ID code: '4H8K' 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' --------------------------------------------------------------------------------- 2167 C1' C C 1 beta 2162 2168 2165 2187 C1' G C 2 beta 2182 2188 2185 2210 C1' A C 3 beta 2205 2211 2208 2232 C1' C C 4 beta 2227 2233 2230 2252 C1' A C 5 beta 2247 2253 2250 2274 C1' C C 6 beta 2269 2275 2272 2294 C1' C C 7 beta 2289 2295 2292 2314 C1' U C 8 beta 2309 2315 2312 2334 C1' G C 9 beta 2329 2335 2332 2357 C1' A C 10 beta 2352 2358 2355 2379 C1' U C 11 beta 2374 2380 2377 2399 C1' U C 12 beta 2394 2400 2397 2419 C1' C C 13 beta 2414 2420 2417 2439 C1' C C 14 beta 2434 2440 2437 2456 C1' DG D 1 beta 2452 2457 2455 2478 C1' DG D 2 beta 2474 2479 2477 2500 C1' DA D 3 beta 2496 2501 2499 2521 C1' DA D 4 beta 2517 2522 2520 2542 C1' DT D 5 beta 2538 2543 2541 2562 C1' DC D 6 beta 2558 2563 2561 2581 C1' DA D 7 beta 2577 2582 2580 2602 C1' DG D 8 beta 2598 2603 2601 2624 C1' DG D 9 beta 2620 2625 2623 2646 C1' DT D 10 beta 2642 2647 2645 2666 C1' DG D 11 beta 2662 2667 2665 2688 C1' DT D 12 beta 2684 2689 2687 2708 C1' DC D 13 beta 2704 2709 2707 2727 C1' DG D 14 beta 2723 2728 2726 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2165 C2' C C 1 OK 2167 2163 2166 2185 C2' G C 2 OK 2187 2183 2186 2208 C2' A C 3 OK 2210 2206 2209 2230 C2' C C 4 OK 2232 2228 2231 2250 C2' A C 5 OK 2252 2248 2251 2272 C2' C C 6 OK 2274 2270 2273 2292 C2' C C 7 OK 2294 2290 2293 2312 C2' U C 8 OK 2314 2310 2313 2332 C2' G C 9 OK 2334 2330 2333 2355 C2' A C 10 OK 2357 2353 2356 2377 C2' U C 11 OK 2379 2375 2378 2397 C2' U C 12 OK 2399 2395 2398 2417 C2' C C 13 OK 2419 2415 2418 2437 C2' C C 14 OK 2439 2435 2438 2455 C2' DG D 1 2456 2453 2477 C2' DG D 2 2478 2475 2499 C2' DA D 3 2500 2497 2520 C2' DA D 4 2521 2518 2541 C2' DT D 5 2542 2539 2561 C2' DC D 6 2562 2559 2580 C2' DA D 7 2581 2578 2601 C2' DG D 8 2602 2599 2623 C2' DG D 9 2624 2621 2645 C2' DT D 10 2646 2643 2665 C2' DG D 11 2666 2663 2687 C2' DT D 12 2688 2685 2707 C2' DC D 13 2708 2705 2726 C2' DG D 14 2727 2724 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2163 C3' C C 1 OK 2161 2164 2165 2183 C3' G C 2 OK 2181 2184 2185 2206 C3' A C 3 OK 2204 2207 2208 2228 C3' C C 4 OK 2226 2229 2230 2248 C3' A C 5 OK 2246 2249 2250 2270 C3' C C 6 OK 2268 2271 2272 2290 C3' C C 7 OK 2288 2291 2292 2310 C3' U C 8 OK 2308 2311 2312 2330 C3' G C 9 OK 2328 2331 2332 2353 C3' A C 10 OK 2351 2354 2355 2375 C3' U C 11 OK 2373 2376 2377 2395 C3' U C 12 OK 2393 2396 2397 2415 C3' C C 13 OK 2413 2416 2417 2435 C3' C C 14 OK 2433 2436 2437 2453 C3' DG D 1 OK 2451 2454 2455 2475 C3' DG D 2 OK 2473 2476 2477 2497 C3' DA D 3 OK 2495 2498 2499 2518 C3' DA D 4 OK 2516 2519 2520 2539 C3' DT D 5 OK 2537 2540 2541 2559 C3' DC D 6 OK 2557 2560 2561 2578 C3' DA D 7 OK 2576 2579 2580 2599 C3' DG D 8 OK 2597 2600 2601 2621 C3' DG D 9 OK 2619 2622 2623 2643 C3' DT D 10 OK 2641 2644 2645 2663 C3' DG D 11 OK 2661 2664 2665 2685 C3' DT D 12 OK 2683 2686 2687 2705 C3' DC D 13 OK 2703 2706 2707 2724 C3' DG D 14 OK 2722 2725 2726 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2161 C4' C C 1 OK 2163 2160 2162 2181 C4' G C 2 OK 2183 2180 2182 