ID code: '1A66' 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' --------------------------------------------------------------------------------- 2843 C1' C B 315 beta 2839 2844 2842 2874 C1' G B 316 beta 2870 2875 2873 2907 C1' A B 317 beta 2903 2908 2906 2939 C1' G B 318 beta 2935 2940 2938 2972 C1' G B 319 beta 2968 2973 2971 3005 C1' A B 320 beta 3001 3006 3004 3037 C1' A B 321 beta 3033 3038 3036 3069 C1' A B 322 beta 3065 3070 3068 3101 C1' A B 323 beta 3097 3102 3100 3133 C1' T B 324 beta 3129 3134 3132 3165 C1' T B 325 beta 3161 3166 3164 3197 C1' G B 326 beta 3193 3198 3196 3229 C1' C C 340 beta 3225 3230 3228 3260 C1' A C 341 beta 3256 3261 3259 3292 C1' A C 342 beta 3288 3293 3291 3324 C1' T C 343 beta 3320 3325 3323 3356 C1' T C 344 beta 3352 3357 3355 3388 C1' T C 345 beta 3384 3389 3387 3420 C1' T C 346 beta 3416 3421 3419 3452 C1' C C 347 beta 3448 3453 3451 3482 C1' C C 348 beta 3478 3483 3481 3512 C1' T C 349 beta 3508 3513 3511 3544 C1' C C 350 beta 3540 3545 3543 3574 C1' G C 351 beta 3570 3575 3573 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2842 C2' C B 315 2843 2840 2873 C2' G B 316 2874 2871 2906 C2' A B 317 2907 2904 2938 C2' G B 318 2939 2936 2971 C2' G B 319 2972 2969 3004 C2' A B 320 3005 3002 3036 C2' A B 321 3037 3034 3068 C2' A B 322 3069 3066 3100 C2' A B 323 3101 3098 3132 C2' T B 324 3133 3130 3164 C2' T B 325 3165 3162 3196 C2' G B 326 3197 3194 3228 C2' C C 340 3229 3226 3259 C2' A C 341 3260 3257 3291 C2' A C 342 3292 3289 3323 C2' T C 343 3324 3321 3355 C2' T C 344 3356 3353 3387 C2' T C 345 3388 3385 3419 C2' T C 346 3420 3417 3451 C2' C C 347 3452 3449 3481 C2' C C 348 3482 3479 3511 C2' T C 349 3512 3509 3543 C2' C C 350 3544 3541 3573 C2' G C 351 3574 3571 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2840 C3' C B 315 OK 2838 2841 2842 2871 C3' G B 316 OK 2869 2872 2873 2904 C3' A B 317 OK 2902 2905 2906 2936 C3' G B 318 OK 2934 2937 2938 2969 C3' G B 319 OK 2967 2970 2971 3002 C3' A B 320 OK 3000 3003 3004 3034 C3' A B 321 OK 3032 3035 3036 3066 C3' A B 322 OK 3064 3067 3068 3098 C3' A B 323 OK 3096 3099 3100 3130 C3' T B 324 OK 3128 3131 3132 3162 C3' T B 325 OK 3160 3163 3164 3194 C3' G B 326 OK 3192 3195 3196 3226 C3' C C 340 OK 3224 3227 3228 3257 C3' A C 341 OK 3255 3258 3259 3289 C3' A C 342 OK 3287 3290 3291 3321 C3' T C 343 OK 3319 3322 3323 3353 C3' T C 344 OK 3351 3354 3355 3385 C3' T C 345 OK 3383 3386 3387 3417 C3' T C 346 OK 3415 3418 3419 3449 C3' C C 347 OK 3447 3450 3451 3479 C3' C C 348 OK 3477 3480 3481 3509 C3' T C 349 OK 3507 3510 3511 3541 C3' C C 350 OK 3539 3542 3543 3571 C3' G C 351 OK 3569 3572 