ID code: '5HP3' 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' --------------------------------------------------------------------------------- 3095 C1' U B 1 beta 3090 3096 3093 3115 C1' U B 2 beta 3110 3116 3113 3135 C1' C B 3 beta 3130 3136 3133 3155 C1' C B 4 beta 3150 3156 3153 3175 C1' C B 5 beta 3170 3176 3173 3195 C1' C B 6 beta 3190 3196 3193 3215 C1' A B 7 beta 3210 3216 3213 3237 C1' C B 8 beta 3232 3238 3235 3257 C1' A B 9 beta 3252 3258 3255 3279 C1' U B 10 beta 3274 3280 3277 3299 C1' U B 11 beta 3294 3300 3297 3315 C1' 8AZ B 12 beta 3314 3316 3326 3341 C1' G B 13 beta 3336 3342 3339 3364 C1' A B 14 beta 3359 3365 3362 3386 C1' C B 15 beta 3381 3387 3384 3406 C1' G B 16 beta 3401 3407 3404 3429 C1' U B 17 beta 3424 3430 3427 3449 C1' U B 18 beta 3444 3450 3447 3469 C1' C B 19 beta 3464 3470 3467 3489 C1' A B 20 beta 3484 3490 3487 3511 C1' G B 21 beta 3506 3512 3509 3534 C1' U B 22 beta 3529 3535 3532 3554 C1' C B 23 beta 3549 3555 3552 3572 C1' G C 1 beta 3567 3573 3570 3595 C1' A C 2 beta 3590 3596 3593 3617 C1' C C 3 beta 3612 3618 3615 3637 C1' U C 4 beta 3632 3638 3635 3657 C1' G C 5 beta 3652 3658 3655 3680 C1' A C 6 beta 3675 3681 3678 3702 C1' A C 7 beta 3697 3703 3700 3724 C1' C C 8 beta 3719 3725 3722 3744 C1' G C 9 beta 3739 3745 3742 3767 C1' A C 10 beta 3762 3768 3765 3789 C1' C C 11 beta 3784 3790 3787 3809 C1' C C 12 beta 3804 3810 3807 3829 C1' A C 13 beta 3824 3830 3827 3851 C1' A C 14 beta 3846 3852 3849 3873 C1' U C 15 beta 3868 3874 3871 3893 C1' G C 16 beta 3888 3894 3891 3916 C1' U C 17 beta 3911 3917 3914 3936 C1' G C 18 beta 3931 3937 3934 3959 C1' G C 19 beta 3954 3960 3957 3982 C1' G C 20 beta 3977 3983 3980 4005 C1' G C 21 beta 4000 4006 4003 4028 C1' A C 22 beta 4023 4029 4026 4050 C1' A C 23 beta 4045 4051 4048 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3093 C2' U B 1 OK 3095 3091 3094 3113 C2' U B 2 OK 3115 3111 3114 3133 C2' C B 3 OK 3135 3131 3134 3153 C2' C B 4 OK 3155 3151 3154 3173 C2' C B 5 OK 3175 3171 3174 3193 C2' C B 6 OK 3195 3191 3194 3213 C2' A B 7 OK 3215 3211 3214 3235 C2' C B 8 OK 3237 3233 3236 3255 C2' A B 9 OK 3257 3253 3256 3277 C2' U B 10 OK 3279 3275 3278 3297 C2' U B 11 OK 3299 3295 3298 3326 C2' 8AZ B 12 OK 3315 3328 3327 3339 C2' G B 13 OK 3341 3337 3340 3362 C2' A B 14 OK 3364 3360 3363 3384 C2' C B 15 OK 3386 3382 3385 3404 C2' G B 16 OK 3406 3402 3405 3427 C2' U B 17 OK 3429 3425 3428 3447 C2' U B 18 OK 3449 3445 3448 3467 C2' C B 19 OK 3469 3465 3468 3487 C2' A B 20 OK 3489 3485 3488 3509 C2' G B 21 OK 3511 3507 3510 3532 C2' U B 22 OK 