ID code: '4NDF' 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' --------------------------------------------------------------------------------- 3051 C1' G D 1 beta 3046 3052 3049 3073 C1' DT D 2 beta 3069 3074 3072 3093 C1' DT D 3 beta 3089 3094 3092 3113 C1' DA D 4 beta 3109 3114 3112 3134 C1' DT D 5 beta 3130 3135 3133 3154 C1' DG D 6 beta 3150 3155 3153 3176 C1' DA D 7 beta 3172 3177 3175 3197 C1' DT D 8 beta 3193 3198 3196 3217 C1' DT D 9 beta 3213 3218 3216 3237 C1' DC D 10 beta 3233 3238 3236 3254 C1' DG E 1 beta 3250 3255 3253 3276 C1' DA E 2 beta 3272 3277 3275 3297 C1' DA E 3 beta 3293 3298 3296 3318 C1' DT E 4 beta 3314 3319 3317 3458 C1' DA E 8 beta 3454 3459 3457 3479 C1' DA E 9 beta 3475 3480 3478 3500 C1' DC E 10 beta 3496 3501 3499 3522 C1' G G 1 beta 3517 3523 3520 3544 C1' DT G 2 beta 3540 3545 3543 3564 C1' DT G 3 beta 3560 3565 3563 3584 C1' DA G 4 beta 3580 3585 3583 3605 C1' DT G 5 beta 3601 3606 3604 3625 C1' DG G 6 beta 3621 3626 3624 3647 C1' DA G 7 beta 3643 3648 3646 3668 C1' DT G 8 beta 3664 3669 3667 3688 C1' DT G 9 beta 3684 3689 3687 3708 C1' DC G 10 beta 3704 3709 3707 3725 C1' DG H 1 beta 3721 3726 3724 3747 C1' DA H 2 beta 3743 3748 3746 3768 C1' DA H 3 beta 3764 3769 3767 3789 C1' DT H 4 beta 3785 3790 3788 3809 C1' DC H 5 beta 3805 3810 3808 3828 C1' DA H 6 beta 3824 3829 3827 3849 C1' DT H 7 beta 3845 3850 3848 3869 C1' DA H 8 beta 3865 3870 3868 3890 C1' DA H 9 beta 3886 3891 3889 3911 C1' DC H 10 beta 3907 3912 3910 3933 C1' AMP A 401 beta 3928 3934 3931 3962 C1' AMP B 401 beta 3957 3963 3960 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3049 C2' G D 1 OK 3051 3047 3050 3072 C2' DT D 2 3073 3070 3092 C2' DT D 3 3093 3090 3112 C2' DA D 4 3113 3110 3133 C2' DT D 5 3134 3131 3153 C2' DG D 6 3154 3151 3175 C2' DA D 7 3176 3173 3196 C2' DT D 8 3197 3194 3216 C2' DT D 9 3217 3214 3236 C2' DC D 10 3237 3234 3253 C2' DG E 1 3254 3251 3275 C2' DA E 2 3276 3273 3296 C2' DA E 3 3297 3294 3317 C2' DT E 4 3318 3315 3457 C2' DA E 8 3458 3455 3478 C2' DA E 9 3479 3476 3499 C2' DC E 10 3500 3497 3520 C2' G G 1 OK 3522 3518 3521 3543 C2' DT G 2 3544 3541 3563 C2' DT G 3 3564 3561 3583 C2' DA G 4 3584 3581 3604 C2' DT G 5 3605 3602 3624 C2' DG G 6 3625 3622 3646 C2' DA G 7 3647 3644 3667 C2' DT G 8 3668 3665 3687 C2' DT G 9 3688 3685 3707 C2' DC G 10 3708 3705 3724 C2' DG H 1 3725 3722 3746 C2' DA H 2 3747 3744 3767 C2' DA H 3 3768 3765 3788 C2' DT H 4 3789 3786 3808 C2' DC H 5 3809 3806 3827 C2' DA H 6 3828 3825 3848 C2' DT H 7 3849 3846 3868 C2' DA H 8 3869 3866 3889 C2' DA H 9 3890 3887 3910 C2' DC H 10 3911 3908 3931 C2' AMP A 401 OK 3933 3929 3932 3960 C2' AMP B 401 OK 3962 3958 3961 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3047 C3' G D 1 OK 3045 3048 3049 3070 C3' DT D 2 OK 3068 3071 3072 3090 C3' DT D 3 OK 3088 3091 3092 3110 C3' DA D 4 OK 3108 3111 3112 3131 C3' DT D 5 OK 3129 3132 3133 3151 