2' A C -28 2404 2401 2426 C2' T C -27 2427 2424 2447 C2' G C -26 2448 2445 2472 C2' C C -25 2473 2470 2493 C2' T C -24 2494 2491 2514 C2' T C -23 2515 2512 2535 C2' T C -22 2536 2533 2556 C2' T C -21 2557 2554 2577 C2' T C -20 2578 2575 2598 C2' T C -19 2599 2596 2619 C2' G C -18 2620 2617 2644 C2' G C -17 2645 2642 2669 C2' C C -16 2670 2667 2715 C2' G D 16 2716 2713 2740 C2' C D 17 2741 2738 2761 C2' C D 18 2762 2759 2782 C2' A D 19 2783 2780 2805 C2' A D 20 2806 2803 2828 C2' A D 21 2829 2826 2851 C2' A D 22 2852 2849 2874 C2' A D 23 2875 2872 2897 C2' A D 24 2898 2895 2920 C2' G D 25 2921 2918 2945 C2' C D 26 2946 2943 2966 C2' A D 27 2967 2964 2989 C2' T D 28 2990 2987 3010 C2' T D 29 3011 3008 3030 C2' G E 30 3031 3028 3056 C2' C E 31 3057 3054 3077 C2' T E 32 3078 3075 3098 C2' T E 33 3099 3096 3119 C2' A E 34 3120 3117 3142 C2' T E 35 3143 3140 3163 C2' C E 36 3164 3161 3184 C2' A E 37 3185 3182 3207 C2' A E 38 3208 3205 3230 C2' T E 39 3231 3228 3251 C2' T E 40 3252 3249 3272 C2' T E 41 3273 3270 3293 C2' G E 42 3294 3291 3318 C2' T E 43 3319 3316 3339 C2' T E 44 3340 3337 3360 C2' G E 45 3361 3358 3385 C2' C E 46 3386 3383 3406 C2' A E 47 3407 3404 3429 C2' C E 48 3430 3427 3450 C2' C E 49 3451 3448 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1922 C3' G C -49 OK 1920 1923 1924 1947 C3' G C -48 OK 1945 1948 1949 1972 C3' T C -47 OK 1970 1973 1974 1993 C3' G C -46 OK 1991 1994 1995 2018 C3' C C -45 OK 2016 2019 2020 2039 C3' A C -44 OK 2037 2040 2041 2062 C3' A C -43 OK 2060 2063 2064 2085 C3' C C -42 OK 2083 2086 2087 2106 C3' A C -41 OK 2104 2107 2108 2129 C3' A C -40 OK 2127 2130 2131 2152 C3' A C -39 OK 2150 2153 2154 2175 C3' T C -38 OK 2173 2176 2177 2196 C3' T C -37 OK 2194 2197 2198 2217 C3' G C -36 OK 2215 2218 2219 2242 C3' A C -35 OK 2240 2243 2244 2265 C3' T C -34 OK 2263 2266 2267 2286 C3' A C -33 OK 2284 2287 2288 2309 C3' A C -32 OK 2307 2310 2311 2332 C3' G C -31 OK 2330 2333 2334 2357 C3' C C -30 OK 2355 2358 2359 2378 C3' A C -29 OK 2376 2379 2380 2401 C3' A C -28 OK 2399 2402 2403 2424 C3' T C -27 OK 2422 2425 2426 2445 C3' G C -26 OK 2443 2446 2447 2470 C3' C C -25 OK 2468 2471 2472 2491 C3' T C -24 OK 2489 2492 2493 2512 C3' T C -23 OK 2510 2513 2514 2533 C3' T C -22 OK 2531 2534 2535 2554 C3' T C -21 OK 2552 2555 2556 2575 C3' T C -20 OK 2573 2576 2577 2596 C3' T C -19 OK 2594 2597 2598 2617 C3' G C -18 OK 2615 2618 2619 2642 C3' G C -17 OK 2640 2643 2644 2667 C3' C C -16 OK 2665 2668 2669 2713 C3' G D 16 OK 2711 2714 2715 2738 C3' C D 17 OK 2736 2739 2740 2759 C3' C D 18 OK 2757 2760 2761 2780 C3' A D 19 OK 2778 2781 2782 2803 C3' A D 20 OK 2801 2804 2805 2826 C3' A D 21 OK 