ID code: '1MNM' 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' --------------------------------------------------------------------------------- 2578 C1' A E 2 beta 2574 2579 2577 2599 C1' T E 3 beta 2595 2600 2598 2619 C1' T E 4 beta 2615 2620 2618 2639 C1' A E 5 beta 2635 2640 2638 2660 C1' C E 6 beta 2656 2661 2659 2679 C1' C E 7 beta 2675 2680 2678 2698 C1' T E 8 beta 2694 2699 2697 2718 C1' A E 9 beta 2714 2719 2717 2739 C1' A E 10 beta 2735 2740 2738 2760 C1' T E 11 beta 2756 2761 2759 2780 C1' A E 12 beta 2776 2781 2779 2801 C1' G E 13 beta 2797 2802 2800 2823 C1' G E 14 beta 2819 2824 2822 2845 C1' G E 15 beta 2841 2846 2844 2867 C1' A E 16 beta 2863 2868 2866 2888 C1' A E 17 beta 2884 2889 2887 2909 C1' A E 18 beta 2905 2910 2908 2930 C1' T E 19 beta 2926 2931 2929 2950 C1' T E 20 beta 2946 2951 2949 2970 C1' T E 21 beta 2966 2971 2969 2990 C1' A E 22 beta 2986 2991 2989 3011 C1' C E 23 beta 3007 3012 3010 3030 C1' A E 24 beta 3026 3031 3029 3051 C1' C E 25 beta 3047 3052 3050 3070 C1' G E 26 beta 3066 3071 3069 3109 C1' C F 28 beta 3105 3110 3108 3128 C1' G F 29 beta 3124 3129 3127 3150 C1' T F 30 beta 3146 3151 3149 3170 C1' G F 31 beta 3166 3171 3169 3192 C1' T F 32 beta 3188 3193 3191 3212 C1' A F 33 beta 3208 3213 3211 3233 C1' A F 34 beta 3229 3234 3232 3254 C1' A F 35 beta 3250 3255 3253 3275 C1' T F 36 beta 3271 3276 3274 3295 C1' T F 37 beta 3291 3296 3294 3315 C1' T F 38 beta 3311 3316 3314 3335 C1' C F 39 beta 3331 3336 3334 3354 C1' C F 40 beta 3350 3355 3353 3373 C1' C F 41 beta 3369 3374 3372 3392 C1' T F 42 beta 3388 3393 3391 3412 C1' A F 43 beta 3408 3413 3411 3433 C1' T F 44 beta 3429 3434 3432 3453 C1' T F 45 beta 3449 3454 3452 3473 C1' A F 46 beta 3469 3474 3472 3494 C1' G F 47 beta 3490 3495 3493 3516 C1' G F 48 beta 3512 3517 3515 3538 C1' T F 49 beta 3534 3539 3537 3558 C1' A F 50 beta 3554 3559 3557 3579 C1' A F 51 beta 3575 3580 3578 3600 C1' T F 52 beta 3596 3601 3599 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2577 C2' A E 2 2578 2575 2598 C2' T E 3 2599 2596 2618 C2' T E 4 2619 2616 2638 C2' A E 5 2639 2636 2659 C2' C E 6 2660 2657 2678 C2' C E 7 2679 2676 2697 C2' T E 8 2698 2695 2717 C2' A E 9 2718 2715 2738 C2' A E 10 2739 2736 2759 C2' T E 11 2760 2757 2779 C2' A E 12 2780 2777 2800 C2' G E 13 2801 2798 2822 C2' G E 14 2823 2820 2844 C2' G E 15 2845 2842 2866 C2' A E 16 2867 2864 2887 C2' A E 17 2888 2885 2908 C2' A E 18 2909 2906 2929 C2' T E 19 2930 2927 2949 C2' T E 20 2950 2947 2969 C2' T E 21 2970 2967 2989 C2' A E 22 2990 2987 3010 C2' C E 23 3011 3008 3029 