2204 C4' A C 3 OK 2206 2203 2205 2226 C4' C C 4 OK 2228 2225 2227 2246 C4' A C 5 OK 2248 2245 2247 2268 C4' C C 6 OK 2270 2267 2269 2288 C4' C C 7 OK 2290 2287 2289 2308 C4' U C 8 OK 2310 2307 2309 2328 C4' G C 9 OK 2330 2327 2329 2351 C4' A C 10 OK 2353 2350 2352 2373 C4' U C 11 OK 2375 2372 2374 2393 C4' U C 12 OK 2395 2392 2394 2413 C4' C C 13 OK 2415 2412 2414 2433 C4' C C 14 OK 2435 2432 2434 2451 C4' DG D 1 OK 2453 2450 2452 2473 C4' DG D 2 OK 2475 2472 2474 2495 C4' DA D 3 OK 2497 2494 2496 2516 C4' DA D 4 OK 2518 2515 2517 2537 C4' DT D 5 OK 2539 2536 2538 2557 C4' DC D 6 OK 2559 2556 2558 2576 C4' DA D 7 OK 2578 2575 2577 2597 C4' DG D 8 OK 2599 2596 2598 2619 C4' DG D 9 OK 2621 2618 2620 2641 C4' DT D 10 OK 2643 2640 2642 2661 C4' DG D 11 OK 2663 2660 2662 2683 C4' DT D 12 OK 2685 2682 2684 2703 C4' DC D 13 OK 2705 2702 2704 2722 C4' DG D 14 OK 2724 2721 2723 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2160 C5' C C 1 2159 2161 2180 C5' G C 2 2179 2181 2203 C5' A C 3 2202 2204 2225 C5' C C 4 2224 2226 2245 C5' A C 5 2244 2246 2267 C5' C C 6 2266 2268 2287 C5' C C 7 2286 2288 2307 C5' U C 8 2306 2308 2327 C5' G C 9 2326 2328 2350 C5' A C 10 2349 2351 2372 C5' U C 11 2371 2373 2392 C5' U C 12 2391 2393 2412 C5' C C 13 2411 2413 2432 C5' C C 14 2431 2433 2450 C5' DG D 1 2449 2451 2472 C5' DG D 2 2471 2473 2494 C5' DA D 3 2493 2495 2515 C5' DA D 4 2514 2516 2536 C5' DT D 5 2535 2537 2556 C5' DC D 6 2555 2557 2575 C5' DA D 7 2574 2576 2596 C5' DG D 8 2595 2597 2618 C5' DG D 9 2617 2619 2640 C5' DT D 10 2639 2641 2660 C5' DG D 11 2659 2661 2682 C5' DT D 12 2681 2683 2702 C5' DC D 13 2701 2703 2721 C5' DG D 14 2720 2722 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2176 P G C 2 distorted distorted 2164 2177 2178 2179 2199 P A C 3 distorted distorted 2184 2200 2201 2202 2221 P C C 4 distorted distorted 2207 2222 2223 2224 2241 P A C 5 distorted distorted 2229 2242 2243 2244 2263 P C C 6 distorted distorted 2249 2264 2265 2266 2283 P C C 7 distorted distorted 2271 2284 2285 2286 2303 P U C 8 distorted distorted 2291 2304 2305 2306 2323 P G C 9 distorted distorted 2311 2324 2325 2326 2346 P A C 10 distorted distorted 2331 2347 2348 2349 2368 P U C 11 distorted distorted 2354 2369 2370 2371 2388 P U C 12 distorted distorted 2376 2389 2390 2391 2408 P C C 13 distorted distorted 2396 2409 2410 2411 2428 P C C 14 distorted distorted 2416 2429 2430 2431 2468 P DG D 2 distorted distorted 2454 2469 2470 2471 2490 P DA D 3 distorted distorted 2476 2491 2492 2493 2511 P DA D 4 distorted distorted 2498 2512 2513 2514 2532 P DT D 5 distorted distorted 2519 2533 2534 2535 2552 P DC D 6 distorted distorted 2540 2553 2554 2555 2571 P DA D 7 distorted distorted 2560 2572 2573 2574 2592 P DG D 8 distorted distorted 2579 2593 2594 2595 2614 P DG D 9 distorted distorted 2600 2615 2616 2617 2636 P DT D 10 distorted distorted 2622 2637 2638 2639 2656 P DG D 11 distorted distorted 2644 2657 2658 2659 2678 P DT D 12 distorted distorted 2664 2679 2680 2681 2698 P DC D 13 distorted distorted 2686 2699 2700 2701 2717 P DG D 14 distorted distorted 2706 2718 2719 2720 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