ID code: '4NDG' 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' --------------------------------------------------------------------------------- 2950 C1' G D 1 beta 2945 2951 2948 2972 C1' DT D 2 beta 2968 2973 2971 2992 C1' DT D 3 beta 2988 2993 2991 3012 C1' DA D 4 beta 3008 3013 3011 3033 C1' DT D 5 beta 3029 3034 3032 3053 C1' DG D 6 beta 3049 3054 3052 3075 C1' DA D 7 beta 3071 3076 3074 3096 C1' DT D 8 beta 3092 3097 3095 3116 C1' DT D 9 beta 3112 3117 3115 3136 C1' DC D 10 beta 3132 3137 3135 3153 C1' DG E 1 beta 3149 3154 3152 3175 C1' DA E 2 beta 3171 3176 3174 3196 C1' DA E 3 beta 3192 3197 3195 3217 C1' DT E 4 beta 3213 3218 3216 3237 C1' DC E 5 beta 3233 3238 3236 3256 C1' DA E 6 beta 3252 3257 3255 3277 C1' DT E 7 beta 3273 3278 3276 3297 C1' DA E 8 beta 3293 3298 3296 3318 C1' DA E 9 beta 3314 3319 3317 3339 C1' DC E 10 beta 3335 3340 3338 3361 C1' G G 1 beta 3356 3362 3359 3383 C1' DT G 2 beta 3379 3384 3382 3403 C1' DT G 3 beta 3399 3404 3402 3423 C1' DA G 4 beta 3419 3424 3422 3444 C1' DT G 5 beta 3440 3445 3443 3464 C1' DG G 6 beta 3460 3465 3463 3486 C1' DA G 7 beta 3482 3487 3485 3507 C1' DT G 8 beta 3503 3508 3506 3527 C1' DT G 9 beta 3523 3528 3526 3547 C1' DC G 10 beta 3543 3548 3546 3564 C1' DG H 1 beta 3560 3565 3563 3586 C1' DA H 2 beta 3582 3587 3585 3607 C1' DA H 3 beta 3603 3608 3606 3628 C1' DT H 4 beta 3624 3629 3627 3648 C1' DC H 5 beta 3644 3649 3647 3667 C1' DA H 6 beta 3663 3668 3666 3688 C1' DT H 7 beta 3684 3689 3687 3708 C1' DA H 8 beta 3704 3709 3707 3729 C1' DA H 9 beta 3725 3730 3728 3750 C1' DC H 10 beta 3746 3751 3749 3770 C1' V5A A 401 beta 3771 3772 3768 3793 C1' V5A B 401 beta 3794 3795 3791 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2948 C2' G D 1 OK 2950 2946 2949 2971 C2' DT D 2 2972 2969 2991 C2' DT D 3 2992 2989 3011 C2' DA D 4 3012 3009 3032 C2' DT D 5 3033 3030 3052 C2' DG D 6 3053 3050 3074 C2' DA D 7 3075 3072 3095 C2' DT D 8 3096 3093 3115 C2' DT D 9 3116 3113 3135 C2' DC D 10 3136 3133 3152 C2' DG E 1 3153 3150 3174 C2' DA E 2 3175 3172 3195 C2' DA E 3 3196 3193 3216 C2' DT E 4 3217 3214 3236 C2' DC E 5 3237 3234 3255 C2' DA E 6 3256 3253 3276 C2' DT E 7 3277 3274 3296 C2' DA E 8 3297 3294 3317 C2' DA E 9 3318 3315 3338 C2' DC E 10 3339 3336 3359 C2' G G 1 OK 3361 3357 3360 3382 C2' DT G 2 3383 3380 3402 C2' DT G 3 3403 3400 3422 C2' DA G 4 3423 3420 3443 C2' DT G 5 3444 3441 3463 C2' DG G 6 3464 3461 3485 C2' DA G 7 3486 3483 3506 C2' DT G 8 3507 3504 3526 C2' DT G 9 3527 3524 3546 C2' DC G 10 3547 3544 3563 C2' DG H 1 3564 3561 3585 C2' DA H 2 3586 3583 3606 C2' DA H 3 3607 3604 3627 C2' DT H 4 3628 3625 3647 C2' DC H 5 3648 3645 3666 C2' DA H 6 3667 3664 3687 C2' DT H 7 3688 3685 3707 C2' DA H 8 3708 3705 3728 C2' DA H 9 3729 3726 3749 C2' DC H 10 3750 3747 3768 C2' V5A A 401 OK 3770 3766 3769 3791 C2' V5A B 401 OK 3793 3789 3792 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2946 C3' G D 1 OK 2944 2947 2948 2969 C3' DT D 2 OK 2967 2970 2971 2989 C3' DT D 3 OK 2987 2990 2991 3009 C3' DA D 4 OK 3007 3010 3011 3030 C3' DT