C2' A E 24 3030 3027 3050 C2' C E 25 3051 3048 3069 C2' G E 26 3070 3067 3108 C2' C F 28 3109 3106 3127 C2' G F 29 3128 3125 3149 C2' T F 30 3150 3147 3169 C2' G F 31 3170 3167 3191 C2' T F 32 3192 3189 3211 C2' A F 33 3212 3209 3232 C2' A F 34 3233 3230 3253 C2' A F 35 3254 3251 3274 C2' T F 36 3275 3272 3294 C2' T F 37 3295 3292 3314 C2' T F 38 3315 3312 3334 C2' C F 39 3335 3332 3353 C2' C F 40 3354 3351 3372 C2' C F 41 3373 3370 3391 C2' T F 42 3392 3389 3411 C2' A F 43 3412 3409 3432 C2' T F 44 3433 3430 3452 C2' T F 45 3453 3450 3472 C2' A F 46 3473 3470 3493 C2' G F 47 3494 3491 3515 C2' G F 48 3516 3513 3537 C2' T F 49 3538 3535 3557 C2' A F 50 3558 3555 3578 C2' A F 51 3579 3576 3599 C2' T F 52 3600 3597 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2575 C3' A E 2 OK 2573 2576 2577 2596 C3' T E 3 OK 2594 2597 2598 2616 C3' T E 4 OK 2614 2617 2618 2636 C3' A E 5 OK 2634 2637 2638 2657 C3' C E 6 OK 2655 2658 2659 2676 C3' C E 7 OK 2674 2677 2678 2695 C3' T E 8 OK 2693 2696 2697 2715 C3' A E 9 OK 2713 2716 2717 2736 C3' A E 10 OK 2734 2737 2738 2757 C3' T E 11 OK 2755 2758 2759 2777 C3' A E 12 OK 2775 2778 2779 2798 C3' G E 13 OK 2796 2799 2800 2820 C3' G E 14 OK 2818 2821 2822 2842 C3' G E 15 OK 2840 2843 2844 2864 C3' A E 16 OK 2862 2865 2866 2885 C3' A E 17 OK 2883 2886 2887 2906 C3' A E 18 OK 2904 2907 2908 2927 C3' T E 19 OK 2925 2928 2929 2947 C3' T E 20 OK 2945 2948 2949 2967 C3' T E 21 OK 2965 2968 2969 2987 C3' A E 22 OK 2985 2988 2989 3008 C3' C E 23 OK 3006 3009 3010 3027 C3' A E 24 OK 3025 3028 3029 3048 C3' C E 25 OK 3046 3049 3050 3067 C3' G E 26 OK 3065 3068 3069 3106 C3' C F 28 OK 3104 3107 3108 3125 C3' G F 29 OK 3123 3126 3127 3147 C3' T F 30 OK 3145 3148 3149 3167 C3' G F 31 OK 3165 3168 3169 3189 C3' T F 32 OK 3187 3190 3191 3209 C3' A F 33 OK 3207 3210 3211 3230 C3' A F 34 OK 3228 3231 3232 3251 C3' A F 35 OK 3249 3252 3253 3272 C3' T F 36 OK 3270 3273 3274 3292 C3' T F 37 OK 3290 3293 3294 3312 C3' T F 38 OK 3310 3313 3314 3332 C3' C F 39 OK 3330 3333 3334 3351 C3' C F 40 OK 3349 3352 3353 3370 C3' C F 41 OK 3368 3371 3372 3389 C3' T F 42 OK 3387 3390 3391 3409 C3' A F 43 OK 3407 3410 3411 3430 C3' T F 44 OK 3428 3431 3432 3450 C3' T F 45 OK 3448 3451 3452 3470 C3' A F 46 OK 3468 3471 3472 3491 C3' G F 47 OK 3489 3492 3493 3513 C3' G F 48 OK 3511 3514 3515 3535 C3' T F 49 OK 3533 3536 3537 3555 C3' A F 50 OK 3553 3556 3557 3576 C3' A F 51 OK 3574 3577 3578 3597 C3' T F 52 OK 3595 3598 3599 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2573 C4' A E 2 OK 2575 2572 2574 2594 C4' T E 