ID code: '4D26' 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' --------------------------------------------------------------------------------- 3374 C1' U D 1 beta 3369 3375 3372 3394 C1' G D 2 beta 3389 3395 3392 3417 C1' A D 3 beta 3412 3418 3415 3439 C1' C D 4 beta 3434 3440 3437 3459 C1' A D 5 beta 3454 3460 3457 3481 C1' U D 6 beta 3476 3482 3479 3507 C1' ADP A1564 beta 3502 3508 3505 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3372 C2' U D 1 OK 3374 3370 3373 3392 C2' G D 2 OK 3394 3390 3393 3415 C2' A D 3 OK 3417 3413 3416 3437 C2' C D 4 OK 3439 3435 3438 3457 C2' A D 5 OK 3459 3455 3458 3479 C2' U D 6 OK 3481 3477 3480 3505 C2' ADP A1564 OK 3507 3503 3506 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3370 C3' U D 1 OK 3368 3371 3372 3390 C3' G D 2 OK 3388 3391 3392 3413 C3' A D 3 OK 3411 3414 3415 3435 C3' C D 4 OK 3433 3436 3437 3455 C3' A D 5 OK 3453 3456 3457 3477 C3' U D 6 OK 3475 3478 3479 3503 C3' ADP A1564 OK 3501 3504 3505 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3368 C4' U D 1 OK 3370 3367 3369 3388 C4' G D 2 OK 3390 3387 3389 3411 C4' A D 3 OK 3413 3410 3412 3433 C4' C D 4 OK 3435 3432 3434 3453 C4' A D 5 OK 3455 3452 3454 3475 C4' U D 6 OK 3477 3474 3476 3501 C4' ADP A1564 OK 3503 3500 3502 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3367 C5' U D 1 3366 3368 3387 C5' G D 2 3386 3388 3410 C5' A D 3 3409 3411 3432 C5' C D 4 3431 3433 3452 C5' A D 5 3451 3453 3474 C5' U D 6 3473 3475 3500 C5' ADP A1564 3499 3501 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3363 P U D 1 distorted distorted 3364 3365 3366 3383 P G D 2 distorted distorted 3371 3384 3385 3386 3406 P A D 3 distorted distorted 3391 3407 3408 3409 3428 P C D 4 distorted distorted 3414 3429 3430 3431 3448 P A D 5 OK OK 3436 3449 3450 3451 3470 P U D 6 distorted distorted 3456 3471 3472 3473 3518 P PO4 A1565 ---------------------------------------------------------------------------------