3534 3530 3533 3552 C2' C B 23 OK 3554 3550 3553 3570 C2' G C 1 OK 3572 3568 3571 3593 C2' A C 2 OK 3595 3591 3594 3615 C2' C C 3 OK 3617 3613 3616 3635 C2' U C 4 OK 3637 3633 3636 3655 C2' G C 5 OK 3657 3653 3656 3678 C2' A C 6 OK 3680 3676 3679 3700 C2' A C 7 OK 3702 3698 3701 3722 C2' C C 8 OK 3724 3720 3723 3742 C2' G C 9 OK 3744 3740 3743 3765 C2' A C 10 OK 3767 3763 3766 3787 C2' C C 11 OK 3789 3785 3788 3807 C2' C C 12 OK 3809 3805 3808 3827 C2' A C 13 OK 3829 3825 3828 3849 C2' A C 14 OK 3851 3847 3850 3871 C2' U C 15 OK 3873 3869 3872 3891 C2' G C 16 OK 3893 3889 3892 3914 C2' U C 17 OK 3916 3912 3915 3934 C2' G C 18 OK 3936 3932 3935 3957 C2' G C 19 OK 3959 3955 3958 3980 C2' G C 20 OK 3982 3978 3981 4003 C2' G C 21 OK 4005 4001 4004 4026 C2' A C 22 OK 4028 4024 4027 4048 C2' A C 23 OK 4050 4046 4049 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3091 C3' U B 1 OK 3089 3092 3093 3111 C3' U B 2 OK 3109 3112 3113 3131 C3' C B 3 OK 3129 3132 3133 3151 C3' C B 4 OK 3149 3152 3153 3171 C3' C B 5 OK 3169 3172 3173 3191 C3' C B 6 OK 3189 3192 3193 3211 C3' A B 7 OK 3209 3212 3213 3233 C3' C B 8 OK 3231 3234 3235 3253 C3' A B 9 OK 3251 3254 3255 3275 C3' U B 10 OK 3273 3276 3277 3295 C3' U B 11 OK 3293 3296 3297 3328 C3' 8AZ B 12 OK 3313 3329 3326 3337 C3' G B 13 OK 3335 3338 3339 3360 C3' A B 14 OK 3358 3361 3362 3382 C3' C B 15 OK 3380 3383 3384 3402 C3' G B 16 OK 3400 3403 3404 3425 C3' U B 17 OK 3423 3426 3427 3445 C3' U B 18 OK 3443 3446 3447 3465 C3' C B 19 OK 3463 3466 3467 3485 C3' A B 20 OK 3483 3486 3487 3507 C3' G B 21 OK 3505 3508 3509 3530 C3' U B 22 OK 3528 3531 3532 3550 C3' C B 23 OK 3548 3551 3552 3568 C3' G C 1 OK 3566 3569 3570 3591 C3' A C 2 OK 3589 3592 3593 3613 C3' C C 3 OK 3611 3614 3615 3633 C3' U C 4 OK 3631 3634 3635 3653 C3' G C 5 OK 3651 3654 3655 3676 C3' A C 6 OK 3674 3677 3678 3698 C3' A C 7 OK 3696 3699 3700 3720 C3' C C 8 OK 3718 3721 3722 3740 C3' G C 9 OK 3738 3741 3742 3763 C3' A C 10 OK 3761 3764 3765 3785 C3' C C 11 OK 3783 3786 3787 3805 C3' C C 12 OK 3803 3806 3807 3825 C3' A C 13 OK 3823 3826 3827 3847 C3' A C 14 OK 3845 3848 3849 3869 C3' U C 15 OK 3867 3870 3871 3889 C3' G C 16 OK 3887 3890 3891 3912 C3' U C 17 OK 3910 3913 3914 3932 C3' G C 18 OK 3930 3933 3934 3955 C3' G C 19 OK 3953 3956 3957 3978 C3' G C 20 OK 3976 3979 3980 4001 C3' G C 21 OK 3999 4002 4003 4024 C3' A C 22 OK 4022 4025 4026 4046 C3' A C 23 OK 4044 4047 4048 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3089 C4' U B 1 OK 3091 3088 3090 3109 C4' U B 2 OK 3111 3108 3110 3129 C4' C B 3 OK 3131 3128 3130 