ID code: '2UWM' 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' --------------------------------------------------------------------------------- 3267 C1' G C 13 beta 3262 3268 3265 3290 C1' G C 14 beta 3285 3291 3288 3313 C1' C C 15 beta 3308 3314 3311 3333 C1' G C 16 beta 3328 3334 3331 3356 C1' U C 17 beta 3351 3357 3354 3376 C1' U C 18 beta 3371 3377 3374 3396 C1' G C 19 beta 3391 3397 3394 3419 C1' C C 20 beta 3414 3420 3417 3439 C1' C C 21 beta 3434 3440 3437 3459 C1' G C 22 beta 3454 3460 3457 3482 C1' G C 23 beta 3477 3483 3480 3505 C1' U C 24 beta 3500 3506 3503 3525 C1' C C 25 beta 3520 3526 3523 3545 C1' U C 26 beta 3540 3546 3543 3565 C1' G C 27 beta 3560 3566 3563 3588 C1' G C 28 beta 3583 3589 3586 3611 C1' C C 29 beta 3606 3612 3609 3631 C1' A C 30 beta 3626 3632 3629 3653 C1' A C 31 beta 3648 3654 3651 3675 C1' C C 32 beta 3670 3676 3673 3695 C1' G C 33 beta 3690 3696 3693 3718 C1' C C 34 beta 3713 3719 3716 3738 C1' C C 35 beta 3733 3739 3736 3756 C1' G D 13 beta 3751 3757 3754 3779 C1' G D 14 beta 3774 3780 3777 3802 C1' C D 15 beta 3797 3803 3800 3822 C1' G D 16 beta 3817 3823 3820 3845 C1' U D 17 beta 3840 3846 3843 3865 C1' U D 18 beta 3860 3866 3863 3885 C1' G D 19 beta 3880 3886 3883 3908 C1' C D 20 beta 3903 3909 3906 3928 C1' C D 21 beta 3923 3929 3926 3948 C1' G D 22 beta 3943 3949 3946 3971 C1' G D 23 beta 3966 3972 3969 3994 C1' U D 24 beta 3989 3995 3992 4014 C1' C D 25 beta 4009 4015 4012 4034 C1' U D 26 beta 4029 4035 4032 4054 C1' G D 27 beta 4049 4055 4052 4077 C1' G D 28 beta 4072 4078 4075 4100 C1' C D 29 beta 4095 4101 4098 4120 C1' A D 30 beta 4115 4121 4118 4142 C1' A D 31 beta 4137 4143 4140 4164 C1' C D 32 beta 4159 4165 4162 4184 C1' G D 33 beta 4179 4185 4182 4207 C1' C D 34 beta 4202 4208 4205 4227 C1' C D 35 beta 4222 4228 4225 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3265 C2' G C 13 OK 3267 3263 3266 3288 C2' G C 14 OK 3290 3286 3289 3311 C2' C C 15 OK 3313 3309 3312 3331 C2' G C 16 OK 3333 3329 3332 3354 C2' U C 17 OK 3356 3352 3355 3374 C2' U C 18 OK 3376 3372 3375 3394 C2' G C 19 OK 3396 3392 3395 3417 C2' C C 20 OK 3419 3415 3418 3437 C2' C C 21 OK 3439 3435 3438 3457 C2' G C 22 OK 3459 3455 3458 3480 C2' G C 23 OK 3482 3478 3481 3503 C2' U C 24 OK 3505 3501 3504 3523 C2' C C 25 OK 3525 3521 3524 3543 C2' U C 26 OK 3545 3541 3544 3563 C2' G C 27 OK 3565 3561 3564 3586 C2' G C 28 OK 3588 3584 3587 3609 C2' C C 29 OK 3611 3607 3610 3629 C2' A C 30 OK 3631 3627 3630 3651 C2' A C 31 OK 3653 3649 3652 3673 C2' C C 32 OK 3675 3671 3674 3693 C2' G C 33 OK 3695 3691 3694 3716 C2' C C 34 OK 3718 3714 