ID code: '2ADC' 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' --------------------------------------------------------------------------------- 3269 C1' C B 532 alpha beta 3264 3284 3270 3267 3301 C1' U B 533 alpha beta 3296 3316 3302 3299 3331 C1' C B 534 alpha beta 3326 3346 3332 3329 3362 C1' U B 535 alpha beta 3357 3377 3363 3360 3392 C1' C B 536 alpha beta 3387 3407 3393 3390 3423 C1' U B 537 alpha beta 3418 3439 3424 3421 3452 C1' C C 538 alpha beta 3447 3467 3453 3450 3484 C1' U C 539 alpha beta 3479 3499 3485 3482 3514 C1' C C 540 alpha beta 3509 3529 3515 3512 3545 C1' U C 541 alpha beta 3540 3560 3546 3543 3575 C1' C C 542 alpha beta 3570 3590 3576 3573 3606 C1' U C 543 alpha beta 3601 3622 3607 3604 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3267 C2' C B 532 OK OK 3269 3265 3282 3268 3299 C2' U B 533 OK OK 3301 3297 3314 3300 3329 C2' C B 534 OK OK 3331 3327 3344 3330 3360 C2' U B 535 OK OK 3362 3358 3375 3361 3390 C2' C B 536 OK OK 3392 3388 3405 3391 3421 C2' U B 537 OK OK 3423 3419 3437 3422 3450 C2' C C 538 OK OK 3452 3448 3465 3451 3482 C2' U C 539 OK OK 3484 3480 3497 3483 3512 C2' C C 540 OK OK 3514 3510 3527 3513 3543 C2' U C 541 OK OK 3545 3541 3558 3544 3573 C2' C C 542 OK OK 3575 3571 3588 3574 3604 C2' U C 543 OK OK 3606 3602 3620 3605 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3265 C3' C B 532 OK OK 3263 3281 3266 3267 3297 C3' U B 533 OK OK 3295 3313 3298 3299 3327 C3' C B 534 OK OK 3325 3343 3328 3329 3358 C3' U B 535 OK OK 3356 3374 3359 3360 3388 C3' C B 536 OK OK 3386 3404 3389 3390 3419 C3' U B 537 OK OK 3417 3435 3420 3421 3448 C3' C C 538 OK OK 3446 3464 3449 3450 3480 C3' U C 539 OK OK 3478 3496 3481 3482 3510 C3' C C 540 OK OK 3508 3526 3511 3512 3541 C3' U C 541 OK OK 3539 3557 3542 3543 3571 C3' C C 542 OK OK 3569 3587 3572 3573 3602 C3' U C 543 OK OK 3600 3618 3603 3604 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3263 C4' C B 532 OK OK 3265 3280 3262 3264 3295 C4' U B 533 OK OK 3297 3312 3294 3296 3325 C4' C B 534 OK OK 3327 3342 3324 3326 3356 C4' U B 535 OK OK 3358 3373 3355 3357 3386 C4' C B 536 OK OK 3388 3403 3385 3387 3417 C4' U B 537 OK OK 3419 3434 3416 3418 3446 C4' C C 538 OK OK 3448 3463 3445 3447 3478 C4' U C 539 OK OK 3480 3495 3477 3479 3508 C4' C C 540 OK OK 3510 3525 3507 3509 3539 C4' U C 541 OK OK 3541 3556 3538 3540 3569 C4' C C 542 OK OK 3571 3586 3568 3570 3600 C4' U C 543 OK OK 3602 3617 3599 3601 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3262 C5' C B 532 OK OK 3261 3278 3279 3263 3294 C5' U B 533 OK OK 3293 3310 3311 3295 3324 C5' C B 534 OK OK 3323 3340 3341 3325 3355 C5' U B 535 OK OK 3354 3371 3372 3356 3385 C5' C B 536 OK OK 3384 3401 3402 3386 3416 C5' U B 537 OK OK 3415 3432 3433 3417 3445 C5' C C 538 OK OK 3444 3461 3462 3446 3477 C5' U C 539 OK OK 3476 3493 3494 3478 3507 C5' C C 540 OK OK 3506 3523 3524 3508 3538 C5' U C 541 OK OK 3537 3554 3555 3539 3568 C5' C C 542 OK OK 3567 3584 3585 3569 3599 C5' U C 543 OK OK 3598 3615 3616 3600 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3290 P U B 533 distorted distorted 3266 3291 3292 3293 3320 P C B 534 distorted distorted 3298 3321 3322 3323 3351 P U B 535 distorted distorted 3328 3352 3353 3354 3381 P C B 536 distorted distorted 3359 3382 3383 3384 3412 P U B 537 distorted distorted 3389 3413 3414 3415 3473 P U C 539 distorted distorted 3449 3474 3475 3476 3503 P C C 540 distorted distorted 3481 3504 3505 3506 3534 P U C 541 distorted distorted 3511 3535 3536 3537 3564 P C C 542 distorted distorted 3542 3565 3566 3567 3595 P U C 543 distorted distorted 3572 3596 3597 3598 ---------------------------------------------------------------------------------