ID code: '1BHM' 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' --------------------------------------------------------------------------------- 3238 C1' A C 2 beta 3234 3239 3237 3259 C1' T C 3 beta 3255 3260 3258 3279 C1' G C 4 beta 3275 3280 3278 3301 C1' G C 5 beta 3297 3302 3300 3323 C1' A C 6 beta 3319 3324 3322 3344 C1' T C 7 beta 3340 3345 3343 3364 C1' C C 8 beta 3360 3365 3363 3383 C1' C C 9 beta 3379 3384 3382 3402 C1' A C 10 beta 3398 3403 3401 3423 C1' T C 11 beta 3419 3424 3422 3482 C1' A D 2 beta 3478 3483 3481 3503 C1' T D 3 beta 3499 3504 3502 3523 C1' G D 4 beta 3519 3524 3522 3545 C1' G D 5 beta 3541 3546 3544 3567 C1' A D 6 beta 3563 3568 3566 3588 C1' T D 7 beta 3584 3589 3587 3608 C1' C D 8 beta 3604 3609 3607 3627 C1' C D 9 beta 3623 3628 3626 3646 C1' A D 10 beta 3642 3647 3645 3667 C1' T D 11 beta 3663 3668 3666 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3237 C2' A C 2 3238 3235 3258 C2' T C 3 3259 3256 3278 C2' G C 4 3279 3276 3300 C2' G C 5 3301 3298 3322 C2' A C 6 3323 3320 3343 C2' T C 7 3344 3341 3363 C2' C C 8 3364 3361 3382 C2' C C 9 3383 3380 3401 C2' A C 10 3402 3399 3422 C2' T C 11 3423 3420 3481 C2' A D 2 3482 3479 3502 C2' T D 3 3503 3500 3522 C2' G D 4 3523 3520 3544 C2' G D 5 3545 3542 3566 C2' A D 6 3567 3564 3587 C2' T D 7 3588 3585 3607 C2' C D 8 3608 3605 3626 C2' C D 9 3627 3624 3645 C2' A D 10 3646 3643 3666 C2' T D 11 3667 3664 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3235 C3' A C 2 OK 3233 3236 3237 3256 C3' T C 3 OK 3254 3257 3258 3276 C3' G C 4 OK 3274 3277 3278 3298 C3' G C 5 OK 3296 3299 3300 3320 C3' A C 6 OK 3318 3321 3322 3341 C3' T C 7 OK 3339 3342 3343 3361 C3' C C 8 OK 3359 3362 3363 3380 C3' C C 9 OK 3378 3381 3382 3399 C3' A C 10 OK 3397 3400 3401 3420 C3' T C 11 OK 3418 3421 3422 3479 C3' A D 2 OK 3477 3480 3481 3500 C3' T D 3 OK 3498 3501 3502 3520 C3' G D 4 OK 3518 3521 3522 3542 C3' G D 5 OK 3540 3543 3544 3564 C3' A D 6 OK 3562 3565 3566 3585 C3' T D 7 OK 3583 3586 3587 3605 C3' C D 8 OK 3603 3606 3607 3624 C3' C D 9 OK 3622 3625 3626 3643 C3' A D 10 OK 3641 3644 3645 3664 C3' T D 11 OK 3662 3665 3666 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3233 C4' A C 2 OK 3235 3232 3234 3254 C4' T C 3 OK 3256 3253 3255 3274 C4' G C 4 OK 3276 3273 3275 3296 C4' G C 5 OK 3298 3295 3297 3318 C4' A C 6 OK 3320 3317 3319 3339 C4' T C 7 OK 3341 3338 3340 3359 C4' C C 8 OK 3361 3358 3360 3378 C4' C C 9 OK 3380 3377 3379 3397 C4' A C 10 OK 3399 3396 3398 3418 C4' T C 11 OK 3420 3417 3419 3477 C4' A D 2 OK 3479 3476 3478 3498 C4' T D 3 OK 3500 3497 3499 3518 C4' G D 4 OK 3520 3517 3519 3540 C4' G D 5 OK 3542 3539 3541 3562 C4' A D 6 OK 3564 3561 3563 3583 C4' T D 7 OK 3585 3582 3584 3603 C4' C D 8 OK 3605 3602 3604 3622 C4' C D 9 OK 3624 3621 3623 3641 C4' A D 10 OK 3643 3640 3642 3662 C4' T D 11 OK 3664 3661 3663 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3232 C5' A C 2 3231 3233 3253 C5' T C 3 3252 3254 3273 C5' G C 4 3272 3274 3295 C5' G C 5 3294 3296 3317 C5' A C 6 3316 3318 3338 C5' T C 7 3337 3339 3358 C5' C C 8 3357 3359 3377 C5' C C 9 3376 3378 3396 C5' A C 10 3395 3397 3417 C5' T C 11 3416 3418 3476 C5' A D 2 3475 3477 3497 C5' T D 3 3496 3498 3517 C5' G D 4 3516 3518 3539 C5' G D 5 3538 3540 3561 C5' A D 6 3560 3562 3582 C5' T D 7 3581 3583 3602 C5' C D 8 3601 3603 3621 C5' C D 9 3620 3622 3640 C5' A D 10 3639 3641 3661 C5' T D 11 3660 3662 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3249 P T C 3 OK OK 3236 3250 3251 3252 3269 P G C 4 OK OK 3257 3270 3271 3272 3291 P G C 5 OK OK 3277 3292 3293 3294 3313 P A C 6 OK OK 3299 3314 3315 3316 3334 P T C 7 OK OK 3321 3335 3336 3337 3354 P C C 8 OK OK 3342 3355 3356 3357 3373 P C C 9 OK OK 3362 3374 3375 3376 3392 P A C 10 OK OK 3381 3393 3394 3395 3413 P T C 11 OK OK 3400 3414 3415 3416 3493 P T D 3 OK OK 3480 3494 3495 3496 3513 P G D 4 OK OK 3501 3514 3515 3516 3535 P G D 5 OK OK 3521 3536 3537 3538 3557 P A D 6 OK OK 3543 3558 3559 3560 3578 P T D 7 OK OK 3565 3579 3580 3581 3598 P C D 8 OK OK 3586 3599 3600 3601 3617 P C D 9 OK OK 3606 3618 3619 3620 3636 P A D 10 OK OK 3625 3637 3638 3639 3657 P T D 11 OK OK 3644 3658 3659 3660 ---------------------------------------------------------------------------------