3149 C4' C B 4 OK 3151 3148 3150 3169 C4' C B 5 OK 3171 3168 3170 3189 C4' C B 6 OK 3191 3188 3190 3209 C4' A B 7 OK 3211 3208 3210 3231 C4' C B 8 OK 3233 3230 3232 3251 C4' A B 9 OK 3253 3250 3252 3273 C4' U B 10 OK 3275 3272 3274 3293 C4' U B 11 OK 3295 3292 3294 3313 C4' 8AZ B 12 OK 3328 3312 3314 3335 C4' G B 13 OK 3337 3334 3336 3358 C4' A B 14 OK 3360 3357 3359 3380 C4' C B 15 OK 3382 3379 3381 3400 C4' G B 16 OK 3402 3399 3401 3423 C4' U B 17 OK 3425 3422 3424 3443 C4' U B 18 OK 3445 3442 3444 3463 C4' C B 19 OK 3465 3462 3464 3483 C4' A B 20 OK 3485 3482 3484 3505 C4' G B 21 OK 3507 3504 3506 3528 C4' U B 22 OK 3530 3527 3529 3548 C4' C B 23 OK 3550 3547 3549 3566 C4' G C 1 OK 3568 3565 3567 3589 C4' A C 2 OK 3591 3588 3590 3611 C4' C C 3 OK 3613 3610 3612 3631 C4' U C 4 OK 3633 3630 3632 3651 C4' G C 5 OK 3653 3650 3652 3674 C4' A C 6 OK 3676 3673 3675 3696 C4' A C 7 OK 3698 3695 3697 3718 C4' C C 8 OK 3720 3717 3719 3738 C4' G C 9 OK 3740 3737 3739 3761 C4' A C 10 OK 3763 3760 3762 3783 C4' C C 11 OK 3785 3782 3784 3803 C4' C C 12 OK 3805 3802 3804 3823 C4' A C 13 OK 3825 3822 3824 3845 C4' A C 14 OK 3847 3844 3846 3867 C4' U C 15 OK 3869 3866 3868 3887 C4' G C 16 OK 3889 3886 3888 3910 C4' U C 17 OK 3912 3909 3911 3930 C4' G C 18 OK 3932 3929 3931 3953 C4' G C 19 OK 3955 3952 3954 3976 C4' G C 20 OK 3978 3975 3977 3999 C4' G C 21 OK 4001 3998 4000 4022 C4' A C 22 OK 4024 4021 4023 4044 C4' A C 23 OK 4046 4043 4045 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3088 C5' U B 1 3087 3089 3108 C5' U B 2 3107 3109 3128 C5' C B 3 3127 3129 3148 C5' C B 4 3147 3149 3168 C5' C B 5 3167 3169 3188 C5' C B 6 3187 3189 3208 C5' A B 7 3207 3209 3230 C5' C B 8 3229 3231 3250 C5' A B 9 3249 3251 3272 C5' U B 10 3271 3273 3292 C5' U B 11 3291 3293 3312 C5' 8AZ B 12 3311 3313 3334 C5' G B 13 3333 3335 3357 C5' A B 14 3356 3358 3379 C5' C B 15 3378 3380 3399 C5' G B 16 3398 3400 3422 C5' U B 17 3421 3423 3442 C5' U B 18 3441 3443 3462 C5' C B 19 3461 3463 3482 C5' A B 20 3481 3483 3504 C5' G B 21 3503 3505 3527 C5' U B 22 3526 3528 3547 C5' C B 23 3546 3548 3565 C5' G C 1 3564 3566 3588 C5' A C 2 3587 3589 3610 C5' C C 3 3609 3611 3630 C5' U C 4 3629 3631 3650 C5' G C 5 3649 3651 3673 C5' A C 6 3672 3674 3695 C5' A C 7 3694 3696 3717 C5' C C 8 3716 3718 3737 C5' G C 9 3736 3738 3760 C5' A C 10 3759 3761 3782 C5' C C 11 3781 3783 3802 C5' C C 12 3801 3803 3822 C5' A C 13 3821 3823 3844 C5' A C 14 3843 3845 3866 C5' U C 15 3865 3867 3886 C5' G C 16 3885 3887 3909 C5' U C 17 3908 3910 3929 C5' G C 18 3928 3930 3952 C5' G C 19 3951 3953 