D 5 OK 3028 3031 3032 3050 C3' DG D 6 OK 3048 3051 3052 3072 C3' DA D 7 OK 3070 3073 3074 3093 C3' DT D 8 OK 3091 3094 3095 3113 C3' DT D 9 OK 3111 3114 3115 3133 C3' DC D 10 OK 3131 3134 3135 3150 C3' DG E 1 OK 3148 3151 3152 3172 C3' DA E 2 OK 3170 3173 3174 3193 C3' DA E 3 OK 3191 3194 3195 3214 C3' DT E 4 OK 3212 3215 3216 3234 C3' DC E 5 OK 3232 3235 3236 3253 C3' DA E 6 OK 3251 3254 3255 3274 C3' DT E 7 OK 3272 3275 3276 3294 C3' DA E 8 OK 3292 3295 3296 3315 C3' DA E 9 OK 3313 3316 3317 3336 C3' DC E 10 OK 3334 3337 3338 3357 C3' G G 1 OK 3355 3358 3359 3380 C3' DT G 2 OK 3378 3381 3382 3400 C3' DT G 3 OK 3398 3401 3402 3420 C3' DA G 4 OK 3418 3421 3422 3441 C3' DT G 5 OK 3439 3442 3443 3461 C3' DG G 6 OK 3459 3462 3463 3483 C3' DA G 7 OK 3481 3484 3485 3504 C3' DT G 8 OK 3502 3505 3506 3524 C3' DT G 9 OK 3522 3525 3526 3544 C3' DC G 10 OK 3542 3545 3546 3561 C3' DG H 1 OK 3559 3562 3563 3583 C3' DA H 2 OK 3581 3584 3585 3604 C3' DA H 3 OK 3602 3605 3606 3625 C3' DT H 4 OK 3623 3626 3627 3645 C3' DC H 5 OK 3643 3646 3647 3664 C3' DA H 6 OK 3662 3665 3666 3685 C3' DT H 7 OK 3683 3686 3687 3705 C3' DA H 8 OK 3703 3706 3707 3726 C3' DA H 9 OK 3724 3727 3728 3747 C3' DC H 10 OK 3745 3748 3749 3766 C3' V5A A 401 OK 3765 3767 3768 3789 C3' V5A B 401 OK 3788 3790 3791 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2944 C4' G D 1 OK 2946 2943 2945 2967 C4' DT D 2 OK 2969 2966 2968 2987 C4' DT D 3 OK 2989 2986 2988 3007 C4' DA D 4 OK 3009 3006 3008 3028 C4' DT D 5 OK 3030 3027 3029 3048 C4' DG D 6 OK 3050 3047 3049 3070 C4' DA D 7 OK 3072 3069 3071 3091 C4' DT D 8 OK 3093 3090 3092 3111 C4' DT D 9 OK 3113 3110 3112 3131 C4' DC D 10 OK 3133 3130 3132 3148 C4' DG E 1 OK 3150 3147 3149 3170 C4' DA E 2 OK 3172 3169 3171 3191 C4' DA E 3 OK 3193 3190 3192 3212 C4' DT E 4 OK 3214 3211 3213 3232 C4' DC E 5 OK 3234 3231 3233 3251 C4' DA E 6 OK 3253 3250 3252 3272 C4' DT E 7 OK 3274 3271 3273 3292 C4' DA E 8 OK 3294 3291 3293 3313 C4' DA E 9 OK 3315 3312 3314 3334 C4' DC E 10 OK 3336 3333 3335 3355 C4' G G 1 OK 3357 3354 3356 3378 C4' DT G 2 OK 3380 3377 3379 3398 C4' DT G 3 OK 3400 3397 3399 3418 C4' DA G 4 OK 3420 3417 3419 3439 C4' DT G 5 OK 3441 3438 3440 3459 C4' DG G 6 OK 3461 3458 3460 3481 C4' DA G 7 OK 3483 3480 3482 3502 C4' DT G 8 OK 3504 3501 3503 3522 C4' DT G 9 OK 3524 3521 3523 3542 C4' DC G 10 OK 3544 3541 3543 3559 C4' DG H 1 OK 3561 3558 3560 3581 C4' DA H 2 OK 3583 3580 3582 3602 C4' DA H 3 OK 3604 3601 3603 3623 C4' DT H 4 OK 3625 3622 3624 3643 C4' DC H 5 OK 3645 3642 3644 3662 C4' DA H 6 OK 3664 3661 3663 3683 C4' DT H 7 OK 3685 3682 3684 3703 C4' DA H 8 OK 3705 3702 3704 3724 C4' DA H 9 OK 3726 3723 3725 3745 C4' DC H 10 OK 3747 3744 3746 3765 C4' V5A A 401 OK 3766 3764 3771 3788 C4' V5A B 401 OK 3789 3787 3794 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2943 C5' G D 1 2942 2944 2966 C5' DT D 2 2965 2967 2986 C5' DT D 3 2985 2987 3006 C5' DA D 4 3005 3007 3027 C5' DT D 5 3026 3028 3047 C5' DG D 6 3046 3048 3069 C5' DA D 7 3068 3070 3090 C5' DT D 8 3089 3091 3110 C5' DT D 9 