ID code: '5HP2' 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' --------------------------------------------------------------------------------- 3106 C1' U B 1 beta 3101 3107 3104 3126 C1' U B 2 beta 3121 3127 3124 3146 C1' C B 3 beta 3141 3147 3144 3166 C1' C B 4 beta 3161 3167 3164 3186 C1' C B 5 beta 3181 3187 3184 3206 C1' C B 6 beta 3201 3207 3204 3226 C1' A B 7 beta 3221 3227 3224 3248 C1' C B 8 beta 3243 3249 3246 3268 C1' A B 9 beta 3263 3269 3266 3290 C1' U B 10 beta 3285 3291 3288 3310 C1' U B 11 beta 3305 3311 3308 3326 C1' 8AZ B 12 beta 3325 3327 3337 3352 C1' G B 13 beta 3347 3353 3350 3375 C1' A B 14 beta 3370 3376 3373 3397 C1' C B 15 beta 3392 3398 3395 3417 C1' G B 16 beta 3412 3418 3415 3440 C1' U B 17 beta 3435 3441 3438 3460 C1' U B 18 beta 3455 3461 3458 3480 C1' C B 19 beta 3475 3481 3478 3500 C1' A B 20 beta 3495 3501 3498 3522 C1' G B 21 beta 3517 3523 3520 3545 C1' U B 22 beta 3540 3546 3543 3565 C1' C B 23 beta 3560 3566 3563 3583 C1' G C 1 beta 3578 3584 3581 3606 C1' A C 2 beta 3601 3607 3604 3628 C1' C C 3 beta 3623 3629 3626 3648 C1' U C 4 beta 3643 3649 3646 3668 C1' G C 5 beta 3663 3669 3666 3691 C1' A C 6 beta 3686 3692 3689 3713 C1' A C 7 beta 3708 3714 3711 3735 C1' C C 8 beta 3730 3736 3733 3755 C1' G C 9 beta 3750 3756 3753 3778 C1' A C 10 beta 3773 3779 3776 3800 C1' C C 11 beta 3795 3801 3798 3820 C1' U C 12 beta 3815 3821 3818 3840 C1' A C 13 beta 3835 3841 3838 3862 C1' A C 14 beta 3857 3863 3860 3884 C1' U C 15 beta 3879 3885 3882 3904 C1' G C 16 beta 3899 3905 3902 3927 C1' U C 17 beta 3922 3928 3925 3947 C1' G C 18 beta 3942 3948 3945 3970 C1' G C 19 beta 3965 3971 3968 3993 C1' G C 20 beta 3988 3994 3991 4016 C1' G C 21 beta 4011 4017 4014 4039 C1' A C 22 beta 4034 4040 4037 4061 C1' A C 23 beta 4056 4062 4059 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3104 C2' U B 1 OK 3106 3102 3105 3124 C2' U B 2 OK 3126 3122 3125 3144 C2' C B 3 OK 3146 3142 3145 3164 C2' C B 4 OK 3166 3162 3165 3184 C2' C B 5 OK 3186 3182 3185 3204 C2' C B 6 OK 3206 3202 3205 3224 C2' A B 7 OK 3226 3222 3225 3246 C2' C B 8 OK 3248 3244 3247 3266 C2' A B 9 OK 3268 3264 3267 3288 C2' U B 10 OK 3290 3286 3289 3308 C2' U B 11 OK 3310 3306 3309 3337 C2' 8AZ B 12 OK 3326 3339 3338 3350 C2' G B 13 OK 3352 3348 3351 3373 C2' A B 14 OK 3375 3371 3374 3395 C2' C B 15 OK 3397 3393 3396 3415 C2' G B 16 OK 3417 3413 3416 3438 C2' U B 17 OK 3440 3436 3439 3458 C2' U B 18 OK 3460 3456 3459 3478 C2' C B 19 OK 3480 3476 3479 3498 C2' A B 20 OK 3500 3496 3499 3520 C2' G B 21 OK 3522 3518 3521 3543 C2' U B 22 OK 