3717 3736 C2' C C 35 OK 3738 3734 3737 3754 C2' G D 13 OK 3756 3752 3755 3777 C2' G D 14 OK 3779 3775 3778 3800 C2' C D 15 OK 3802 3798 3801 3820 C2' G D 16 OK 3822 3818 3821 3843 C2' U D 17 OK 3845 3841 3844 3863 C2' U D 18 OK 3865 3861 3864 3883 C2' G D 19 OK 3885 3881 3884 3906 C2' C D 20 OK 3908 3904 3907 3926 C2' C D 21 OK 3928 3924 3927 3946 C2' G D 22 OK 3948 3944 3947 3969 C2' G D 23 OK 3971 3967 3970 3992 C2' U D 24 OK 3994 3990 3993 4012 C2' C D 25 OK 4014 4010 4013 4032 C2' U D 26 OK 4034 4030 4033 4052 C2' G D 27 OK 4054 4050 4053 4075 C2' G D 28 OK 4077 4073 4076 4098 C2' C D 29 OK 4100 4096 4099 4118 C2' A D 30 OK 4120 4116 4119 4140 C2' A D 31 OK 4142 4138 4141 4162 C2' C D 32 OK 4164 4160 4163 4182 C2' G D 33 OK 4184 4180 4183 4205 C2' C D 34 OK 4207 4203 4206 4225 C2' C D 35 OK 4227 4223 4226 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3263 C3' G C 13 OK 3261 3264 3265 3286 C3' G C 14 OK 3284 3287 3288 3309 C3' C C 15 OK 3307 3310 3311 3329 C3' G C 16 OK 3327 3330 3331 3352 C3' U C 17 OK 3350 3353 3354 3372 C3' U C 18 OK 3370 3373 3374 3392 C3' G C 19 OK 3390 3393 3394 3415 C3' C C 20 OK 3413 3416 3417 3435 C3' C C 21 OK 3433 3436 3437 3455 C3' G C 22 OK 3453 3456 3457 3478 C3' G C 23 OK 3476 3479 3480 3501 C3' U C 24 OK 3499 3502 3503 3521 C3' C C 25 OK 3519 3522 3523 3541 C3' U C 26 OK 3539 3542 3543 3561 C3' G C 27 OK 3559 3562 3563 3584 C3' G C 28 OK 3582 3585 3586 3607 C3' C C 29 OK 3605 3608 3609 3627 C3' A C 30 OK 3625 3628 3629 3649 C3' A C 31 OK 3647 3650 3651 3671 C3' C C 32 OK 3669 3672 3673 3691 C3' G C 33 OK 3689 3692 3693 3714 C3' C C 34 OK 3712 3715 3716 3734 C3' C C 35 OK 3732 3735 3736 3752 C3' G D 13 OK 3750 3753 3754 3775 C3' G D 14 OK 3773 3776 3777 3798 C3' C D 15 OK 3796 3799 3800 3818 C3' G D 16 OK 3816 3819 3820 3841 C3' U D 17 OK 3839 3842 3843 3861 C3' U D 18 OK 3859 3862 3863 3881 C3' G D 19 OK 3879 3882 3883 3904 C3' C D 20 OK 3902 3905 3906 3924 C3' C D 21 OK 3922 3925 3926 3944 C3' G D 22 OK 3942 3945 3946 3967 C3' G D 23 OK 3965 3968 3969 3990 C3' U D 24 OK 3988 3991 3992 4010 C3' C D 25 OK 4008 4011 4012 4030 C3' U D 26 OK 4028 4031 4032 4050 C3' G D 27 OK 4048 4051 4052 4073 C3' G D 28 OK 4071 4074 4075 4096 C3' C D 29 OK 4094 4097 4098 4116 C3' A D 30 OK 4114 4117 4118 4138 C3' A D 31 OK 4136 4139 4140 4160 C3' C D 32 OK 4158 4161 4162 4180 C3' G D 33 OK 4178 4181 4182 4203 C3' C D 34 OK 4201 4204 4205 4223 C3' C D 35 OK 4221 4224 4225 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3261 C4' G C 13 OK 3263 3260 3262 3284 C4' G C 14 OK 3286 3283 3285 3307 C4' C C 15 OK 3309 3306 3308 3327 C4' G