ID code: '2M2W' 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' --------------------------------------------------------------------------------- 3016 C1' DG B 1 alpha beta 3012 3034 3017 3015 3050 C1' DG B 2 alpha beta 3046 3068 3051 3049 3083 C1' DC B 3 alpha beta 3079 3098 3084 3082 3113 C1' DG B 4 alpha beta 3109 3131 3114 3112 3146 C1' DA B 5 alpha beta 3142 3163 3147 3145 3178 C1' DA B 6 alpha beta 3174 3195 3179 3177 3210 C1' DG B 7 alpha beta 3206 3228 3211 3209 3243 C1' DC B 8 alpha beta 3239 3258 3244 3242 3273 C1' DC B 9 alpha beta 3269 3288 3274 3272 3303 C1' DG B 10 alpha beta 3299 3321 3304 3302 3336 C1' DG B 11 alpha beta 3332 3354 3337 3335 3369 C1' DG B 12 alpha beta 3365 3387 3370 3368 3402 C1' DT B 13 alpha beta 3398 3418 3403 3401 3434 C1' DG B 14 alpha beta 3430 3452 3435 3433 3467 C1' DC B 15 alpha beta 3463 3482 3468 3466 3497 C1' DG B 16 alpha beta 3493 3515 3498 3496 3530 C1' DA B 17 alpha beta 3526 3547 3531 3529 3562 C1' DA B 18 alpha beta 3558 3579 3563 3561 3594 C1' DG B 19 alpha beta 3590 3612 3595 3593 3627 C1' DC B 20 alpha beta 3623 3642 3628 3626 3657 C1' DA B 21 alpha beta 3653 3674 3658 3656 3689 C1' DC B 22 alpha beta 3685 3704 3690 3688 3717 C1' DOC B 23 alpha beta 3721 3731 3709 3718 3759 C1' DGT A 201 beta 3755 3760 3758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3015 C2' DG B 1 OK OK 3016 3013 3032 3033 3049 C2' DG B 2 OK OK 3050 3047 3066 3067 3082 C2' DC B 3 OK OK 3083 3080 3096 3097 3112 C2' DG B 4 OK OK 3113 3110 3129 3130 3145 C2' DA B 5 OK OK 3146 3143 3161 3162 3177 C2' DA B 6 OK OK 3178 3175 3193 3194 3209 C2' DG B 7 OK OK 3210 3207 3226 3227 3242 C2' DC B 8 OK OK 3243 3240 3256 3257 3272 C2' DC B 9 OK OK 3273 3270 3286 3287 3302 C2' DG B 10 OK OK 3303 3300 3319 3320 3335 C2' DG B 11 OK OK 3336 3333 3352 3353 3368 C2' DG B 12 OK OK 3369 3366 3385 3386 3401 C2' DT B 13 OK OK 3402 3399 3416 3417 3433 C2' DG B 14 OK OK 3434 3431 3450 3451 3466 C2' DC B 15 OK OK 3467 3464 3480 3481 3496 C2' DG B 16 OK OK 3497 3494 3513 3514 3529 C2' DA B 17 OK OK 3530 3527 3545 3546 3561 C2' DA B 18 OK OK 3562 3559 3577 3578 3593 C2' DG B 19 OK OK 3594 3591 3610 3611 3626 C2' DC B 20 OK OK 3627 3624 3640 3641 3656 C2' DA B 21 OK OK 3657 3654 3672 3673 3688 C2' DC B 22 OK OK 3689 3686 3702 3703 3718 C2' DOC B 23 OK OK 3717 3719 3732 3733 3758 C2' DGT A 201 3759 3756 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3013 C3' DG B 1 OK OK 3011 3031 3014 3015 3047 C3' DG B 2 OK OK 3045 3065 3048 3049 3080 C3' DC B 3 OK OK 3078 3095 3081 3082 3110 C3' DG B 4 OK OK 3108 3128 3111 3112 3143 C3' DA B 5 OK OK 3141 3160 3144 3145 3175 C3' DA B 6 OK OK 3173 3192 3176 3177 3207 C3' DG B 7 OK OK 3205 3225 3208 3209 3240 C3' DC B 8 OK OK 3238 3255 3241 3242 3270 C3' DC B 9 OK OK 3268 3285 3271 3272 3300 C3' DG B 10 OK OK 3298 3318 3301 3302 3333 C3' DG B 11 OK OK 3331 3351 3334 3335 3366 C3' DG B 12 OK OK 3364 3384 3367 3368 3399 C3' DT B 13 OK OK 3397 3415 3400 3401 3431 C3' DG B 14 OK OK 3429 3449 3432 3433 3464 C3' DC B 15 OK OK 3462 3479 3465 3466 3494 C3' DG B 16 OK OK 3492 3512 3495 3496 3527 C3' DA B 17 OK OK 3525 3544 3528 3529 3559 C3' DA B 18 OK OK 3557 3576 3560 3561 3591 C3' DG B 19 OK OK 3589 3609 3592 3593 3624 C3' DC B 20 OK OK 3622 3639 3625 3626 3654 C3' DA B 21 OK OK 3652 3671 3655 3656 3686 C3' DC B 22 OK OK 3684 3701 3687 3688 3719 C3' DOC B 23 3720 3718 3756 C3' DGT A 201 OK 3754 3757 3758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3011 