ID code: '4XWW' 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' --------------------------------------------------------------------------------- 8362 C1' U D 1 beta 8357 8363 8360 8382 C1' U D 2 beta 8377 8383 8380 8402 C1' U D 3 beta 8397 8403 8400 8422 C1' U D 4 beta 8417 8423 8420 8442 C1' U D 5 beta 8437 8443 8440 8462 C1' U D 6 beta 8457 8463 8460 8484 C1' U E 1 beta 8479 8485 8482 8504 C1' U E 2 beta 8499 8505 8502 8524 C1' U E 3 beta 8519 8525 8522 8544 C1' U E 4 beta 8539 8545 8542 8564 C1' U E 5 beta 8559 8565 8562 8584 C1' U E 6 beta 8579 8585 8582 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8360 C2' U D 1 OK 8362 8358 8361 8380 C2' U D 2 OK 8382 8378 8381 8400 C2' U D 3 OK 8402 8398 8401 8420 C2' U D 4 OK 8422 8418 8421 8440 C2' U D 5 OK 8442 8438 8441 8460 C2' U D 6 OK 8462 8458 8461 8482 C2' U E 1 OK 8484 8480 8483 8502 C2' U E 2 OK 8504 8500 8503 8522 C2' U E 3 OK 8524 8520 8523 8542 C2' U E 4 OK 8544 8540 8543 8562 C2' U E 5 OK 8564 8560 8563 8582 C2' U E 6 OK 8584 8580 8583 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8358 C3' U D 1 OK 8356 8359 8360 8378 C3' U D 2 OK 8376 8379 8380 8398 C3' U D 3 OK 8396 8399 8400 8418 C3' U D 4 OK 8416 8419 8420 8438 C3' U D 5 OK 8436 8439 8440 8458 C3' U D 6 OK 8456 8459 8460 8480 C3' U E 1 OK 8478 8481 8482 8500 C3' U E 2 OK 8498 8501 8502 8520 C3' U E 3 OK 8518 8521 8522 8540 C3' U E 4 OK 8538 8541 8542 8560 C3' U E 5 OK 8558 8561 8562 8580 C3' U E 6 OK 8578 8581 8582 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8356 C4' U D 1 OK 8358 8355 8357 8376 C4' U D 2 OK 8378 8375 8377 8396 C4' U D 3 OK 8398 8395 8397 8416 C4' U D 4 OK 8418 8415 8417 8436 C4' U D 5 OK 8438 8435 8437 8456 C4' U D 6 OK 8458 8455 8457 8478 C4' U E 1 OK 8480 8477 8479 8498 C4' U E 2 OK 8500 8497 8499 8518 C4' U E 3 OK 8520 8517 8519 8538 C4' U E 4 OK 8540 8537 8539 8558 C4' U E 5 OK 8560 8557 8559 8578 C4' U E 6 OK 8580 8577 8579 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8355 C5' U D 1 8354 8356 8375 C5' U D 2 8374 8376 8395 C5' U D 3 8394 8396 8415 C5' U D 4 8414 8416 8435 C5' U D 5 8434 8436 8455 C5' U D 6 8454 8456 8477 C5' U E 1 8476 8478 8497 C5' U E 2 8496 8498 8517 C5' U E 3 8516 8518 8537 C5' U E 4 8536 8538 8557 C5' U E 5 8556 8558 8577 C5' U E 6 8576 8578 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8351 P U D 1 distorted distorted 8350 8352 8353 8354 8371 P U D 2 distorted distorted 8359 8372 8373 8374 8391 P U D 3 distorted distorted 8379 8392 8393 8394 8411 P U D 4 distorted distorted 8399 8412 8413 8414 8431 P U D 5 distorted distorted 8419 8432 8433 8434 8451 P U D 6 distorted distorted 8439 8452 8453 8454 8473 P U E 1 distorted distorted 8472 8474 8475 8476 8493 P U E 2 distorted distorted 8481 8494 8495 8496 8513 P U E 3 distorted distorted 8501 8514 8515 8516 8533 P U E 4 distorted distorted 8521 8534 8535 8536 8553 P U E 5 distorted distorted 8541 8554 8555 8556 8573 P U E 6 distorted distorted 8561 8574 8575 8576 ---------------------------------------------------------------------------------