3573 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2838 C4' C B 315 OK 2840 2837 2839 2869 C4' G B 316 OK 2871 2868 2870 2902 C4' A B 317 OK 2904 2901 2903 2934 C4' G B 318 OK 2936 2933 2935 2967 C4' G B 319 OK 2969 2966 2968 3000 C4' A B 320 OK 3002 2999 3001 3032 C4' A B 321 OK 3034 3031 3033 3064 C4' A B 322 OK 3066 3063 3065 3096 C4' A B 323 OK 3098 3095 3097 3128 C4' T B 324 OK 3130 3127 3129 3160 C4' T B 325 OK 3162 3159 3161 3192 C4' G B 326 OK 3194 3191 3193 3224 C4' C C 340 OK 3226 3223 3225 3255 C4' A C 341 OK 3257 3254 3256 3287 C4' A C 342 OK 3289 3286 3288 3319 C4' T C 343 OK 3321 3318 3320 3351 C4' T C 344 OK 3353 3350 3352 3383 C4' T C 345 OK 3385 3382 3384 3415 C4' T C 346 OK 3417 3414 3416 3447 C4' C C 347 OK 3449 3446 3448 3477 C4' C C 348 OK 3479 3476 3478 3507 C4' T C 349 OK 3509 3506 3508 3539 C4' C C 350 OK 3541 3538 3540 3569 C4' G C 351 OK 3571 3568 3570 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2837 C5' C B 315 2836 2838 2868 C5' G B 316 2867 2869 2901 C5' A B 317 2900 2902 2933 C5' G B 318 2932 2934 2966 C5' G B 319 2965 2967 2999 C5' A B 320 2998 3000 3031 C5' A B 321 3030 3032 3063 C5' A B 322 3062 3064 3095 C5' A B 323 3094 3096 3127 C5' T B 324 3126 3128 3159 C5' T B 325 3158 3160 3191 C5' G B 326 3190 3192 3223 C5' C C 340 3222 3224 3254 C5' A C 341 3253 3255 3286 C5' A C 342 3285 3287 3318 C5' T C 343 3317 3319 3350 C5' T C 344 3349 3351 3382 C5' T C 345 3381 3383 3414 C5' T C 346 3413 3415 3446 C5' C C 347 3445 3447 3476 C5' C C 348 3475 3477 3506 C5' T C 349 3505 3507 3538 C5' C C 350 3537 3539 3568 C5' G C 351 3567 3569 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2864 P G B 316 OK OK 2841 2865 2866 2867 2897 P A B 317 OK OK 2872 2898 2899 2900 2929 P G B 318 OK OK 2905 2930 2931 2932 2962 P G B 319 OK OK 2937 2963 2964 2965 2995 P A B 320 OK OK 2970 2996 2997 2998 3027 P A B 321 OK OK 3003 3028 3029 3030 3059 P A B 322 OK OK 3035 3060 3061 3062 3091 P A B 323 OK OK 3067 3092 3093 3094 3123 P T B 324 OK OK 3099 3124 3125 3126 3155 P T B 325 OK OK 3131 3156 3157 3158 3187 P G B 326 OK OK 3163 3188 3189 3190 3250 P A C 341 OK OK 3227 3251 3252 3253 3282 P A C 342 OK OK 3258 3283 3284 3285 3314 P T C 343 OK OK 3290 3315 3316 3317 3346 P T C 344 OK OK 3322 3347 3348 3349 3378 P T C 345 OK OK 3354 3379 3380 3381 3410 P T C 346 OK OK 3386 3411 3412 3413 3442 P C C 347 OK OK 3418 3443 3444 3445 3472 P C C 348 OK OK 3450 3473 3474 3475 3502 P T C 349 OK OK 3480 3503 3504 3505 3534 P C C 350 OK OK 3510 3535 3536 3537 3564 P G C 351 OK OK 3542 3565 3566 3567 ---------------------------------------------------------------------------------