ID code: '4D25' 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' --------------------------------------------------------------------------------- 3387 C1' U D 1 beta 3382 3388 3385 3407 C1' G D 2 beta 3402 3408 3405 3430 C1' A D 3 beta 3425 3431 3428 3452 C1' C D 4 beta 3447 3453 3450 3472 C1' A D 5 beta 3467 3473 3470 3494 C1' U D 6 beta 3489 3495 3492 3524 C1' ANP A1564 beta 3519 3525 3522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3385 C2' U D 1 OK 3387 3383 3386 3405 C2' G D 2 OK 3407 3403 3406 3428 C2' A D 3 OK 3430 3426 3429 3450 C2' C D 4 OK 3452 3448 3451 3470 C2' A D 5 OK 3472 3468 3471 3492 C2' U D 6 OK 3494 3490 3493 3522 C2' ANP A1564 OK 3524 3520 3523 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3383 C3' U D 1 OK 3381 3384 3385 3403 C3' G D 2 OK 3401 3404 3405 3426 C3' A D 3 OK 3424 3427 3428 3448 C3' C D 4 OK 3446 3449 3450 3468 C3' A D 5 OK 3466 3469 3470 3490 C3' U D 6 OK 3488 3491 3492 3520 C3' ANP A1564 OK 3518 3521 3522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3381 C4' U D 1 OK 3383 3380 3382 3401 C4' G D 2 OK 3403 3400 3402 3424 C4' A D 3 OK 3426 3423 3425 3446 C4' C D 4 OK 3448 3445 3447 3466 C4' A D 5 OK 3468 3465 3467 3488 C4' U D 6 OK 3490 3487 3489 3518 C4' ANP A1564 OK 3520 3517 3519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3380 C5' U D 1 3379 3381 3400 C5' G D 2 3399 3401 3423 C5' A D 3 3422 3424 3445 C5' C D 4 3444 3446 3465 C5' A D 5 3464 3466 3487 C5' U D 6 3486 3488 3517 C5' ANP A1564 3516 3518 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3376 P U D 1 distorted distorted 3377 3378 3379 3396 P G D 2 distorted distorted 3384 3397 3398 3399 3419 P A D 3 distorted distorted 3404 3420 3421 3422 3441 P C D 4 distorted distorted 3427 3442 3443 3444 3461 P A D 5 OK OK 3449 3462 3463 3464 3483 P U D 6 distorted distorted 3469 3484 3485 3486 ---------------------------------------------------------------------------------