3545 3541 3544 3563 C2' C B 23 OK 3565 3561 3564 3581 C2' G C 1 OK 3583 3579 3582 3604 C2' A C 2 OK 3606 3602 3605 3626 C2' C C 3 OK 3628 3624 3627 3646 C2' U C 4 OK 3648 3644 3647 3666 C2' G C 5 OK 3668 3664 3667 3689 C2' A C 6 OK 3691 3687 3690 3711 C2' A C 7 OK 3713 3709 3712 3733 C2' C C 8 OK 3735 3731 3734 3753 C2' G C 9 OK 3755 3751 3754 3776 C2' A C 10 OK 3778 3774 3777 3798 C2' C C 11 OK 3800 3796 3799 3818 C2' U C 12 OK 3820 3816 3819 3838 C2' A C 13 OK 3840 3836 3839 3860 C2' A C 14 OK 3862 3858 3861 3882 C2' U C 15 OK 3884 3880 3883 3902 C2' G C 16 OK 3904 3900 3903 3925 C2' U C 17 OK 3927 3923 3926 3945 C2' G C 18 OK 3947 3943 3946 3968 C2' G C 19 OK 3970 3966 3969 3991 C2' G C 20 OK 3993 3989 3992 4014 C2' G C 21 OK 4016 4012 4015 4037 C2' A C 22 OK 4039 4035 4038 4059 C2' A C 23 OK 4061 4057 4060 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3102 C3' U B 1 OK 3100 3103 3104 3122 C3' U B 2 OK 3120 3123 3124 3142 C3' C B 3 OK 3140 3143 3144 3162 C3' C B 4 OK 3160 3163 3164 3182 C3' C B 5 OK 3180 3183 3184 3202 C3' C B 6 OK 3200 3203 3204 3222 C3' A B 7 OK 3220 3223 3224 3244 C3' C B 8 OK 3242 3245 3246 3264 C3' A B 9 OK 3262 3265 3266 3286 C3' U B 10 OK 3284 3287 3288 3306 C3' U B 11 OK 3304 3307 3308 3339 C3' 8AZ B 12 OK 3324 3340 3337 3348 C3' G B 13 OK 3346 3349 3350 3371 C3' A B 14 OK 3369 3372 3373 3393 C3' C B 15 OK 3391 3394 3395 3413 C3' G B 16 OK 3411 3414 3415 3436 C3' U B 17 OK 3434 3437 3438 3456 C3' U B 18 OK 3454 3457 3458 3476 C3' C B 19 OK 3474 3477 3478 3496 C3' A B 20 OK 3494 3497 3498 3518 C3' G B 21 OK 3516 3519 3520 3541 C3' U B 22 OK 3539 3542 3543 3561 C3' C B 23 OK 3559 3562 3563 3579 C3' G C 1 OK 3577 3580 3581 3602 C3' A C 2 OK 3600 3603 3604 3624 C3' C C 3 OK 3622 3625 3626 3644 C3' U C 4 OK 3642 3645 3646 3664 C3' G C 5 OK 3662 3665 3666 3687 C3' A C 6 OK 3685 3688 3689 3709 C3' A C 7 OK 3707 3710 3711 3731 C3' C C 8 OK 3729 3732 3733 3751 C3' G C 9 OK 3749 3752 3753 3774 C3' A C 10 OK 3772 3775 3776 3796 C3' C C 11 OK 3794 3797 3798 3816 C3' U C 12 OK 3814 3817 3818 3836 C3' A C 13 OK 3834 3837 3838 3858 C3' A C 14 OK 3856 3859 3860 3880 C3' U C 15 OK 3878 3881 3882 3900 C3' G C 16 OK 3898 3901 3902 3923 C3' U C 17 OK 3921 3924 3925 3943 C3' G C 18 OK 3941 3944 3945 3966 C3' G C 19 OK 3964 3967 3968 3989 C3' G C 20 OK 3987 3990 3991 4012 C3' G C 21 OK 4010 4013 4014 4035 C3' A C 22 OK 4033 4036 4037 4057 C3' A C 23 OK 4055 4058 4059 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3100 C4' U B 1 OK 3102 3099 3101 3120 C4' U B 2 OK 3122 3119 3121 3140 C4' C B 3 OK 3142 3139 3141 