ID code: '5L2X' 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' --------------------------------------------------------------------------------- 2149 C1' DA C 2 beta 2145 2150 2148 2170 C1' DT C 3 beta 2166 2171 2169 2190 C1' DC C 4 beta 2186 2191 2189 2209 C1' DG C 5 beta 2205 2210 2208 2231 C1' DC C 6 beta 2227 2232 2230 2249 C1' 5IU C 7 beta 2254 2240 2250 2270 C1' DA C 8 beta 2266 2271 2269 2291 C1' DC C 9 beta 2287 2292 2290 2310 C1' DC C 10 beta 2306 2311 2309 2329 C1' DA C 11 beta 2325 2330 2328 2350 C1' DC C 12 beta 2346 2351 2349 2369 C1' DA C 13 beta 2365 2370 2368 2391 C1' DG D 8 beta 2387 2392 2390 2413 C1' DG D 9 beta 2409 2414 2412 2435 C1' DT D 10 beta 2431 2436 2434 2455 C1' DA D 11 beta 2451 2456 2454 2476 C1' DG D 12 beta 2472 2477 2475 2498 C1' DC D 13 beta 2494 2499 2497 2516 C1' DDG D 14 beta 2513 2517 2515 4550 C1' DT G 3 beta 4546 4551 4549 4570 C1' DC G 4 beta 4566 4571 4569 4589 C1' DG G 5 beta 4585 4590 4588 4611 C1' DC G 6 beta 4607 4612 4610 4629 C1' 5IU G 7 beta 4634 4620 4630 4650 C1' DA G 8 beta 4646 4651 4649 4671 C1' DC G 9 beta 4667 4672 4670 4690 C1' DC G 10 beta 4686 4691 4689 4710 C1' DG H 8 beta 4706 4711 4709 4732 C1' DG H 9 beta 4728 4733 4731 4754 C1' DT H 10 beta 4750 4755 4753 4774 C1' DA H 11 beta 4770 4775 4773 4795 C1' DG H 12 beta 4791 4796 4794 4817 C1' DC H 13 beta 4813 4818 4816 4835 C1' DDG H 14 beta 4832 4836 4834 4867 C1' DTP A 401 beta 4863 4868 4866 4898 C1' DTP B 401 beta 4894 4899 4897 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2148 C2' DA C 2 2149 2146 2169 C2' DT C 3 2170 2167 2189 C2' DC C 4 2190 2187 2208 C2' DG C 5 2209 2206 2230 C2' DC C 6 2231 2228 2250 C2' 5IU C 7 2249 2251 2269 C2' DA C 8 2270 2267 2290 C2' DC C 9 2291 2288 2309 C2' DC C 10 2310 2307 2328 C2' DA C 11 2329 2326 2349 C2' DC C 12 2350 2347 2368 C2' DA C 13 2369 2366 2390 C2' DG D 8 2391 2388 2412 C2' DG D 9 2413 2410 2434 C2' DT D 10 2435 2432 2454 C2' DA D 11 2455 2452 2475 C2' DG D 12 2476 2473 2497 C2' DC D 13 2498 2495 2515 C2' DDG D 14 2516 2514 4549 C2' DT G 3 4550 4547 4569 C2' DC G 4 4570 4567 4588 C2' DG G 5 4589 4586 4610 C2' DC G 6 4611 4608 4630 C2' 5IU G 7 4629 4631 4649 C2' DA G 8 4650 4647 4670 C2' DC G 9 4671 4668 4689 C2' DC G 10 4690 4687 4709 C2' DG H 8 4710 4707 4731 C2' DG H 9 4732 4729 4753 C2' DT H 10 4754 4751 4773 C2' DA H 11 4774 4771 4794 C2' DG H 12 4795 4792 4816 C2' DC H 13 4817 4814 4834 C2' DDG H 14 4835 4833 4866 C2' DTP A 401 4867 4864 4897 C2' DTP B 401 4898 4895 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2146 C3' DA C 2 OK 2144 2147 2148 2167 C3' DT C 3 OK 2165 2168 2169 2187 C3' DC C 4 OK 2185 2188 2189 2206 C3' DG C 5 OK 2204 2207 2208 2228 C3' DC