3975 C5' G C 20 3974 3976 3998 C5' G C 21 3997 3999 4021 C5' A C 22 4020 4022 4043 C5' A C 23 4042 4044 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3104 P U B 2 distorted distorted 3092 3105 3106 3107 3124 P C B 3 distorted distorted 3112 3125 3126 3127 3144 P C B 4 distorted distorted 3132 3145 3146 3147 3164 P C B 5 distorted distorted 3152 3165 3166 3167 3184 P C B 6 distorted distorted 3172 3185 3186 3187 3204 P A B 7 distorted distorted 3192 3205 3206 3207 3226 P C B 8 distorted distorted 3212 3227 3228 3229 3246 P A B 9 distorted distorted 3234 3247 3248 3249 3268 P U B 10 distorted distorted 3254 3269 3270 3271 3288 P U B 11 distorted distorted 3276 3289 3290 3291 3308 P 8AZ B 12 distorted distorted 3296 3310 3309 3311 3330 P G B 13 distorted distorted 3329 3331 3332 3333 3353 P A B 14 distorted distorted 3338 3354 3355 3356 3375 P C B 15 distorted distorted 3361 3376 3377 3378 3395 P G B 16 distorted distorted 3383 3396 3397 3398 3418 P U B 17 distorted distorted 3403 3419 3420 3421 3438 P U B 18 distorted distorted 3426 3439 3440 3441 3458 P C B 19 distorted distorted 3446 3459 3460 3461 3478 P A B 20 distorted distorted 3466 3479 3480 3481 3500 P G B 21 distorted distorted 3486 3501 3502 3503 3523 P U B 22 distorted distorted 3508 3524 3525 3526 3543 P C B 23 distorted distorted 3531 3544 3545 3546 3584 P A C 2 distorted distorted 3569 3585 3586 3587 3606 P C C 3 distorted distorted 3592 3607 3608 3609 3626 P U C 4 distorted distorted 3614 3627 3628 3629 3646 P G C 5 distorted distorted 3634 3647 3648 3649 3669 P A C 6 distorted distorted 3654 3670 3671 3672 3691 P A C 7 distorted distorted 3677 3692 3693 3694 3713 P C C 8 distorted distorted 3699 3714 3715 3716 3733 P G C 9 distorted distorted 3721 3734 3735 3736 3756 P A C 10 distorted distorted 3741 3757 3758 3759 3778 P C C 11 distorted distorted 3764 3779 3780 3781 3798 P C C 12 distorted distorted 3786 3799 3800 3801 3818 P A C 13 distorted distorted 3806 3819 3820 3821 3840 P A C 14 distorted distorted 3826 3841 3842 3843 3862 P U C 15 distorted distorted 3848 3863 3864 3865 3882 P G C 16 distorted distorted 3870 3883 3884 3885 3905 P U C 17 distorted distorted 3890 3906 3907 3908 3925 P G C 18 distorted distorted 3913 3926 3927 3928 3948 P G C 19 distorted distorted 3933 3949 3950 3951 3971 P G C 20 distorted distorted 3956 3972 3973 3974 3994 P G C 21 distorted distorted 3979 3995 3996 3997 4017 P A C 22 distorted distorted 4002 4018 4019 4020 4039 P A C 23 distorted distorted 4025 4040 4041 4042 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