C3' DG D 6 OK 3149 3152 3153 3173 C3' DA D 7 OK 3171 3174 3175 3194 C3' DT D 8 OK 3192 3195 3196 3214 C3' DT D 9 OK 3212 3215 3216 3234 C3' DC D 10 OK 3232 3235 3236 3251 C3' DG E 1 OK 3249 3252 3253 3273 C3' DA E 2 OK 3271 3274 3275 3294 C3' DA E 3 OK 3292 3295 3296 3315 C3' DT E 4 OK 3313 3316 3317 3455 C3' DA E 8 OK 3453 3456 3457 3476 C3' DA E 9 OK 3474 3477 3478 3497 C3' DC E 10 OK 3495 3498 3499 3518 C3' G G 1 OK 3516 3519 3520 3541 C3' DT G 2 OK 3539 3542 3543 3561 C3' DT G 3 OK 3559 3562 3563 3581 C3' DA G 4 OK 3579 3582 3583 3602 C3' DT G 5 OK 3600 3603 3604 3622 C3' DG G 6 OK 3620 3623 3624 3644 C3' DA G 7 OK 3642 3645 3646 3665 C3' DT G 8 OK 3663 3666 3667 3685 C3' DT G 9 OK 3683 3686 3687 3705 C3' DC G 10 OK 3703 3706 3707 3722 C3' DG H 1 OK 3720 3723 3724 3744 C3' DA H 2 OK 3742 3745 3746 3765 C3' DA H 3 OK 3763 3766 3767 3786 C3' DT H 4 OK 3784 3787 3788 3806 C3' DC H 5 OK 3804 3807 3808 3825 C3' DA H 6 OK 3823 3826 3827 3846 C3' DT H 7 OK 3844 3847 3848 3866 C3' DA H 8 OK 3864 3867 3868 3887 C3' DA H 9 OK 3885 3888 3889 3908 C3' DC H 10 OK 3906 3909 3910 3929 C3' AMP A 401 OK 3927 3930 3931 3958 C3' AMP B 401 OK 3956 3959 3960 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3045 C4' G D 1 OK 3047 3044 3046 3068 C4' DT D 2 OK 3070 3067 3069 3088 C4' DT D 3 OK 3090 3087 3089 3108 C4' DA D 4 OK 3110 3107 3109 3129 C4' DT D 5 OK 3131 3128 3130 3149 C4' DG D 6 OK 3151 3148 3150 3171 C4' DA D 7 OK 3173 3170 3172 3192 C4' DT D 8 OK 3194 3191 3193 3212 C4' DT D 9 OK 3214 3211 3213 3232 C4' DC D 10 OK 3234 3231 3233 3249 C4' DG E 1 OK 3251 3248 3250 3271 C4' DA E 2 OK 3273 3270 3272 3292 C4' DA E 3 OK 3294 3291 3293 3313 C4' DT E 4 OK 3315 3312 3314 3453 C4' DA E 8 OK 3455 3452 3454 3474 C4' DA E 9 OK 3476 3473 3475 3495 C4' DC E 10 OK 3497 3494 3496 3516 C4' G G 1 OK 3518 3515 3517 3539 C4' DT G 2 OK 3541 3538 3540 3559 C4' DT G 3 OK 3561 3558 3560 3579 C4' DA G 4 OK 3581 3578 3580 3600 C4' DT G 5 OK 3602 3599 3601 3620 C4' DG G 6 OK 3622 3619 3621 3642 C4' DA G 7 OK 3644 3641 3643 3663 C4' DT G 8 OK 3665 3662 3664 3683 C4' DT G 9 OK 3685 3682 3684 3703 C4' DC G 10 OK 3705 3702 3704 3720 C4' DG H 1 OK 3722 3719 3721 3742 C4' DA H 2 OK 3744 3741 3743 3763 C4' DA H 3 OK 3765 3762 3764 3784 C4' DT H 4 OK 3786 3783 3785 3804 C4' DC H 5 OK 3806 3803 3805 3823 C4' DA H 6 OK 3825 3822 3824 3844 C4' DT H 7 OK 3846 3843 3845 3864 C4' DA H 8 OK 3866 3863 3865 3885 C4' DA H 9 OK 3887 3884 3886 3906 C4' DC H 10 OK 3908 3905 3907 3927 C4' AMP A 401 OK 3929 3926 3928 3956 C4' AMP B 401 OK 3958 3955 3957 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3044 C5' G D 1 3043 3045 3067 C5' DT D 2 3066 3068 3087 C5' DT D 3 3086 3088 3107 C5' DA D 4 3106 3108 3128 C5' DT D 5 3127 3129 3148 C5' DG D 6 3147 3149 3170 C5' DA D 7 3169 3171 3191 C5' DT D 8 3190 3192 3211 C5' DT D 9 3210 3212 3231 C5' DC D 10 3230 3232 3248 C5' DG E 1 3247 3249 3270 C5' DA E 2 