C 6 OK 2226 2229 2230 2251 C3' 5IU C 7 OK 2252 2253 2250 2267 C3' DA C 8 OK 2265 2268 2269 2288 C3' DC C 9 OK 2286 2289 2290 2307 C3' DC C 10 OK 2305 2308 2309 2326 C3' DA C 11 OK 2324 2327 2328 2347 C3' DC C 12 OK 2345 2348 2349 2366 C3' DA C 13 OK 2364 2367 2368 2388 C3' DG D 8 OK 2386 2389 2390 2410 C3' DG D 9 OK 2408 2411 2412 2432 C3' DT D 10 OK 2430 2433 2434 2452 C3' DA D 11 OK 2450 2453 2454 2473 C3' DG D 12 OK 2471 2474 2475 2495 C3' DC D 13 OK 2493 2496 2497 2514 C3' DDG D 14 2512 2515 4547 C3' DT G 3 OK 4545 4548 4549 4567 C3' DC G 4 OK 4565 4568 4569 4586 C3' DG G 5 OK 4584 4587 4588 4608 C3' DC G 6 OK 4606 4609 4610 4631 C3' 5IU G 7 OK 4632 4633 4630 4647 C3' DA G 8 OK 4645 4648 4649 4668 C3' DC G 9 OK 4666 4669 4670 4687 C3' DC G 10 OK 4685 4688 4689 4707 C3' DG H 8 OK 4705 4708 4709 4729 C3' DG H 9 OK 4727 4730 4731 4751 C3' DT H 10 OK 4749 4752 4753 4771 C3' DA H 11 OK 4769 4772 4773 4792 C3' DG H 12 OK 4790 4793 4794 4814 C3' DC H 13 OK 4812 4815 4816 4833 C3' DDG H 14 4831 4834 4864 C3' DTP A 401 OK 4862 4865 4866 4895 C3' DTP B 401 OK 4893 4896 4897 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2144 C4' DA C 2 OK 2146 2143 2145 2165 C4' DT C 3 OK 2167 2164 2166 2185 C4' DC C 4 OK 2187 2184 2186 2204 C4' DG C 5 OK 2206 2203 2205 2226 C4' DC C 6 OK 2228 2225 2227 2252 C4' 5IU C 7 OK 2251 2255 2254 2265 C4' DA C 8 OK 2267 2264 2266 2286 C4' DC C 9 OK 2288 2285 2287 2305 C4' DC C 10 OK 2307 2304 2306 2324 C4' DA C 11 OK 2326 2323 2325 2345 C4' DC C 12 OK 2347 2344 2346 2364 C4' DA C 13 OK 2366 2363 2365 2386 C4' DG D 8 OK 2388 2385 2387 2408 C4' DG D 9 OK 2410 2407 2409 2430 C4' DT D 10 OK 2432 2429 2431 2450 C4' DA D 11 OK 2452 2449 2451 2471 C4' DG D 12 OK 2473 2470 2472 2493 C4' DC D 13 OK 2495 2492 2494 2512 C4' DDG D 14 OK 2514 2511 2513 4545 C4' DT G 3 OK 4547 4544 4546 4565 C4' DC G 4 OK 4567 4564 4566 4584 C4' DG G 5 OK 4586 4583 4585 4606 C4' DC G 6 OK 4608 4605 4607 4632 C4' 5IU G 7 OK 4631 4635 4634 4645 C4' DA G 8 OK 4647 4644 4646 4666 C4' DC G 9 OK 4668 4665 4667 4685 C4' DC G 10 OK 4687 4684 4686 4705 C4' DG H 8 OK 4707 4704 4706 4727 C4' DG H 9 OK 4729 4726 4728 4749 C4' DT H 10 OK 4751 4748 4750 4769 C4' DA H 11 OK 4771 4768 4770 4790 C4' DG H 12 OK 4792 4789 4791 4812 C4' DC H 13 OK 4814 4811 4813 4831 C4' DDG H 14 OK 4833 4830 4832 4862 C4' DTP A 401 OK 4864 4861 4863 4893 C4' DTP B 401 OK 4895 4892 4894 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2143 C5' DA C 2 2142 2144 2164 C5' DT C 3 2163 2165 2184 C5' DC C 4 2183 2185 2203 C5' DG C 5 2202 2204 2225 C5' DC C 6 2224 2226 2255 C5' 5IU C 7 2256 2252 2264 C5' DA C 8 2263 2265 2285 C5' DC C 9 2284 2286 2304 C5' DC C 10 2303 2305 2323 