C4' DG B 1 OK OK 3013 3030 3010 3012 3045 C4' DG B 2 OK OK 3047 3064 3044 3046 3078 C4' DC B 3 OK OK 3080 3094 3077 3079 3108 C4' DG B 4 OK OK 3110 3127 3107 3109 3141 C4' DA B 5 OK OK 3143 3159 3140 3142 3173 C4' DA B 6 OK OK 3175 3191 3172 3174 3205 C4' DG B 7 OK OK 3207 3224 3204 3206 3238 C4' DC B 8 OK OK 3240 3254 3237 3239 3268 C4' DC B 9 OK OK 3270 3284 3267 3269 3298 C4' DG B 10 OK OK 3300 3317 3297 3299 3331 C4' DG B 11 OK OK 3333 3350 3330 3332 3364 C4' DG B 12 OK OK 3366 3383 3363 3365 3397 C4' DT B 13 OK OK 3399 3414 3396 3398 3429 C4' DG B 14 OK OK 3431 3448 3428 3430 3462 C4' DC B 15 OK OK 3464 3478 3461 3463 3492 C4' DG B 16 OK OK 3494 3511 3491 3493 3525 C4' DA B 17 OK OK 3527 3543 3524 3526 3557 C4' DA B 18 OK OK 3559 3575 3556 3558 3589 C4' DG B 19 OK OK 3591 3608 3588 3590 3622 C4' DC B 20 OK OK 3624 3638 3621 3623 3652 C4' DA B 21 OK OK 3654 3670 3651 3653 3684 C4' DC B 22 OK OK 3686 3700 3683 3685 3720 C4' DOC B 23 OK OK 3719 3736 3722 3721 3754 C4' DGT A 201 OK 3756 3753 3755 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3010 C5' DG B 1 OK OK 3009 3028 3029 3011 3044 C5' DG B 2 OK OK 3043 3062 3063 3045 3077 C5' DC B 3 OK OK 3076 3092 3093 3078 3107 C5' DG B 4 OK OK 3106 3125 3126 3108 3140 C5' DA B 5 OK OK 3139 3157 3158 3141 3172 C5' DA B 6 OK OK 3171 3189 3190 3173 3204 C5' DG B 7 OK OK 3203 3222 3223 3205 3237 C5' DC B 8 OK OK 3236 3252 3253 3238 3267 C5' DC B 9 OK OK 3266 3282 3283 3268 3297 C5' DG B 10 OK OK 3296 3315 3316 3298 3330 C5' DG B 11 OK OK 3329 3348 3349 3331 3363 C5' DG B 12 OK OK 3362 3381 3382 3364 3396 C5' DT B 13 OK OK 3395 3412 3413 3397 3428 C5' DG B 14 OK OK 3427 3446 3447 3429 3461 C5' DC B 15 OK OK 3460 3476 3477 3462 3491 C5' DG B 16 OK OK 3490 3509 3510 3492 3524 C5' DA B 17 OK OK 3523 3541 3542 3525 3556 C5' DA B 18 OK OK 3555 3573 3574 3557 3588 C5' DG B 19 OK OK 3587 3606 3607 3589 3621 C5' DC B 20 OK OK 3620 3636 3637 3622 3651 C5' DA B 21 OK OK 3650 3668 3669 3652 3683 C5' DC B 22 OK OK 3682 3698 3699 3684 3722 C5' DOC B 23 OK OK 3723 3737 3738 3720 3753 C5' DGT A 201 3752 3754 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3006 P DG B 1 OK OK 3007 3008 3009 3040 P DG B 2 distorted distorted 3014 3041 3042 3043 3073 P DC B 3 distorted distorted 3048 3074 3075 3076 3103 P DG B 4 distorted distorted 3081 3104 3105 3106 3136 P DA B 5 distorted distorted 3111 3137 3138 3139 3168 P DA B 6 distorted distorted 3144 3169 3170 3171 3200 P DG B 7 distorted distorted 3176 3201 3202 3203 3233 P DC B 8 distorted distorted 3208 3234 3235 3236 3263 P DC B 9 distorted distorted 3241 3264 3265 3266 3293 P DG B 10 distorted distorted 3271 3294 3295 3296 3326 P DG B 11 distorted distorted 3301 3327 3328 3329 3359 P DG B 12 distorted distorted 3334 3360 3361 3362 3392 P DT B 13 distorted distorted 3367 3393 3394 3395 3424 P DG B 14 distorted distorted 3400 3425 3426 3427 3457 P DC B 15 distorted distorted 3432 3458 3459 3460 3487 P DG B 16 distorted distorted 3465 3488 3489 3490 3520 P DA B 17 distorted distorted 3495 3521 3522 3523 3552 P DA B 18 distorted distorted 3528 3553 3554 3555 3584 P DG B 19 distorted distorted 3560 3585 3586 3587 3617 P DC B 20 distorted distorted 3592 3618 3619 3620 3647 P DA B 21 distorted distorted 3625 3648 3649 3650 3679 P DC B 22 distorted distorted 3655 3680 3681 3682 3724 P DOC B 23 distorted distorted 3687 3725 3726 3723 ---------------------------------------------------------------------------------