ID code: '5E08' 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' --------------------------------------------------------------------------------- 3395 C1' G N 1 beta 3390 3396 3393 3418 C1' U N 2 beta 3413 3419 3416 3438 C1' A N 3 beta 3433 3439 3436 3460 C1' U N 4 beta 3455 3461 3458 3480 C1' G N 5 beta 3475 3481 3478 3503 C1' C N 6 beta 3498 3504 3501 3523 C1' A N 7 beta 3518 3524 3521 3545 C1' U N 8 beta 3540 3546 3543 3565 C1' A N 9 beta 3560 3566 3563 3587 C1' G N 10 beta 3582 3588 3585 3610 C1' G N 11 beta 3605 3611 3608 3633 C1' C N 12 beta 3628 3634 3631 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3393 C2' G N 1 OK 3395 3391 3394 3416 C2' U N 2 OK 3418 3414 3417 3436 C2' A N 3 OK 3438 3434 3437 3458 C2' U N 4 OK 3460 3456 3459 3478 C2' G N 5 OK 3480 3476 3479 3501 C2' C N 6 OK 3503 3499 3502 3521 C2' A N 7 OK 3523 3519 3522 3543 C2' U N 8 OK 3545 3541 3544 3563 C2' A N 9 OK 3565 3561 3564 3585 C2' G N 10 OK 3587 3583 3586 3608 C2' G N 11 OK 3610 3606 3609 3631 C2' C N 12 OK 3633 3629 3632 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3391 C3' G N 1 OK 3389 3392 3393 3414 C3' U N 2 OK 3412 3415 3416 3434 C3' A N 3 OK 3432 3435 3436 3456 C3' U N 4 OK 3454 3457 3458 3476 C3' G N 5 OK 3474 3477 3478 3499 C3' C N 6 OK 3497 3500 3501 3519 C3' A N 7 OK 3517 3520 3521 3541 C3' U N 8 OK 3539 3542 3543 3561 C3' A N 9 OK 3559 3562 3563 3583 C3' G N 10 OK 3581 3584 3585 3606 C3' G N 11 OK 3604 3607 3608 3629 C3' C N 12 OK 3627 3630 3631 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3389 C4' G N 1 OK 3391 3388 3390 3412 C4' U N 2 OK 3414 3411 3413 3432 C4' A N 3 OK 3434 3431 3433 3454 C4' U N 4 OK 3456 3453 3455 3474 C4' G N 5 OK 3476 3473 3475 3497 C4' C N 6 OK 3499 3496 3498 3517 C4' A N 7 OK 3519 3516 3518 3539 C4' U N 8 OK 3541 3538 3540 3559 C4' A N 9 OK 3561 3558 3560 3581 C4' G N 10 OK 3583 3580 3582 3604 C4' G N 11 OK 3606 3603 3605 3627 C4' C N 12 OK 3629 3626 3628 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3388 C5' G N 1 3387 3389 3411 C5' U N 2 3410 3412 3431 C5' A N 3 3430 3432 3453 C5' U N 4 3452 3454 3473 C5' G N 5 3472 3474 3496 C5' C N 6 3495 3497 3516 C5' A N 7 3515 3517 3538 C5' U N 8 3537 3539 3558 C5' A N 9 3557 3559 3580 C5' G N 10 3579 3581 3603 C5' G N 11 3602 3604 3626 C5' C N 12 3625 3627 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3407 P U N 2 distorted distorted 3392 3408 3409 3410 3427 P A N 3 distorted distorted 3415 3428 3429 3430 3449 P U N 4 distorted distorted 3435 3450 3451 3452 3469 P G N 5 distorted distorted 3457 3470 3471 3472 3492 P C N 6 distorted distorted 3477 3493 3494 3495 3512 P A N 7 distorted distorted 3500 3513 3514 3515 3534 P U N 8 distorted distorted 3520 3535 3536 3537 3554 P A N 9 distorted distorted 3542 3555 3556 3557 3576 P G N 10 distorted distorted 3562 3577 3578 3579 3599 P G N 11 distorted distorted 3584 3600 3601 3602 3622 P C N 12 distorted distorted 3607 3623 3624 3625 ---------------------------------------------------------------------------------