ID code: '4PY5' 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' --------------------------------------------------------------------------------- 2046 C1' G B 1 beta 2041 2047 2044 2069 C1' A B 2 beta 2064 2070 2067 2091 C1' G B 3 beta 2086 2092 2089 2114 C1' U B 4 beta 2109 2115 2112 2134 C1' G B 5 beta 2129 2135 2132 2157 C1' C B 6 beta 2152 2158 2155 2177 C1' G B 7 beta 2172 2178 2175 2200 C1' A B 8 beta 2195 2201 2198 2222 C1' C B 9 beta 2217 2223 2220 2242 C1' A B 10 beta 2237 2243 2240 2264 C1' C B 11 beta 2259 2265 2262 2284 C1' C B 12 beta 2279 2285 2282 2304 C1' U B 13 beta 2299 2305 2302 2324 C1' G B 14 beta 2319 2325 2322 2347 C1' A B 15 beta 2342 2348 2345 2369 C1' U B 16 beta 2364 2370 2367 2389 C1' U B 17 beta 2384 2390 2387 2409 C1' C B 18 beta 2404 2410 2407 2429 C1' C B 19 beta 2424 2430 2427 2446 C1' DG C 1 beta 2442 2447 2445 2468 C1' DG C 2 beta 2464 2469 2467 2490 C1' DA C 3 beta 2486 2491 2489 2511 C1' DA C 4 beta 2507 2512 2510 2532 C1' DT C 5 beta 2528 2533 2531 2552 C1' DC C 6 beta 2548 2553 2551 2571 C1' DA C 7 beta 2567 2572 2570 2592 C1' DG C 8 beta 2588 2593 2591 2614 C1' DG C 9 beta 2610 2615 2613 2636 C1' DT C 10 beta 2632 2637 2635 2656 C1' DG C 11 beta 2652 2657 2655 2678 C1' DT C 12 beta 2674 2679 2677 2698 C1' DC C 13 beta 2694 2699 2697 2717 C1' DG C 14 beta 2713 2718 2716 2739 C1' DC C 15 beta 2735 2740 2738 2758 C1' DA C 16 beta 2754 2759 2757 2779 C1' DC C 17 beta 2775 2780 2778 2798 C1' DT C 18 beta 2794 2799 2797 2818 C1' DC C 19 beta 2814 2819 2817 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2044 C2' G B 1 OK 2046 2042 2045 2067 C2' A B 2 OK 2069 2065 2068 2089 C2' G B 3 OK 2091 2087 2090 2112 C2' U B 4 OK 2114 2110 2113 2132 C2' G B 5 OK 2134 2130 2133 2155 C2' C B 6 OK 2157 2153 2156 2175 C2' G B 7 OK 2177 2173 2176 2198 C2' A B 8 OK 2200 2196 2199 2220 C2' C B 9 OK 2222 2218 2221 2240 C2' A B 10 OK 2242 2238 2241 2262 C2' C B 11 OK 2264 2260 2263 2282 C2' C B 12 OK 2284 2280 2283 2302 C2' U B 13 OK 2304 2300 2303 2322 C2' G B 14 OK 2324 2320 2323 2345 C2' A B 15 OK 2347 2343 2346 2367 C2' U B 16 OK 2369 2365 2368 2387 C2' U B 17 OK 2389 2385 2388 2407 C2' C B 18 OK 2409 2405 2408 2427 C2' C B 19 OK 2429 2425 2428 2445 C2' DG C 1 2446 2443 2467 C2' DG C 2 2468 2465 2489 C2' DA C 3 2490 2487 2510 C2' DA C 4 2511 2508 2531 C2' DT C 5 2532 2529 2551 C2' DC C 6 2552 2549 2570 C2' DA C 7 2571 2568 2591 C2' DG C 8 2592 2589 2613 C2' DG C 9 2614 2611 2635 C2' DT C 10 2636 2633 2655 C2' DG C 11 2656 2653 2677 C2' DT C 12 2678 2675 2697 C2' DC C 13 2698 2695 2716 C2' DG C 14 2717 2714 2738 C2' DC C 15 2739 2736 2757 C2' DA C 16 2758 2755 2778 C2' DC C 17 2779 2776 2797 C2' DT C 18 2798 2795 2817 C2' DC C 19 2818 2815 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2042 C3' G B 1 OK 2040 2043 2044 2065 C3' A B 2 OK 2063 2066 2067 2087 C3' G