2824 2827 2828 2849 C3' A D 22 OK 2847 2850 2851 2872 C3' A D 23 OK 2870 2873 2874 2895 C3' A D 24 OK 2893 2896 2897 2918 C3' G D 25 OK 2916 2919 2920 2943 C3' C D 26 OK 2941 2944 2945 2964 C3' A D 27 OK 2962 2965 2966 2987 C3' T D 28 OK 2985 2988 2989 3008 C3' T D 29 OK 3006 3009 3010 3028 C3' G E 30 OK 3026 3029 3030 3054 C3' C E 31 OK 3052 3055 3056 3075 C3' T E 32 OK 3073 3076 3077 3096 C3' T E 33 OK 3094 3097 3098 3117 C3' A E 34 OK 3115 3118 3119 3140 C3' T E 35 OK 3138 3141 3142 3161 C3' C E 36 OK 3159 3162 3163 3182 C3' A E 37 OK 3180 3183 3184 3205 C3' A E 38 OK 3203 3206 3207 3228 C3' T E 39 OK 3226 3229 3230 3249 C3' T E 40 OK 3247 3250 3251 3270 C3' T E 41 OK 3268 3271 3272 3291 C3' G E 42 OK 3289 3292 3293 3316 C3' T E 43 OK 3314 3317 3318 3337 C3' T E 44 OK 3335 3338 3339 3358 C3' G E 45 OK 3356 3359 3360 3383 C3' C E 46 OK 3381 3384 3385 3404 C3' A E 47 OK 3402 3405 3406 3427 C3' C E 48 OK 3425 3428 3429 3448 C3' C E 49 OK 3446 3449 3450 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1920 C4' G C -49 OK 1922 1919 1921 1945 C4' G C -48 OK 1947 1944 1946 1970 C4' T C -47 OK 1972 1969 1971 1991 C4' G C -46 OK 1993 1990 1992 2016 C4' C C -45 OK 2018 2015 2017 2037 C4' A C -44 OK 2039 2036 2038 2060 C4' A C -43 OK 2062 2059 2061 2083 C4' C C -42 OK 2085 2082 2084 2104 C4' A C -41 OK 2106 2103 2105 2127 C4' A C -40 OK 2129 2126 2128 2150 C4' A C -39 OK 2152 2149 2151 2173 C4' T C -38 OK 2175 2172 2174 2194 C4' T C -37 OK 2196 2193 2195 2215 C4' G C -36 OK 2217 2214 2216 2240 C4' A C -35 OK 2242 2239 2241 2263 C4' T C -34 OK 2265 2262 2264 2284 C4' A C -33 OK 2286 2283 2285 2307 C4' A C -32 OK 2309 2306 2308 2330 C4' G C -31 OK 2332 2329 2331 2355 C4' C C -30 OK 2357 2354 2356 2376 C4' A C -29 OK 2378 2375 2377 2399 C4' A C -28 OK 2401 2398 2400 2422 C4' T C -27 OK 2424 2421 2423 2443 C4' G C -26 OK 2445 2442 2444 2468 C4' C C -25 OK 2470 2467 2469 2489 C4' T C -24 OK 2491 2488 2490 2510 C4' T C -23 OK 2512 2509 2511 2531 C4' T C -22 OK 2533 2530 2532 2552 C4' T C -21 OK 2554 2551 2553 2573 C4' T C -20 OK 2575 2572 2574 2594 C4' T C -19 OK 2596 2593 2595 2615 C4' G C -18 OK 2617 2614 2616 2640 C4' G C -17 OK 2642 2639 2641 2665 C4' C C -16 OK 2667 2664 2666 2711 C4' G D 16 OK 2713 2710 2712 2736 C4' C D 17 OK 2738 2735 2737 2757 C4' C D 18 OK 2759 2756 2758 2778 C4' A D 19 OK 2780 2777 2779 2801 C4' A D 20 OK 2803 2800 2802 2824 C4' A D 21 OK 2826 2823 2825 2847 C4' A D 22 OK 2849 2846 2848 2870 C4' A D 23 OK 2872 2869 2871 2893 C4' A D 24 OK 2895 2892 2894 2916 C4' G D 25 OK 2918 2915 2917 2941 C4' C D 26 OK 2943 2940 2942 2962 C4' A D 27 OK 2964 2961 2963 2985 C4' T D 28 OK 2987 2984 2986 3006 C4' T