ID code: '1O27' 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' --------------------------------------------------------------------------------- 7235 C1' BRU A 603 beta 7240 7226 7236 7287 C1' FAD A 615 7288 7309 C1' BRU B 608 beta 7314 7300 7310 7361 C1' FAD B 610 7362 7414 C1' FAD C 605 7415 7436 C1' BRU C 613 beta 7441 7427 7437 7488 C1' FAD D 600 7489 7510 C1' BRU D 618 beta 7515 7501 7511 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7236 C2' BRU A 603 7235 7237 7288 C2' FAD A 615 OK 7287 7290 7289 7310 C2' BRU B 608 7309 7311 7362 C2' FAD B 610 OK 7361 7364 7363 7415 C2' FAD C 605 OK 7414 7417 7416 7437 C2' BRU C 613 7436 7438 7489 C2' FAD D 600 OK 7488 7491 7490 7511 C2' BRU D 618 7510 7512 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7237 C3' BRU A 603 OK 7238 7239 7236 7290 C3' FAD A 615 OK 7292 7291 7288 7311 C3' BRU B 608 OK 7312 7313 7310 7364 C3' FAD B 610 OK 7366 7365 7362 7417 C3' FAD C 605 OK 7419 7418 7415 7438 C3' BRU C 613 OK 7439 7440 7437 7491 C3' FAD D 600 OK 7493 7492 7489 7512 C3' BRU D 618 OK 7513 7514 7511 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7238 C4' BRU A 603 OK 7237 7241 7240 7292 C4' FAD A 615 OK 7290 7294 7293 7312 C4' BRU B 608 OK 7311 7315 7314 7366 C4' FAD B 610 OK 7364 7368 7367 7419 C4' FAD C 605 OK 7417 7421 7420 7439 C4' BRU C 613 OK 7438 7442 7441 7493 C4' FAD D 600 OK 7491 7495 7494 7513 C4' BRU D 618 OK 7512 7516 7515 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7241 C5' BRU A 603 7242 7238 7294 C5' FAD A 615 7295 7292 7315 C5' BRU B 608 7316 7312 7368 C5' FAD B 610 7369 7366 7421 C5' FAD C 605 7422 7419 7442 C5' BRU C 613 7443 7439 7495 C5' FAD D 600 7496 7493 7516 C5' BRU D 618 7517 7513 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7243 P BRU A 603 distorted distorted 7244 7245 7242 7296 P FAD A 615 distorted distorted 7297 7298 7295 7317 P BRU B 608 distorted distorted 7318 7319 7316 7370 P FAD B 610 distorted distorted 7371 7372 7369 7423 P FAD C 605 distorted distorted 7424 7425 7422 7444 P BRU C 613 distorted distorted 7445 7446 7443 7497 P FAD D 600 distorted distorted 7498 7499 7496 7518 P BRU D 618 distorted distorted 7519 7520 7517 ---------------------------------------------------------------------------------