3160 C4' C B 4 OK 3162 3159 3161 3180 C4' C B 5 OK 3182 3179 3181 3200 C4' C B 6 OK 3202 3199 3201 3220 C4' A B 7 OK 3222 3219 3221 3242 C4' C B 8 OK 3244 3241 3243 3262 C4' A B 9 OK 3264 3261 3263 3284 C4' U B 10 OK 3286 3283 3285 3304 C4' U B 11 OK 3306 3303 3305 3324 C4' 8AZ B 12 OK 3339 3323 3325 3346 C4' G B 13 OK 3348 3345 3347 3369 C4' A B 14 OK 3371 3368 3370 3391 C4' C B 15 OK 3393 3390 3392 3411 C4' G B 16 OK 3413 3410 3412 3434 C4' U B 17 OK 3436 3433 3435 3454 C4' U B 18 OK 3456 3453 3455 3474 C4' C B 19 OK 3476 3473 3475 3494 C4' A B 20 OK 3496 3493 3495 3516 C4' G B 21 OK 3518 3515 3517 3539 C4' U B 22 OK 3541 3538 3540 3559 C4' C B 23 OK 3561 3558 3560 3577 C4' G C 1 OK 3579 3576 3578 3600 C4' A C 2 OK 3602 3599 3601 3622 C4' C C 3 OK 3624 3621 3623 3642 C4' U C 4 OK 3644 3641 3643 3662 C4' G C 5 OK 3664 3661 3663 3685 C4' A C 6 OK 3687 3684 3686 3707 C4' A C 7 OK 3709 3706 3708 3729 C4' C C 8 OK 3731 3728 3730 3749 C4' G C 9 OK 3751 3748 3750 3772 C4' A C 10 OK 3774 3771 3773 3794 C4' C C 11 OK 3796 3793 3795 3814 C4' U C 12 OK 3816 3813 3815 3834 C4' A C 13 OK 3836 3833 3835 3856 C4' A C 14 OK 3858 3855 3857 3878 C4' U C 15 OK 3880 3877 3879 3898 C4' G C 16 OK 3900 3897 3899 3921 C4' U C 17 OK 3923 3920 3922 3941 C4' G C 18 OK 3943 3940 3942 3964 C4' G C 19 OK 3966 3963 3965 3987 C4' G C 20 OK 3989 3986 3988 4010 C4' G C 21 OK 4012 4009 4011 4033 C4' A C 22 OK 4035 4032 4034 4055 C4' A C 23 OK 4057 4054 4056 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3099 C5' U B 1 3098 3100 3119 C5' U B 2 3118 3120 3139 C5' C B 3 3138 3140 3159 C5' C B 4 3158 3160 3179 C5' C B 5 3178 3180 3199 C5' C B 6 3198 3200 3219 C5' A B 7 3218 3220 3241 C5' C B 8 3240 3242 3261 C5' A B 9 3260 3262 3283 C5' U B 10 3282 3284 3303 C5' U B 11 3302 3304 3323 C5' 8AZ B 12 3322 3324 3345 C5' G B 13 3344 3346 3368 C5' A B 14 3367 3369 3390 C5' C B 15 3389 3391 3410 C5' G B 16 3409 3411 3433 C5' U B 17 3432 3434 3453 C5' U B 18 3452 3454 3473 C5' C B 19 3472 3474 3493 C5' A B 20 3492 3494 3515 C5' G B 21 3514 3516 3538 C5' U B 22 3537 3539 3558 C5' C B 23 3557 3559 3576 C5' G C 1 3575 3577 3599 C5' A C 2 3598 3600 3621 C5' C C 3 3620 3622 3641 C5' U C 4 3640 3642 3661 C5' G C 5 3660 3662 3684 C5' A C 6 3683 3685 3706 C5' A C 7 3705 3707 3728 C5' C C 8 3727 3729 3748 C5' G C 9 3747 3749 3771 C5' A C 10 3770 3772 3793 C5' C C 11 3792 3794 3813 C5' U C 12 3812 3814 3833 C5' A C 13 3832 3834 3855 C5' A C 14 3854 3856 3877 C5' U C 15 3876 3878 3897 C5' G C 16 3896 3898 3920 C5' U C 17 3919 3921 3940 C5' G C 18 3939 3941 3963 C5' G C 19 3962 3964 