3 OK 2596 2593 2595 2614 C4' T E 4 OK 2616 2613 2615 2634 C4' A E 5 OK 2636 2633 2635 2655 C4' C E 6 OK 2657 2654 2656 2674 C4' C E 7 OK 2676 2673 2675 2693 C4' T E 8 OK 2695 2692 2694 2713 C4' A E 9 OK 2715 2712 2714 2734 C4' A E 10 OK 2736 2733 2735 2755 C4' T E 11 OK 2757 2754 2756 2775 C4' A E 12 OK 2777 2774 2776 2796 C4' G E 13 OK 2798 2795 2797 2818 C4' G E 14 OK 2820 2817 2819 2840 C4' G E 15 OK 2842 2839 2841 2862 C4' A E 16 OK 2864 2861 2863 2883 C4' A E 17 OK 2885 2882 2884 2904 C4' A E 18 OK 2906 2903 2905 2925 C4' T E 19 OK 2927 2924 2926 2945 C4' T E 20 OK 2947 2944 2946 2965 C4' T E 21 OK 2967 2964 2966 2985 C4' A E 22 OK 2987 2984 2986 3006 C4' C E 23 OK 3008 3005 3007 3025 C4' A E 24 OK 3027 3024 3026 3046 C4' C E 25 OK 3048 3045 3047 3065 C4' G E 26 OK 3067 3064 3066 3104 C4' C F 28 OK 3106 3103 3105 3123 C4' G F 29 OK 3125 3122 3124 3145 C4' T F 30 OK 3147 3144 3146 3165 C4' G F 31 OK 3167 3164 3166 3187 C4' T F 32 OK 3189 3186 3188 3207 C4' A F 33 OK 3209 3206 3208 3228 C4' A F 34 OK 3230 3227 3229 3249 C4' A F 35 OK 3251 3248 3250 3270 C4' T F 36 OK 3272 3269 3271 3290 C4' T F 37 OK 3292 3289 3291 3310 C4' T F 38 OK 3312 3309 3311 3330 C4' C F 39 OK 3332 3329 3331 3349 C4' C F 40 OK 3351 3348 3350 3368 C4' C F 41 OK 3370 3367 3369 3387 C4' T F 42 OK 3389 3386 3388 3407 C4' A F 43 OK 3409 3406 3408 3428 C4' T F 44 OK 3430 3427 3429 3448 C4' T F 45 OK 3450 3447 3449 3468 C4' A F 46 OK 3470 3467 3469 3489 C4' G F 47 OK 3491 3488 3490 3511 C4' G F 48 OK 3513 3510 3512 3533 C4' T F 49 OK 3535 3532 3534 3553 C4' A F 50 OK 3555 3552 3554 3574 C4' A F 51 OK 3576 3573 3575 3595 C4' T F 52 OK 3597 3594 3596 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2572 C5' A E 2 2571 2573 2593 C5' T E 3 2592 2594 2613 C5' T E 4 2612 2614 2633 C5' A E 5 2632 2634 2654 C5' C E 6 2653 2655 2673 C5' C E 7 2672 2674 2692 C5' T E 8 2691 2693 2712 C5' A E 9 2711 2713 2733 C5' A E 10 2732 2734 2754 C5' T E 11 2753 2755 2774 C5' A E 12 2773 2775 2795 C5' G E 13 2794 2796 2817 C5' G E 14 2816 2818 2839 C5' G E 15 2838 2840 2861 C5' A E 16 2860 2862 2882 C5' A E 17 2881 2883 2903 C5' A E 18 2902 2904 2924 C5' T E 19 2923 2925 2944 C5' T E 20 2943 2945 2964 C5' T E 21 2963 2965 2984 C5' A E 22 2983 2985 3005 C5' C E 23 3004 3006 3024 C5' A E 24 3023 3025 3045 C5' C E 25 3044 3046 3064 C5' G E 26 3063 3065 3103 C5' C F 28 3102 3104 3122 C5' G F 29 3121 3123 3144 C5' T F 30 3143 3145 3164 C5' G F 31 3163 3165 3186 C5' T F 32 3185 3187 3206 C5' A F 33 3205 3207 3227 C5' A F 34 3226 3228 3248 C5' A F 35 3247 3249 3269 C5' T F 36 3268 