ID code: '4FWT' 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' --------------------------------------------------------------------------------- 9301 C1' C G2003 beta 9296 9302 9299 9321 C1' U G2004 beta 9316 9322 9319 9341 C1' A G2005 beta 9336 9342 9339 9363 C1' C G2006 beta 9358 9364 9361 9383 C1' C G2007 beta 9378 9384 9381 9402 C1' C G2008 beta 9398 9403 9400 9420 C1' G T2101 beta 9415 9421 9418 9443 C1' G T2102 beta 9438 9444 9441 9466 C1' G T2103 beta 9461 9467 9464 9489 C1' U T2104 beta 9484 9490 9487 9509 C1' A T2105 beta 9504 9510 9507 9531 C1' G T2106 beta 9526 9532 9529 9564 C1' GTP A2501 beta 9559 9565 9562 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 9299 C2' C G2003 OK 9301 9297 9300 9319 C2' U G2004 OK 9321 9317 9320 9339 C2' A G2005 OK 9341 9337 9340 9361 C2' C G2006 OK 9363 9359 9362 9381 C2' C G2007 OK 9383 9379 9382 9400 C2' C G2008 OK 9402 9399 9401 9418 C2' G T2101 OK 9420 9416 9419 9441 C2' G T2102 OK 9443 9439 9442 9464 C2' G T2103 OK 9466 9462 9465 9487 C2' U T2104 OK 9489 9485 9488 9507 C2' A T2105 OK 9509 9505 9508 9529 C2' G T2106 OK 9531 9527 9530 9562 C2' GTP A2501 OK 9564 9560 9563 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9297 C3' C G2003 OK 9295 9298 9299 9317 C3' U G2004 OK 9315 9318 9319 9337 C3' A G2005 OK 9335 9338 9339 9359 C3' C G2006 OK 9357 9360 9361 9379 C3' C G2007 OK 9377 9380 9381 9399 C3' C G2008 9397 9400 9416 C3' G T2101 OK 9414 9417 9418 9439 C3' G T2102 OK 9437 9440 9441 9462 C3' G T2103 OK 9460 9463 9464 9485 C3' U T2104 OK 9483 9486 9487 9505 C3' A T2105 OK 9503 9506 9507 9527 C3' G T2106 OK 9525 9528 9529 9560 C3' GTP A2501 OK 9558 9561 9562 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 9295 C4' C G2003 OK 9297 9294 9296 9315 C4' U G2004 OK 9317 9314 9316 9335 C4' A G2005 OK 9337 9334 9336 9357 C4' C G2006 OK 9359 9356 9358 9377 C4' C G2007 OK 9379 9376 9378 9397 C4' C G2008 OK 9399 9396 9398 9414 C4' G T2101 OK 9416 9413 9415 9437 C4' G T2102 OK 9439 9436 9438 9460 C4' G T2103 OK 9462 9459 9461 9483 C4' U T2104 OK 9485 9482 9484 9503 C4' A T2105 OK 9505 9502 9504 9525 C4' G T2106 OK 9527 9524 9526 9558 C4' GTP A2501 OK 9560 9557 9559 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 9294 C5' C G2003 9293 9295 9314 C5' U G2004 9313 9315 9334 C5' A G2005 9333 9335 9356 C5' C G2006 9355 9357 9376 C5' C G2007 9375 9377 9396 C5' C G2008 9395 9397 9413 C5' G T2101 9412 9414 9436 C5' G T2102 9435 9437 9459 C5' G T2103 9458 9460 9482 C5' U T2104 9481 9483 9502 C5' A T2105 9501 9503 9524 C5' G T2106 9523 9525 9557 C5' GTP A2501 9556 9558 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 9290 P C G2003 distorted distorted 9289 9291 9292 9293 9310 P U G2004 distorted distorted 9298 9311 9312 9313 9330 P A G2005 distorted distorted 9318 9331 9332 9333 9352 P C G2006 distorted distorted 9338 9353 9354 9355 9372 P C G2007 distorted distorted 9360 9373 9374 9375 9392 P C G2008 distorted distorted 9380 9393 9394 9395 9432 P G T2102 distorted distorted 9417 9433 9434 9435 9455 P G T2103 distorted distorted 9440 9456 9457 9458 9478 P U T2104 distorted distorted 9463 9479 9480 9481 9498 P A T2105 distorted distorted 9486 9499 9500 9501 9520 P G T2106 distorted distorted 9506 9521 9522 9523 ---------------------------------------------------------------------------------