3269 3271 3291 C5' DA E 3 3290 3292 3312 C5' DT E 4 3311 3313 3452 C5' DA E 8 3451 3453 3473 C5' DA E 9 3472 3474 3494 C5' DC E 10 3493 3495 3515 C5' G G 1 3514 3516 3538 C5' DT G 2 3537 3539 3558 C5' DT G 3 3557 3559 3578 C5' DA G 4 3577 3579 3599 C5' DT G 5 3598 3600 3619 C5' DG G 6 3618 3620 3641 C5' DA G 7 3640 3642 3662 C5' DT G 8 3661 3663 3682 C5' DT G 9 3681 3683 3702 C5' DC G 10 3701 3703 3719 C5' DG H 1 3718 3720 3741 C5' DA H 2 3740 3742 3762 C5' DA H 3 3761 3763 3783 C5' DT H 4 3782 3784 3803 C5' DC H 5 3802 3804 3822 C5' DA H 6 3821 3823 3843 C5' DT H 7 3842 3844 3863 C5' DA H 8 3862 3864 3884 C5' DA H 9 3883 3885 3905 C5' DC H 10 3904 3906 3926 C5' AMP A 401 3925 3927 3955 C5' AMP B 401 3954 3956 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3040 P G D 1 distorted distorted 3041 3042 3043 3063 P DT D 2 distorted distorted 3048 3064 3065 3066 3083 P DT D 3 distorted distorted 3071 3084 3085 3086 3103 P DA D 4 distorted distorted 3091 3104 3105 3106 3124 P DT D 5 distorted distorted 3111 3125 3126 3127 3144 P DG D 6 distorted distorted 3132 3145 3146 3147 3166 P DA D 7 distorted distorted 3152 3167 3168 3169 3187 P DT D 8 distorted distorted 3174 3188 3189 3190 3207 P DT D 9 distorted distorted 3195 3208 3209 3210 3227 P DC D 10 distorted distorted 3215 3228 3229 3230 3266 P DA E 2 distorted distorted 3252 3267 3268 3269 3287 P DA E 3 distorted distorted 3274 3288 3289 3290 3308 P DT E 4 distorted distorted 3295 3309 3310 3311 3328 P DC E 5 3316 3329 P DC E 5 3316 3366 P DA E 6 3367 P DA E 6 3408 P DT E 7 3409 P DT E 7 3448 P DA E 8 distorted distorted 3449 3450 3451 3469 P DA E 9 distorted distorted 3456 3470 3471 3472 3490 P DC E 10 distorted distorted 3477 3491 3492 3493 3511 P G G 1 OK OK 3512 3513 3514 3534 P DT G 2 distorted distorted 3519 3535 3536 3537 3554 P DT G 3 distorted distorted 3542 3555 3556 3557 3574 P DA G 4 distorted distorted 3562 3575 3576 3577 3595 P DT G 5 distorted distorted 3582 3596 3597 3598 3615 P DG G 6 distorted distorted 3603 3616 3617 3618 3637 P DA G 7 distorted distorted 3623 3638 3639 3640 3658 P DT G 8 distorted distorted 3645 3659 3660 3661 3678 P DT G 9 distorted distorted 3666 3679 3680 3681 3698 P DC G 10 distorted distorted 3686 3699 3700 3701 3737 P DA H 2 distorted distorted 3723 3738 3739 3740 3758 P DA H 3 distorted distorted 3745 3759 3760 3761 3779 P DT H 4 distorted distorted 3766 3780 3781 3782 3799 P DC H 5 distorted distorted 3787 3800 3801 3802 3818 P DA H 6 distorted distorted 3807 3819 3820 3821 3839 P DT H 7 distorted distorted 3826 3840 3841 3842 3859 P DA H 8 distorted distorted 3847 3860 3861 3862 3880 P DA H 9 distorted distorted 3867 3881 3882 3883 3901 P DC H 10 distorted distorted 3888 3902 3903 3904 3921 P AMP A 401 distorted distorted 3922 3923 3925 3950 P AMP B 401 OK OK 3951 3952 3954 ---------------------------------------------------------------------------------