D 29 OK 3008 3005 3007 3026 C4' G E 30 OK 3028 3025 3027 3052 C4' C E 31 OK 3054 3051 3053 3073 C4' T E 32 OK 3075 3072 3074 3094 C4' T E 33 OK 3096 3093 3095 3115 C4' A E 34 OK 3117 3114 3116 3138 C4' T E 35 OK 3140 3137 3139 3159 C4' C E 36 OK 3161 3158 3160 3180 C4' A E 37 OK 3182 3179 3181 3203 C4' A E 38 OK 3205 3202 3204 3226 C4' T E 39 OK 3228 3225 3227 3247 C4' T E 40 OK 3249 3246 3248 3268 C4' T E 41 OK 3270 3267 3269 3289 C4' G E 42 OK 3291 3288 3290 3314 C4' T E 43 OK 3316 3313 3315 3335 C4' T E 44 OK 3337 3334 3336 3356 C4' G E 45 OK 3358 3355 3357 3381 C4' C E 46 OK 3383 3380 3382 3402 C4' A E 47 OK 3404 3401 3403 3425 C4' C E 48 OK 3427 3424 3426 3446 C4' C E 49 OK 3448 3445 3447 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1919 C5' G C -49 1918 1920 1944 C5' G C -48 1943 1945 1969 C5' T C -47 1968 1970 1990 C5' G C -46 1989 1991 2015 C5' C C -45 2014 2016 2036 C5' A C -44 2035 2037 2059 C5' A C -43 2058 2060 2082 C5' C C -42 2081 2083 2103 C5' A C -41 2102 2104 2126 C5' A C -40 2125 2127 2149 C5' A C -39 2148 2150 2172 C5' T C -38 2171 2173 2193 C5' T C -37 2192 2194 2214 C5' G C -36 2213 2215 2239 C5' A C -35 2238 2240 2262 C5' T C -34 2261 2263 2283 C5' A C -33 2282 2284 2306 C5' A C -32 2305 2307 2329 C5' G C -31 2328 2330 2354 C5' C C -30 2353 2355 2375 C5' A C -29 2374 2376 2398 C5' A C -28 2397 2399 2421 C5' T C -27 2420 2422 2442 C5' G C -26 2441 2443 2467 C5' C C -25 2466 2468 2488 C5' T C -24 2487 2489 2509 C5' T C -23 2508 2510 2530 C5' T C -22 2529 2531 2551 C5' T C -21 2550 2552 2572 C5' T C -20 2571 2573 2593 C5' T C -19 2592 2594 2614 C5' G C -18 2613 2615 2639 C5' G C -17 2638 2640 2664 C5' C C -16 2663 2665 2710 C5' G D 16 2709 2711 2735 C5' C D 17 2734 2736 2756 C5' C D 18 2755 2757 2777 C5' A D 19 2776 2778 2800 C5' A D 20 2799 2801 2823 C5' A D 21 2822 2824 2846 C5' A D 22 2845 2847 2869 C5' A D 23 2868 2870 2892 C5' A D 24 2891 2893 2915 C5' G D 25 2914 2916 2940 C5' C D 26 2939 2941 2961 C5' A D 27 2960 2962 2984 C5' T D 28 2983 2985 3005 C5' T D 29 3004 3006 3025 C5' G E 30 3024 3026 3051 C5' C E 31 3050 3052 3072 C5' T E 32 3071 3073 3093 C5' T E 33 3092 3094 3114 C5' A E 34 3113 3115 3137 C5' T E 35 3136 3138 3158 C5' C E 36 3157 3159 3179 C5' A E 37 3178 3180 3202 C5' A E 38 3201 3203 3225 C5' T E 39 3224 3226 3246 C5' T E 40 3245 3247 3267 C5' T E 41 3266 3268 3288 C5' G E 42 3287 3289 3313 C5' T E 43 3312 3314 3334 C5' T E 44 3333 3335 3355 C5' G E 45 3354 3356 3380 C5' C E 46 3379 3381 3401 C5' A E 47 3400 3402 3424 C5' C E 48 3423 3425 3445 C5' C E 49 3444 3446 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1940 P G C -48 OK OK 1923 1941 1942 1943 1965 P T C -47 OK OK 1948 1966 1967 1968 1986 P G C -46 OK OK 1973 1987 1988 1989 2011 P C C -45 OK OK 1994 2012 2013 2014 2032 P A C -44 OK OK 2019 2033 2034 2035 2055 P A C -43 OK OK 2040 2056 2057 2058 2078 P C C -42 OK OK 2063 2079 2080 2081 2099 P A C -41 OK OK 2086 2100 2101 2102 2122 P A C -40 OK OK 2107 2123 2124 2125 2145 P A C -39 OK OK 2130 2146 2147 2148 2168 P T C -38 OK OK 2153 2169 2170 2171 2189 P T C -37 OK OK 2176 2190 2191 2192 2210 P G C -36 OK OK 2197 2211 2212 2213 2235 P A C -35 OK OK 2218 2236 2237 2238 2258 P T C -34 OK OK 2243 2259 2260 2261 2279 P A C -33 OK OK 2266 2280 2281 2282 2302 P A C -32 OK OK 2287 2303 2304 2305 2325 P G C -31 OK OK 2310 2326 2327 2328 2350 P C C -30 OK OK 2333 2351 2352 2353 2371 P A C -29 OK OK 2358 2372 2373 2374 2394 P A C -28 OK OK 2379 2395 2396 2397 2417 P T C -27 OK OK 2402 2418 2419 2420 2438 P G C -26 OK OK 2425 2439 2440 2441 2463 P C C -25 OK OK 2446 2464 2465 2466 2484 P T C -24 OK OK 2471 2485 2486 2487 2505 P T C -23 OK OK 2492 2506 2507 2508 2526 P T C -22 OK OK 2513 2527 2528 2529 2547 P T C -21 OK OK 2534 2548 2549 2550 2568 P T C -20 OK OK 2555 2569 2570 2571 2589 P T C -19 OK OK 2576 2590 2591 2592 2610 P G C -18 OK OK 2597 2611 2612 2613 2635 P G C -17 OK OK 2618 2636 2637 2638 2660 P C C -16 OK OK 2643 2661 2662 2663 2731 P C D 17 OK OK 2714 2732 2733 2734 2752 P C D 18 OK OK 2739 2753 2754 2755 2773 P A D 19 OK OK 2760 2774 2775 2776 2796 P A D 20 OK OK 2781 2797 2798 2799 2819 P A D 21 OK OK 2804 2820 2821 2822 2842 P A D 22 OK OK 2827 2843 2844 2845 2865 P A D 23 OK OK 2850 2866 2867 2868 2888 P A D 24 OK OK 2873 2889 2890 2891 2911 P G D 25 OK OK 2896 2912 2913 2914 2936 P C D 26 OK OK 2919 2937 2938 2939 2957 P A D 27 OK OK 2944 2958 2959 2960 2980 P T D 28 OK OK 2965 2981 2982 2983 3001 P T D 29 OK OK 2988 3002 3003 3004 3047 P C E 31 OK OK 3029 3048 3049 3050 3068 P T E 32 OK OK 3055 3069 3070 3071 3089 P T E 33 OK OK 3076 3090 3091 3092 3110 P A E 34 OK OK 3097 3111 3112 3113 3133 P T E 35 OK OK 3118 3134 3135 3136 3154 P C E 36 OK OK 3141 3155 3156 3157 3175 P A E 37 OK OK 3162 3176 3177 3178 3198 P A E 38 OK OK 3183 3199 3200 3201 3221 P T E 39 OK OK 3206 3222 3223 3224 3242 P T E 40 OK OK 3229 3243 3244 3245 3263 P T E 41 OK OK 3250 3264 3265 3266 3284 P G E 42 OK OK 3271 3285 3286 3287 3309 P T E 43 OK OK 3292 3310 3311 3312 3330 P T E 44 OK OK 3317 3331 3332 3333 3351 P G E 45 OK OK 3338 3352 3353 3354 3376 P C E 46 OK OK 3359 3377 3378 3379 3397 P A E 47 OK OK 3384 3398 3399 3400 3420 P C E 48 OK OK 3405 3421 3422 3423 3441 P C E 49 OK OK 3428 3442 3443 3444 ---------------------------------------------------------------------------------