3270 3289 C5' T F 37 3288 3290 3309 C5' T F 38 3308 3310 3329 C5' C F 39 3328 3330 3348 C5' C F 40 3347 3349 3367 C5' C F 41 3366 3368 3386 C5' T F 42 3385 3387 3406 C5' A F 43 3405 3407 3427 C5' T F 44 3426 3428 3447 C5' T F 45 3446 3448 3467 C5' A F 46 3466 3468 3488 C5' G F 47 3487 3489 3510 C5' G F 48 3509 3511 3532 C5' T F 49 3531 3533 3552 C5' A F 50 3551 3553 3573 C5' A F 51 3572 3574 3594 C5' T F 52 3593 3595 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2589 P T E 3 OK OK 2576 2590 2591 2592 2609 P T E 4 OK OK 2597 2610 2611 2612 2629 P A E 5 OK OK 2617 2630 2631 2632 2650 P C E 6 OK OK 2637 2651 2652 2653 2669 P C E 7 OK OK 2658 2670 2671 2672 2688 P T E 8 OK OK 2677 2689 2690 2691 2708 P A E 9 distorted distorted 2696 2709 2710 2711 2729 P A E 10 distorted distorted 2716 2730 2731 2732 2750 P T E 11 distorted distorted 2737 2751 2752 2753 2770 P A E 12 OK OK 2758 2771 2772 2773 2791 P G E 13 OK OK 2778 2792 2793 2794 2813 P G E 14 OK OK 2799 2814 2815 2816 2835 P G E 15 distorted distorted 2821 2836 2837 2838 2857 P A E 16 OK OK 2843 2858 2859 2860 2878 P A E 17 OK OK 2865 2879 2880 2881 2899 P A E 18 OK OK 2886 2900 2901 2902 2920 P T E 19 OK OK 2907 2921 2922 2923 2940 P T E 20 OK OK 2928 2941 2942 2943 2960 P T E 21 OK OK 2948 2961 2962 2963 2980 P A E 22 distorted distorted 2968 2981 2982 2983 3001 P C E 23 OK OK 2988 3002 3003 3004 3020 P A E 24 OK OK 3009 3021 3022 3023 3041 P C E 25 OK OK 3028 3042 3043 3044 3060 P G E 26 OK OK 3049 3061 3062 3063 3118 P G F 29 OK OK 3107 3119 3120 3121 3140 P T F 30 OK OK 3126 3141 3142 3143 3160 P G F 31 OK OK 3148 3161 3162 3163 3182 P T F 32 OK OK 3168 3183 3184 3185 3202 P A F 33 OK OK 3190 3203 3204 3205 3223 P A F 34 OK OK 3210 3224 3225 3226 3244 P A F 35 OK OK 3231 3245 3246 3247 3265 P T F 36 OK OK 3252 3266 3267 3268 3285 P T F 37 OK OK 3273 3286 3287 3288 3305 P T F 38 OK OK 3293 3306 3307 3308 3325 P C F 39 OK OK 3313 3326 3327 3328 3344 P C F 40 distorted distorted 3333 3345 3346 3347 3363 P C F 41 OK OK 3352 3364 3365 3366 3382 P T F 42 OK OK 3371 3383 3384 3385 3402 P A F 43 OK OK 3390 3403 3404 3405 3423 P T F 44 distorted distorted 3410 3424 3425 3426 3443 P T F 45 distorted distorted 3431 3444 3445 3446 3463 P A F 46 distorted distorted 3451 3464 3465 3466 3484 P G F 47 OK OK 3471 3485 3486 3487 3506 P G F 48 OK OK 3492 3507 3508 3509 3528 P T F 49 OK OK 3514 3529 3530 3531 3548 P A F 50 OK OK 3536 3549 3550 3551 3569 P A F 51 OK OK 3556 3570 3571 3572 3590 P T F 52 OK OK 3577 3591 3592 3593 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