B 3 OK 2085 2088 2089 2110 C3' U B 4 OK 2108 2111 2112 2130 C3' G B 5 OK 2128 2131 2132 2153 C3' C B 6 OK 2151 2154 2155 2173 C3' G B 7 OK 2171 2174 2175 2196 C3' A B 8 OK 2194 2197 2198 2218 C3' C B 9 OK 2216 2219 2220 2238 C3' A B 10 OK 2236 2239 2240 2260 C3' C B 11 OK 2258 2261 2262 2280 C3' C B 12 OK 2278 2281 2282 2300 C3' U B 13 OK 2298 2301 2302 2320 C3' G B 14 OK 2318 2321 2322 2343 C3' A B 15 OK 2341 2344 2345 2365 C3' U B 16 OK 2363 2366 2367 2385 C3' U B 17 OK 2383 2386 2387 2405 C3' C B 18 OK 2403 2406 2407 2425 C3' C B 19 OK 2423 2426 2427 2443 C3' DG C 1 OK 2441 2444 2445 2465 C3' DG C 2 OK 2463 2466 2467 2487 C3' DA C 3 OK 2485 2488 2489 2508 C3' DA C 4 OK 2506 2509 2510 2529 C3' DT C 5 OK 2527 2530 2531 2549 C3' DC C 6 OK 2547 2550 2551 2568 C3' DA C 7 OK 2566 2569 2570 2589 C3' DG C 8 OK 2587 2590 2591 2611 C3' DG C 9 OK 2609 2612 2613 2633 C3' DT C 10 OK 2631 2634 2635 2653 C3' DG C 11 OK 2651 2654 2655 2675 C3' DT C 12 OK 2673 2676 2677 2695 C3' DC C 13 OK 2693 2696 2697 2714 C3' DG C 14 OK 2712 2715 2716 2736 C3' DC C 15 OK 2734 2737 2738 2755 C3' DA C 16 OK 2753 2756 2757 2776 C3' DC C 17 OK 2774 2777 2778 2795 C3' DT C 18 OK 2793 2796 2797 2815 C3' DC C 19 OK 2813 2816 2817 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2040 C4' G B 1 OK 2042 2039 2041 2063 C4' A B 2 OK 2065 2062 2064 2085 C4' G B 3 OK 2087 2084 2086 2108 C4' U B 4 OK 2110 2107 2109 2128 C4' G B 5 OK 2130 2127 2129 2151 C4' C B 6 OK 2153 2150 2152 2171 C4' G B 7 OK 2173 2170 2172 2194 C4' A B 8 OK 2196 2193 2195 2216 C4' C B 9 OK 2218 2215 2217 2236 C4' A B 10 OK 2238 2235 2237 2258 C4' C B 11 OK 2260 2257 2259 2278 C4' C B 12 OK 2280 2277 2279 2298 C4' U B 13 OK 2300 2297 2299 2318 C4' G B 14 OK 2320 2317 2319 2341 C4' A B 15 OK 2343 2340 2342 2363 C4' U B 16 OK 2365 2362 2364 2383 C4' U B 17 OK 2385 2382 2384 2403 C4' C B 18 OK 2405 2402 2404 2423 C4' C B 19 OK 2425 2422 2424 2441 C4' DG C 1 OK 2443 2440 2442 2463 C4' DG C 2 OK 2465 2462 2464 2485 C4' DA C 3 OK 2487 2484 2486 2506 C4' DA C 4 OK 2508 2505 2507 2527 C4' DT C 5 OK 2529 2526 2528 2547 C4' DC C 6 OK 2549 2546 2548 2566 C4' DA C 7 OK 2568 2565 2567 2587 C4' DG C 8 OK 2589 2586 2588 2609 C4' DG C 9 OK 2611 2608 2610 2631 C4' DT C 10 OK 2633 2630 2632 2651 C4' DG C 11 OK 2653 2650 2652 2673 C4' DT C 12 OK 2675 2672 2674 2693 C4' DC C 13 OK 2695 2692 2694 2712 C4' DG C 14 OK 2714 2711 2713 2734 C4' DC C 15 OK 2736 2733 2735 2753 C4' DA C 16 OK 2755 2752 2754 2774 C4' DC C 17 OK 2776 2773 2775 2793 C4' DT C 18 OK 2795 2792 2794 2813 C4' DC C 19 OK 2815 2812 2814 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2039 C5' G B 1 2038 2040 2062 C5' A B 2 2061 2063 2084 C5' G B 3 2083 2085 2107 C5' U B 4 2106 2108 2127 C5' G B 5 2126 2128 2150 C5' C B 6 2149 2151 2170 C5' G B 7 2169 2171 2193 C5' A B 8 2192 2194 2215 C5' C B 9 2214 2216 