3109 3111 3130 C5' DC D 10 3129 3131 3147 C5' DG E 1 3146 3148 3169 C5' DA E 2 3168 3170 3190 C5' DA E 3 3189 3191 3211 C5' DT E 4 3210 3212 3231 C5' DC E 5 3230 3232 3250 C5' DA E 6 3249 3251 3271 C5' DT E 7 3270 3272 3291 C5' DA E 8 3290 3292 3312 C5' DA E 9 3311 3313 3333 C5' DC E 10 3332 3334 3354 C5' G G 1 3353 3355 3377 C5' DT G 2 3376 3378 3397 C5' DT G 3 3396 3398 3417 C5' DA G 4 3416 3418 3438 C5' DT G 5 3437 3439 3458 C5' DG G 6 3457 3459 3480 C5' DA G 7 3479 3481 3501 C5' DT G 8 3500 3502 3521 C5' DT G 9 3520 3522 3541 C5' DC G 10 3540 3542 3558 C5' DG H 1 3557 3559 3580 C5' DA H 2 3579 3581 3601 C5' DA H 3 3600 3602 3622 C5' DT H 4 3621 3623 3642 C5' DC H 5 3641 3643 3661 C5' DA H 6 3660 3662 3682 C5' DT H 7 3681 3683 3702 C5' DA H 8 3701 3703 3723 C5' DA H 9 3722 3724 3744 C5' DC H 10 3743 3745 3764 C5' V5A A 401 3763 3765 3787 C5' V5A B 401 3786 3788 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2939 P G D 1 distorted distorted 2940 2941 2942 2962 P DT D 2 distorted distorted 2947 2963 2964 2965 2982 P DT D 3 distorted distorted 2970 2983 2984 2985 3002 P DA D 4 distorted distorted 2990 3003 3004 3005 3023 P DT D 5 distorted distorted 3010 3024 3025 3026 3043 P DG D 6 distorted distorted 3031 3044 3045 3046 3065 P DA D 7 distorted distorted 3051 3066 3067 3068 3086 P DT D 8 distorted distorted 3073 3087 3088 3089 3106 P DT D 9 distorted distorted 3094 3107 3108 3109 3126 P DC D 10 distorted distorted 3114 3127 3128 3129 3165 P DA E 2 distorted distorted 3151 3166 3167 3168 3186 P DA E 3 distorted distorted 3173 3187 3188 3189 3207 P DT E 4 distorted distorted 3194 3208 3209 3210 3227 P DC E 5 distorted distorted 3215 3228 3229 3230 3246 P DA E 6 distorted distorted 3235 3247 3248 3249 3267 P DT E 7 distorted distorted 3254 3268 3269 3270 3287 P DA E 8 distorted distorted 3275 3288 3289 3290 3308 P DA E 9 distorted distorted 3295 3309 3310 3311 3329 P DC E 10 distorted distorted 3316 3330 3331 3332 3350 P G G 1 distorted distorted 3351 3352 3353 3373 P DT G 2 distorted distorted 3358 3374 3375 3376 3393 P DT G 3 distorted distorted 3381 3394 3395 3396 3413 P DA G 4 distorted distorted 3401 3414 3415 3416 3434 P DT G 5 distorted distorted 3421 3435 3436 3437 3454 P DG G 6 distorted distorted 3442 3455 3456 3457 3476 P DA G 7 distorted distorted 3462 3477 3478 3479 3497 P DT G 8 distorted distorted 3484 3498 3499 3500 3517 P DT G 9 distorted distorted 3505 3518 3519 3520 3537 P DC G 10 distorted distorted 3525 3538 3539 3540 3576 P DA H 2 distorted distorted 3562 3577 3578 3579 3597 P DA H 3 distorted distorted 3584 3598 3599 3600 3618 P DT H 4 distorted distorted 3605 3619 3620 3621 3638 P DC H 5 distorted distorted 3626 3639 3640 3641 3657 P DA H 6 distorted distorted 3646 3658 3659 3660 3678 P DT H 7 distorted distorted 3665 3679 3680 3681 3698 P DA H 8 distorted distorted 3686 3699 3700 3701 3719 P DA H 9 distorted distorted 3706 3720 3721 3722 3740 P DC H 10 distorted distorted 3727 3741 3742 3743 ---------------------------------------------------------------------------------