ID code: '5H1L' 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' --------------------------------------------------------------------------------- 5388 C1' A B 1 beta 5383 5389 5386 5410 C1' U B 2 beta 5405 5411 5408 5430 C1' U B 3 beta 5425 5431 5428 5450 C1' U B 4 beta 5445 5451 5448 5470 C1' U B 5 beta 5465 5471 5468 5490 C1' U B 6 beta 5485 5491 5488 5510 C1' G B 7 beta 5505 5511 5508 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5386 C2' A B 1 OK 5388 5384 5387 5408 C2' U B 2 OK 5410 5406 5409 5428 C2' U B 3 OK 5430 5426 5429 5448 C2' U B 4 OK 5450 5446 5449 5468 C2' U B 5 OK 5470 5466 5469 5488 C2' U B 6 OK 5490 5486 5489 5508 C2' G B 7 OK 5510 5506 5509 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5384 C3' A B 1 OK 5382 5385 5386 5406 C3' U B 2 OK 5404 5407 5408 5426 C3' U B 3 OK 5424 5427 5428 5446 C3' U B 4 OK 5444 5447 5448 5466 C3' U B 5 OK 5464 5467 5468 5486 C3' U B 6 OK 5484 5487 5488 5506 C3' G B 7 OK 5504 5507 5508 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5382 C4' A B 1 OK 5384 5381 5383 5404 C4' U B 2 OK 5406 5403 5405 5424 C4' U B 3 OK 5426 5423 5425 5444 C4' U B 4 OK 5446 5443 5445 5464 C4' U B 5 OK 5466 5463 5465 5484 C4' U B 6 OK 5486 5483 5485 5504 C4' G B 7 OK 5506 5503 5505 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5381 C5' A B 1 5380 5382 5403 C5' U B 2 5402 5404 5423 C5' U B 3 5422 5424 5443 C5' U B 4 5442 5444 5463 C5' U B 5 5462 5464 5483 C5' U B 6 5482 5484 5503 C5' G B 7 5502 5504 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5399 P U B 2 distorted distorted 5385 5400 5401 5402 5419 P U B 3 distorted distorted 5407 5420 5421 5422 5439 P U B 4 distorted distorted 5427 5440 5441 5442 5459 P U B 5 distorted distorted 5447 5460 5461 5462 5479 P U B 6 distorted distorted 5467 5480 5481 5482 5499 P G B 7 distorted distorted 5487 5500 5501 5502 ---------------------------------------------------------------------------------