2235 C5' A B 10 2234 2236 2257 C5' C B 11 2256 2258 2277 C5' C B 12 2276 2278 2297 C5' U B 13 2296 2298 2317 C5' G B 14 2316 2318 2340 C5' A B 15 2339 2341 2362 C5' U B 16 2361 2363 2382 C5' U B 17 2381 2383 2402 C5' C B 18 2401 2403 2422 C5' C B 19 2421 2423 2440 C5' DG C 1 2439 2441 2462 C5' DG C 2 2461 2463 2484 C5' DA C 3 2483 2485 2505 C5' DA C 4 2504 2506 2526 C5' DT C 5 2525 2527 2546 C5' DC C 6 2545 2547 2565 C5' DA C 7 2564 2566 2586 C5' DG C 8 2585 2587 2608 C5' DG C 9 2607 2609 2630 C5' DT C 10 2629 2631 2650 C5' DG C 11 2649 2651 2672 C5' DT C 12 2671 2673 2692 C5' DC C 13 2691 2693 2711 C5' DG C 14 2710 2712 2733 C5' DC C 15 2732 2734 2752 C5' DA C 16 2751 2753 2773 C5' DC C 17 2772 2774 2792 C5' DT C 18 2791 2793 2812 C5' DC C 19 2811 2813 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2058 P A B 2 distorted distorted 2043 2059 2060 2061 2080 P G B 3 distorted distorted 2066 2081 2082 2083 2103 P U B 4 distorted distorted 2088 2104 2105 2106 2123 P G B 5 distorted distorted 2111 2124 2125 2126 2146 P C B 6 distorted distorted 2131 2147 2148 2149 2166 P G B 7 distorted distorted 2154 2167 2168 2169 2189 P A B 8 distorted distorted 2174 2190 2191 2192 2211 P C B 9 distorted distorted 2197 2212 2213 2214 2231 P A B 10 distorted distorted 2219 2232 2233 2234 2253 P C B 11 distorted distorted 2239 2254 2255 2256 2273 P C B 12 distorted distorted 2261 2274 2275 2276 2293 P U B 13 distorted distorted 2281 2294 2295 2296 2313 P G B 14 distorted distorted 2301 2314 2315 2316 2336 P A B 15 distorted distorted 2321 2337 2338 2339 2358 P U B 16 distorted distorted 2344 2359 2360 2361 2378 P U B 17 distorted distorted 2366 2379 2380 2381 2398 P C B 18 distorted distorted 2386 2399 2400 2401 2418 P C B 19 distorted distorted 2406 2419 2420 2421 2458 P DG C 2 distorted distorted 2444 2459 2460 2461 2480 P DA C 3 distorted distorted 2466 2481 2482 2483 2501 P DA C 4 distorted distorted 2488 2502 2503 2504 2522 P DT C 5 distorted distorted 2509 2523 2524 2525 2542 P DC C 6 distorted distorted 2530 2543 2544 2545 2561 P DA C 7 distorted distorted 2550 2562 2563 2564 2582 P DG C 8 distorted distorted 2569 2583 2584 2585 2604 P DG C 9 distorted distorted 2590 2605 2606 2607 2626 P DT C 10 distorted distorted 2612 2627 2628 2629 2646 P DG C 11 distorted distorted 2634 2647 2648 2649 2668 P DT C 12 distorted distorted 2654 2669 2670 2671 2688 P DC C 13 distorted distorted 2676 2689 2690 2691 2707 P DG C 14 distorted distorted 2696 2708 2709 2710 2729 P DC C 15 distorted distorted 2715 2730 2731 2732 2748 P DA C 16 distorted distorted 2737 2749 2750 2751 2769 P DC C 17 distorted distorted 2756 2770 2771 2772 2788 P DT C 18 distorted distorted 2777 2789 2790 2791 2808 P DC C 19 distorted distorted 2796 2809 2810 2811 ---------------------------------------------------------------------------------