ID code: '1MJO' 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' --------------------------------------------------------------------------------- 3412 C1' T F 0 beta 3408 3413 3411 3432 C1' A F 1 beta 3428 3433 3431 3453 C1' G F 2 beta 3449 3454 3452 3475 C1' A F 3 beta 3471 3476 3474 3496 C1' C F 4 beta 3492 3497 3495 3515 C1' G F 5 beta 3511 3516 3514 3537 C1' T F 6 beta 3533 3538 3536 3557 C1' C F 7 beta 3553 3558 3556 3576 C1' A F 8 beta 3572 3577 3575 3597 C1' T F 9 beta 3593 3598 3596 3617 C1' G F 10 beta 3613 3618 3616 3639 C1' A F 11 beta 3635 3640 3638 3660 C1' C F 12 beta 3656 3661 3659 3679 C1' G F 13 beta 3675 3680 3678 3701 C1' T F 14 beta 3697 3702 3700 3721 C1' C F 15 beta 3717 3722 3720 3740 C1' T F 16 beta 3736 3741 3739 3760 C1' A F 17 beta 3756 3761 3759 3799 C1' T G 0 beta 3795 3800 3798 3819 C1' A G 1 beta 3815 3820 3818 3840 C1' G G 2 beta 3836 3841 3839 3862 C1' A G 3 beta 3858 3863 3861 3883 C1' C G 4 beta 3879 3884 3882 3902 C1' G G 5 beta 3898 3903 3901 3924 C1' T G 6 beta 3920 3925 3923 3944 C1' C G 7 beta 3940 3945 3943 3963 C1' A G 8 beta 3959 3964 3962 3984 C1' T G 9 beta 3980 3985 3983 4004 C1' G G 10 beta 4000 4005 4003 4026 C1' A G 11 beta 4022 4027 4025 4047 C1' C G 12 beta 4043 4048 4046 4066 C1' G G 13 beta 4062 4067 4065 4088 C1' T G 14 beta 4084 4089 4087 4108 C1' C G 15 beta 4104 4109 4107 4127 C1' T G 16 beta 4123 4128 4126 4147 C1' A G 17 beta 4143 4148 4146 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3411 C2' T F 0 3412 3409 3431 C2' A F 1 3432 3429 3452 C2' G F 2 3453 3450 3474 C2' A F 3 3475 3472 3495 C2' C F 4 3496 3493 3514 C2' G F 5 3515 3512 3536 C2' T F 6 3537 3534 3556 C2' C F 7 3557 3554 3575 C2' A F 8 3576 3573 3596 C2' T F 9 3597 3594 3616 C2' G F 10 3617 3614 3638 C2' A F 11 3639 3636 3659 C2' C F 12 3660 3657 3678 C2' G F 13 3679 3676 3700 C2' T F 14 3701 3698 3720 C2' C F 15 3721 3718 3739 C2' T F 16 3740 3737 3759 C2' A F 17 3760 3757 3798 C2' T G 0 3799 3796 3818 C2' A G 1 3819 3816 3839 C2' G G 2 3840 3837 3861 C2' A G 3 3862 3859 3882 C2' C G 4 3883 3880 3901 C2' G G 5 3902 3899 3923 C2' T G 6 3924 3921 3943 C2' C G 7 3944 3941 3962 C2' A G 8 3963 3960 3983 C2' T G 9 3984 3981 4003 C2' G G 10 4004 4001 4025 C2' A G 11 4026 4023 4046 C2' C G 12 4047 4044 4065 C2' G G 13 4066 4063 4087 C2' T G 14 4088 4085 4107 C2' C G 15 4108 4105 4126 C2' T G 16 4127 4124 4146 C2' A G 17 4147 4144 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3409 C3' T F 0 OK 3407 3410 3411 3429 C3' A F 1 OK 3427 3430 3431 3450 C3' G F 2 OK 3448 3451 3452 3472 C3' A F 3 OK 3470 3473 3474 3493 C3' C F 4 OK 3491 3494 