C 16 OK 3329 3326 3328 3350 C4' U C 17 OK 3352 3349 3351 3370 C4' U C 18 OK 3372 3369 3371 3390 C4' G C 19 OK 3392 3389 3391 3413 C4' C C 20 OK 3415 3412 3414 3433 C4' C C 21 OK 3435 3432 3434 3453 C4' G C 22 OK 3455 3452 3454 3476 C4' G C 23 OK 3478 3475 3477 3499 C4' U C 24 OK 3501 3498 3500 3519 C4' C C 25 OK 3521 3518 3520 3539 C4' U C 26 OK 3541 3538 3540 3559 C4' G C 27 OK 3561 3558 3560 3582 C4' G C 28 OK 3584 3581 3583 3605 C4' C C 29 OK 3607 3604 3606 3625 C4' A C 30 OK 3627 3624 3626 3647 C4' A C 31 OK 3649 3646 3648 3669 C4' C C 32 OK 3671 3668 3670 3689 C4' G C 33 OK 3691 3688 3690 3712 C4' C C 34 OK 3714 3711 3713 3732 C4' C C 35 OK 3734 3731 3733 3750 C4' G D 13 OK 3752 3749 3751 3773 C4' G D 14 OK 3775 3772 3774 3796 C4' C D 15 OK 3798 3795 3797 3816 C4' G D 16 OK 3818 3815 3817 3839 C4' U D 17 OK 3841 3838 3840 3859 C4' U D 18 OK 3861 3858 3860 3879 C4' G D 19 OK 3881 3878 3880 3902 C4' C D 20 OK 3904 3901 3903 3922 C4' C D 21 OK 3924 3921 3923 3942 C4' G D 22 OK 3944 3941 3943 3965 C4' G D 23 OK 3967 3964 3966 3988 C4' U D 24 OK 3990 3987 3989 4008 C4' C D 25 OK 4010 4007 4009 4028 C4' U D 26 OK 4030 4027 4029 4048 C4' G D 27 OK 4050 4047 4049 4071 C4' G D 28 OK 4073 4070 4072 4094 C4' C D 29 OK 4096 4093 4095 4114 C4' A D 30 OK 4116 4113 4115 4136 C4' A D 31 OK 4138 4135 4137 4158 C4' C D 32 OK 4160 4157 4159 4178 C4' G D 33 OK 4180 4177 4179 4201 C4' C D 34 OK 4203 4200 4202 4221 C4' C D 35 OK 4223 4220 4222 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3260 C5' G C 13 3259 3261 3283 C5' G C 14 3282 3284 3306 C5' C C 15 3305 3307 3326 C5' G C 16 3325 3327 3349 C5' U C 17 3348 3350 3369 C5' U C 18 3368 3370 3389 C5' G C 19 3388 3390 3412 C5' C C 20 3411 3413 3432 C5' C C 21 3431 3433 3452 C5' G C 22 3451 3453 3475 C5' G C 23 3474 3476 3498 C5' U C 24 3497 3499 3518 C5' C C 25 3517 3519 3538 C5' U C 26 3537 3539 3558 C5' G C 27 3557 3559 3581 C5' G C 28 3580 3582 3604 C5' C C 29 3603 3605 3624 C5' A C 30 3623 3625 3646 C5' A C 31 3645 3647 3668 C5' C C 32 3667 3669 3688 C5' G C 33 3687 3689 3711 C5' C C 34 3710 3712 3731 C5' C C 35 3730 3732 3749 C5' G D 13 3748 3750 3772 C5' G D 14 3771 3773 3795 C5' C D 15 3794 3796 3815 C5' G D 16 3814 3816 3838 C5' U D 17 3837 3839 3858 C5' U D 18 3857 3859 3878 C5' G D 19 3877 3879 3901 C5' C D 20 3900 3902 3921 C5' C D 21 3920 3922 3941 C5' G D 22 3940 3942 3964 C5' G D 23 3963 3965 3987 C5' U D 24 3986 3988 4007 C5' C D 25 4006 4008 4027 C5' U D 26 4026 4028 4047 C5' G D 27 4046 4048 4070 C5' G D 28 4069 4071 4093 C5' C D 29 4092 4094 4113 C5' A D 30 4112 4114 4135 C5' A D 31 4134 4136 4157 C5' C