3986 C5' G C 20 3985 3987 4009 C5' G C 21 4008 4010 4032 C5' A C 22 4031 4033 4054 C5' A C 23 4053 4055 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3115 P U B 2 distorted distorted 3103 3116 3117 3118 3135 P C B 3 distorted distorted 3123 3136 3137 3138 3155 P C B 4 distorted distorted 3143 3156 3157 3158 3175 P C B 5 distorted distorted 3163 3176 3177 3178 3195 P C B 6 distorted distorted 3183 3196 3197 3198 3215 P A B 7 distorted distorted 3203 3216 3217 3218 3237 P C B 8 distorted distorted 3223 3238 3239 3240 3257 P A B 9 distorted distorted 3245 3258 3259 3260 3279 P U B 10 distorted distorted 3265 3280 3281 3282 3299 P U B 11 distorted distorted 3287 3300 3301 3302 3319 P 8AZ B 12 distorted distorted 3307 3321 3320 3322 3341 P G B 13 distorted distorted 3340 3342 3343 3344 3364 P A B 14 distorted distorted 3349 3365 3366 3367 3386 P C B 15 distorted distorted 3372 3387 3388 3389 3406 P G B 16 distorted distorted 3394 3407 3408 3409 3429 P U B 17 distorted distorted 3414 3430 3431 3432 3449 P U B 18 distorted distorted 3437 3450 3451 3452 3469 P C B 19 distorted distorted 3457 3470 3471 3472 3489 P A B 20 distorted distorted 3477 3490 3491 3492 3511 P G B 21 distorted distorted 3497 3512 3513 3514 3534 P U B 22 distorted distorted 3519 3535 3536 3537 3554 P C B 23 distorted distorted 3542 3555 3556 3557 3595 P A C 2 distorted distorted 3580 3596 3597 3598 3617 P C C 3 distorted distorted 3603 3618 3619 3620 3637 P U C 4 distorted distorted 3625 3638 3639 3640 3657 P G C 5 distorted distorted 3645 3658 3659 3660 3680 P A C 6 distorted distorted 3665 3681 3682 3683 3702 P A C 7 distorted distorted 3688 3703 3704 3705 3724 P C C 8 distorted distorted 3710 3725 3726 3727 3744 P G C 9 distorted distorted 3732 3745 3746 3747 3767 P A C 10 distorted distorted 3752 3768 3769 3770 3789 P C C 11 distorted distorted 3775 3790 3791 3792 3809 P U C 12 distorted distorted 3797 3810 3811 3812 3829 P A C 13 distorted distorted 3817 3830 3831 3832 3851 P A C 14 distorted distorted 3837 3852 3853 3854 3873 P U C 15 distorted distorted 3859 3874 3875 3876 3893 P G C 16 distorted distorted 3881 3894 3895 3896 3916 P U C 17 distorted distorted 3901 3917 3918 3919 3936 P G C 18 distorted distorted 3924 3937 3938 3939 3959 P G C 19 distorted distorted 3944 3960 3961 3962 3982 P G C 20 distorted distorted 3967 3983 3984 3985 4005 P G C 21 distorted distorted 3990 4006 4007 4008 4028 P A C 22 distorted distorted 4013 4029 4030 4031 4050 P A C 23 distorted distorted 4036 4051 4052 4053 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