3495 3512 C3' G F 5 OK 3510 3513 3514 3534 C3' T F 6 OK 3532 3535 3536 3554 C3' C F 7 OK 3552 3555 3556 3573 C3' A F 8 OK 3571 3574 3575 3594 C3' T F 9 OK 3592 3595 3596 3614 C3' G F 10 OK 3612 3615 3616 3636 C3' A F 11 OK 3634 3637 3638 3657 C3' C F 12 OK 3655 3658 3659 3676 C3' G F 13 OK 3674 3677 3678 3698 C3' T F 14 OK 3696 3699 3700 3718 C3' C F 15 OK 3716 3719 3720 3737 C3' T F 16 OK 3735 3738 3739 3757 C3' A F 17 OK 3755 3758 3759 3796 C3' T G 0 OK 3794 3797 3798 3816 C3' A G 1 OK 3814 3817 3818 3837 C3' G G 2 OK 3835 3838 3839 3859 C3' A G 3 OK 3857 3860 3861 3880 C3' C G 4 OK 3878 3881 3882 3899 C3' G G 5 OK 3897 3900 3901 3921 C3' T G 6 OK 3919 3922 3923 3941 C3' C G 7 OK 3939 3942 3943 3960 C3' A G 8 OK 3958 3961 3962 3981 C3' T G 9 OK 3979 3982 3983 4001 C3' G G 10 OK 3999 4002 4003 4023 C3' A G 11 OK 4021 4024 4025 4044 C3' C G 12 OK 4042 4045 4046 4063 C3' G G 13 OK 4061 4064 4065 4085 C3' T G 14 OK 4083 4086 4087 4105 C3' C G 15 OK 4103 4106 4107 4124 C3' T G 16 OK 4122 4125 4126 4144 C3' A G 17 OK 4142 4145 4146 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3407 C4' T F 0 OK 3409 3406 3408 3427 C4' A F 1 OK 3429 3426 3428 3448 C4' G F 2 OK 3450 3447 3449 3470 C4' A F 3 OK 3472 3469 3471 3491 C4' C F 4 OK 3493 3490 3492 3510 C4' G F 5 OK 3512 3509 3511 3532 C4' T F 6 OK 3534 3531 3533 3552 C4' C F 7 OK 3554 3551 3553 3571 C4' A F 8 OK 3573 3570 3572 3592 C4' T F 9 OK 3594 3591 3593 3612 C4' G F 10 OK 3614 3611 3613 3634 C4' A F 11 OK 3636 3633 3635 3655 C4' C F 12 OK 3657 3654 3656 3674 C4' G F 13 OK 3676 3673 3675 3696 C4' T F 14 OK 3698 3695 3697 3716 C4' C F 15 OK 3718 3715 3717 3735 C4' T F 16 OK 3737 3734 3736 3755 C4' A F 17 OK 3757 3754 3756 3794 C4' T G 0 OK 3796 3793 3795 3814 C4' A G 1 OK 3816 3813 3815 3835 C4' G G 2 OK 3837 3834 3836 3857 C4' A G 3 OK 3859 3856 3858 3878 C4' C G 4 OK 3880 3877 3879 3897 C4' G G 5 OK 3899 3896 3898 3919 C4' T G 6 OK 3921 3918 3920 3939 C4' C G 7 OK 3941 3938 3940 3958 C4' A G 8 OK 3960 3957 3959 3979 C4' T G 9 OK 3981 3978 3980 3999 C4' G G 10 OK 4001 3998 4000 4021 C4' A G 11 OK 4023 4020 4022 4042 C4' C G 12 OK 4044 4041 4043 4061 C4' G G 13 OK 4063 4060 4062 4083 C4' T G 14 OK 4085 4082 4084 4103 C4' C G 15 OK 4105 4102 4104 4122 C4' T G 16 OK 4124 4121 4123 4142 C4' A G 17 OK 4144 4141 4143 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3406 C5' T F 0 3405 3407 3426 C5' A F 1 3425 3427 3447 C5' G F 2 3446 3448 3469 C5' A F 3 3468 3470 3490 C5' C F 4 3489 3491 3509 C5' G F 5 3508 3510 3531 C5' T F 6 3530 3532 3551 C5' C F 7 3550 3552 3570 C5' A F 8 3569 3571 3591 C5' T F 9 3590 3592 3611 