C5' DA C 11 2322 2324 2344 C5' DC C 12 2343 2345 2363 C5' DA C 13 2362 2364 2385 C5' DG D 8 2384 2386 2407 C5' DG D 9 2406 2408 2429 C5' DT D 10 2428 2430 2449 C5' DA D 11 2448 2450 2470 C5' DG D 12 2469 2471 2492 C5' DC D 13 2491 2493 2511 C5' DDG D 14 2510 2512 4544 C5' DT G 3 4543 4545 4564 C5' DC G 4 4563 4565 4583 C5' DG G 5 4582 4584 4605 C5' DC G 6 4604 4606 4635 C5' 5IU G 7 4636 4632 4644 C5' DA G 8 4643 4645 4665 C5' DC G 9 4664 4666 4684 C5' DC G 10 4683 4685 4704 C5' DG H 8 4703 4705 4726 C5' DG H 9 4725 4727 4748 C5' DT H 10 4747 4749 4768 C5' DA H 11 4767 4769 4789 C5' DG H 12 4788 4790 4811 C5' DC H 13 4810 4812 4830 C5' DDG H 14 4829 4831 4861 C5' DTP A 401 4860 4862 4892 C5' DTP B 401 4891 4893 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2139 P DA C 2 distorted distorted 2140 2141 2142 2160 P DT C 3 distorted distorted 2147 2161 2162 2163 2180 P DC C 4 distorted distorted 2168 2181 2182 2183 2199 P DG C 5 distorted distorted 2188 2200 2201 2202 2221 P DC C 6 distorted distorted 2207 2222 2223 2224 2257 P 5IU C 7 distorted distorted 2229 2258 2259 2256 2260 P DA C 8 distorted distorted 2253 2261 2262 2263 2281 P DC C 9 distorted distorted 2268 2282 2283 2284 2300 P DC C 10 distorted distorted 2289 2301 2302 2303 2319 P DA C 11 distorted distorted 2308 2320 2321 2322 2340 P DC C 12 distorted distorted 2327 2341 2342 2343 2359 P DA C 13 distorted distorted 2348 2360 2361 2362 2381 P DG D 8 distorted distorted 2382 2383 2384 2403 P DG D 9 distorted distorted 2389 2404 2405 2406 2425 P DT D 10 distorted distorted 2411 2426 2427 2428 2445 P DA D 11 distorted distorted 2433 2446 2447 2448 2466 P DG D 12 distorted distorted 2453 2467 2468 2469 2488 P DC D 13 distorted distorted 2474 2489 2490 2491 2507 P DDG D 14 distorted distorted 2496 2508 2509 2510 4540 P DT G 3 distorted distorted 4541 4542 4543 4560 P DC G 4 distorted distorted 4548 4561 4562 4563 4579 P DG G 5 distorted distorted 4568 4580 4581 4582 4601 P DC G 6 distorted distorted 4587 4602 4603 4604 4637 P 5IU G 7 distorted distorted 4609 4638 4639 4636 4640 P DA G 8 distorted distorted 4633 4641 4642 4643 4661 P DC G 9 distorted distorted 4648 4662 4663 4664 4680 P DC G 10 distorted distorted 4669 4681 4682 4683 4700 P DG H 8 distorted distorted 4701 4702 4703 4722 P DG H 9 distorted distorted 4708 4723 4724 4725 4744 P DT H 10 distorted distorted 4730 4745 4746 4747 4764 P DA H 11 distorted distorted 4752 4765 4766 4767 4785 P DG H 12 distorted distorted 4772 4786 4787 4788 4807 P DC H 13 distorted distorted 4793 4808 4809 4810 4826 P DDG H 14 distorted distorted 4815 4827 4828 4829 ---------------------------------------------------------------------------------