D 32 4156 4158 4177 C5' G D 33 4176 4178 4200 C5' C D 34 4199 4201 4220 C5' C D 35 4219 4221 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3279 P G C 14 distorted distorted 3264 3280 3281 3282 3302 P C C 15 distorted distorted 3287 3303 3304 3305 3322 P G C 16 distorted distorted 3310 3323 3324 3325 3345 P U C 17 distorted distorted 3330 3346 3347 3348 3365 P U C 18 distorted distorted 3353 3366 3367 3368 3385 P G C 19 distorted distorted 3373 3386 3387 3388 3408 P C C 20 distorted distorted 3393 3409 3410 3411 3428 P C C 21 distorted distorted 3416 3429 3430 3431 3448 P G C 22 distorted distorted 3436 3449 3450 3451 3471 P G C 23 distorted distorted 3456 3472 3473 3474 3494 P U C 24 distorted distorted 3479 3495 3496 3497 3514 P C C 25 distorted distorted 3502 3515 3516 3517 3534 P U C 26 distorted distorted 3522 3535 3536 3537 3554 P G C 27 distorted distorted 3542 3555 3556 3557 3577 P G C 28 distorted distorted 3562 3578 3579 3580 3600 P C C 29 distorted distorted 3585 3601 3602 3603 3620 P A C 30 distorted distorted 3608 3621 3622 3623 3642 P A C 31 distorted distorted 3628 3643 3644 3645 3664 P C C 32 distorted distorted 3650 3665 3666 3667 3684 P G C 33 distorted distorted 3672 3685 3686 3687 3707 P C C 34 distorted distorted 3692 3708 3709 3710 3727 P C C 35 distorted distorted 3715 3728 3729 3730 3768 P G D 14 distorted distorted 3753 3769 3770 3771 3791 P C D 15 distorted distorted 3776 3792 3793 3794 3811 P G D 16 distorted distorted 3799 3812 3813 3814 3834 P U D 17 distorted distorted 3819 3835 3836 3837 3854 P U D 18 distorted distorted 3842 3855 3856 3857 3874 P G D 19 distorted distorted 3862 3875 3876 3877 3897 P C D 20 distorted distorted 3882 3898 3899 3900 3917 P C D 21 distorted distorted 3905 3918 3919 3920 3937 P G D 22 distorted distorted 3925 3938 3939 3940 3960 P G D 23 distorted distorted 3945 3961 3962 3963 3983 P U D 24 distorted distorted 3968 3984 3985 3986 4003 P C D 25 distorted distorted 3991 4004 4005 4006 4023 P U D 26 distorted distorted 4011 4024 4025 4026 4043 P G D 27 distorted distorted 4031 4044 4045 4046 4066 P G D 28 distorted distorted 4051 4067 4068 4069 4089 P C D 29 distorted distorted 4074 4090 4091 4092 4109 P A D 30 distorted distorted 4097 4110 4111 4112 4131 P A D 31 distorted distorted 4117 4132 4133 4134 4153 P C D 32 distorted distorted 4139 4154 4155 4156 4173 P G D 33 distorted distorted 4161 4174 4175 4176 4196 P C D 34 distorted distorted 4181 4197 4198 4199 4216 P C D 35 distorted distorted 4204 4217 4218 4219 ---------------------------------------------------------------------------------