C5' G F 10 3610 3612 3633 C5' A F 11 3632 3634 3654 C5' C F 12 3653 3655 3673 C5' G F 13 3672 3674 3695 C5' T F 14 3694 3696 3715 C5' C F 15 3714 3716 3734 C5' T F 16 3733 3735 3754 C5' A F 17 3753 3755 3793 C5' T G 0 3792 3794 3813 C5' A G 1 3812 3814 3834 C5' G G 2 3833 3835 3856 C5' A G 3 3855 3857 3877 C5' C G 4 3876 3878 3896 C5' G G 5 3895 3897 3918 C5' T G 6 3917 3919 3938 C5' C G 7 3937 3939 3957 C5' A G 8 3956 3958 3978 C5' T G 9 3977 3979 3998 C5' G G 10 3997 3999 4020 C5' A G 11 4019 4021 4041 C5' C G 12 4040 4042 4060 C5' G G 13 4059 4061 4082 C5' T G 14 4081 4083 4102 C5' C G 15 4101 4103 4121 C5' T G 16 4120 4122 4141 C5' A G 17 4140 4142 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3422 P A F 1 distorted distorted 3410 3423 3424 3425 3443 P G F 2 distorted distorted 3430 3444 3445 3446 3465 P A F 3 distorted distorted 3451 3466 3467 3468 3486 P C F 4 distorted distorted 3473 3487 3488 3489 3505 P G F 5 distorted distorted 3494 3506 3507 3508 3527 P T F 6 distorted distorted 3513 3528 3529 3530 3547 P C F 7 distorted distorted 3535 3548 3549 3550 3566 P A F 8 distorted distorted 3555 3567 3568 3569 3587 P T F 9 distorted distorted 3574 3588 3589 3590 3607 P G F 10 distorted distorted 3595 3608 3609 3610 3629 P A F 11 distorted distorted 3615 3630 3631 3632 3650 P C F 12 distorted distorted 3637 3651 3652 3653 3669 P G F 13 distorted distorted 3658 3670 3671 3672 3691 P T F 14 distorted distorted 3677 3692 3693 3694 3711 P C F 15 distorted distorted 3699 3712 3713 3714 3730 P T F 16 distorted distorted 3719 3731 3732 3733 3750 P A F 17 distorted distorted 3738 3751 3752 3753 3809 P A G 1 distorted distorted 3797 3810 3811 3812 3830 P G G 2 distorted distorted 3817 3831 3832 3833 3852 P A G 3 distorted distorted 3838 3853 3854 3855 3873 P C G 4 distorted distorted 3860 3874 3875 3876 3892 P G G 5 distorted distorted 3881 3893 3894 3895 3914 P T G 6 distorted distorted 3900 3915 3916 3917 3934 P C G 7 distorted distorted 3922 3935 3936 3937 3953 P A G 8 distorted distorted 3942 3954 3955 3956 3974 P T G 9 distorted distorted 3961 3975 3976 3977 3994 P G G 10 distorted distorted 3982 3995 3996 3997 4016 P A G 11 distorted distorted 4002 4017 4018 4019 4037 P C G 12 distorted distorted 4024 4038 4039 4040 4056 P G G 13 distorted distorted 4045 4057 4058 4059 4078 P T G 14 distorted distorted 4064 4079 4080 4081 4098 P C G 15 distorted distorted 4086 4099 4100 4101 4117 P T G 16 distorted distorted 4106 4118 4119 4120 4137 P A G 17 distorted distorted 4125 4138 4139 4140 ---------------------------------------------------------------------------------