ID code: '1DZ5' 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' --------------------------------------------------------------------------------- 3343 C1' G C 8 alpha beta 3338 3361 3344 3341 3378 C1' A C 9 alpha beta 3373 3395 3379 3376 3411 C1' G C 10 alpha beta 3406 3429 3412 3409 3445 C1' A C 11 alpha beta 3440 3462 3446 3443 3478 C1' C C 12 alpha beta 3473 3493 3479 3476 3509 C1' A C 13 alpha beta 3504 3526 3510 3507 3542 C1' U C 14 alpha beta 3537 3557 3543 3540 3572 C1' U C 15 alpha beta 3567 3587 3573 3570 3602 C1' G C 16 alpha beta 3597 3620 3603 3600 3636 C1' C C 17 alpha beta 3631 3651 3637 3634 3667 C1' A C 18 alpha beta 3662 3684 3668 3665 3700 C1' C C 19 alpha beta 3695 3715 3701 3698 3731 C1' C C 20 alpha beta 3726 3746 3732 3729 3762 C1' C C 21 alpha beta 3757 3777 3763 3760 3793 C1' G C 22 alpha beta 3788 3811 3794 3791 3827 C1' G C 23 alpha beta 3822 3845 3828 3825 3861 C1' A C 24 alpha beta 3856 3878 3862 3859 3894 C1' G C 25 alpha beta 3889 3912 3895 3892 3928 C1' U C 26 alpha beta 3923 3943 3929 3926 3958 C1' C C 27 alpha beta 3953 3973 3959 3956 3989 C1' U C 28 alpha beta 3984 4004 3990 3987 4019 C1' C C 29 alpha beta 4014 4034 4020 4017 4049 C1' G D 34 alpha beta 4044 4067 4050 4047 4084 C1' A D 35 alpha beta 4079 4101 4085 4082 4117 C1' G D 36 alpha beta 4112 4135 4118 4115 4151 C1' A D 37 alpha beta 4146 4168 4152 4149 4184 C1' C D 38 alpha beta 4179 4199 4185 4182 4215 C1' A D 39 alpha beta 4210 4232 4216 4213 4248 C1' U D 40 alpha beta 4243 4263 4249 4246 4278 C1' U D 41 alpha beta 4273 4293 4279 4276 4308 C1' G D 42 alpha beta 4303 4326 4309 4306 4342 C1' C D 43 alpha beta 4337 4357 4343 4340 4373 C1' A D 44 alpha beta 4368 4390 4374 4371 4406 C1' C D 45 alpha beta 4401 4421 4407 4404 4437 C1' C D 46 alpha beta 4432 4452 4438 4435 4468 C1' C D 47 alpha beta 4463 4483 4469 4466 4499 C1' G D 48 alpha beta 4494 4517 4500 4497 4533 C1' G D 49 alpha beta 4528 4551 4534 4531 4567 C1' A D 50 alpha beta 4562 4584 4568 4565 4600 C1' G D 51 alpha beta 4595 4618 4601 4598 4634 C1' U D 52 alpha beta 4629 4649 4635 4632 4664 C1' C D 53 alpha beta 4659 4679 4665 4662 4695 C1' U D 54 alpha beta 4690 4710 4696 4693 4725 C1' C D 55 alpha beta 4720 4740 4726 4723 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3341 C2' G C 8 OK OK 3343 3339 3359 3342 3376 C2' A C 9 OK OK 3378 3374 3393 3377 3409 C2' G C 10 OK OK 3411 3407 3427 3410 3443 C2' A C 11 OK OK 3445 3441 3460 3444 3476 C2' C C 12 OK OK 3478 3474 3491 3477 3507 C2' A C 13 OK OK 3509 3505 3524 3508 3540 C2' U C 14 OK OK 3542 3538 3555 3541 3570 C2' U C 15 OK OK 3572 3568 3585 3571 3600 C2' G C 16 OK OK 3602 3598 3618 3601 3634 C2' C C 17 OK OK 3636 3632 3649 3635 3665 C2' A C 18 OK OK 3667 3663 3682 3666 3698 C2' C C 19 OK OK 3700 3696 3713 3699 3729 C2' C C 20 OK OK 3731 3727 3744 3730 3760 C2' C C 21 OK OK 3762 3758 3775 3761 3791 C2' G C 22 OK OK 3793 3789 3809 3792 3825 C2' G C 23 OK OK 3827 3823 3843 3826 3859 C2' A C 24 OK OK 3861 3857 3876 3860 3892 C2' G C 25 OK OK 3894 3890 3910 3893 3926 C2' U C 26 OK OK 3928 3924 3941 3927 3956 C2' C C 27 OK OK 3958 3954 3971 3957 3987 C2' U C 28 OK OK 3989 3985 4002 3988 4017 C2' C C 29 OK OK 4019 4015 4032 4018 4047 C2' G D 34 OK OK 4049 4045 4065 4048 4082 C2' A D 35 OK OK 4084 4080 4099 4083 4115 C2' G D 36 OK OK 4117 4113 4133 4116 4149 C2' A D 37 OK OK 4151 4147 4166 4150 4182 C2' C D 38 OK OK 4184 4180 4197 4183 4213 C2' A D 39 OK OK 4215 4211 4230 4214 4246 C2' U D 40 OK OK 4248 4244 4261 4247 4276 C2' U D 41 OK OK 4278 4274 4291 4277 4306 C2' G D 42 OK OK 4308 4304 4324 4307 4340 C2' C D 43 OK OK 4342 4338 4355 4341 4371 C2' A D 44 OK OK 4373 4369 4388 4372 4404 C2' C D 45 OK OK 4406 4402 4419 4405 4435 C2' C D 46 OK OK 4437 4433 4450 4436 4466 C2' C D 47 OK OK 4468 4464 4481 4467 4497 C2' G D 48 OK OK 4499 4495 4515 4498 4531 C2' G D 49 OK OK 4533 4529 4549 4532 4565 C2' A D 50 OK OK 4567 4563 4582 4566 4598 C2' G D 51 OK OK 4600 4596 4616 4599 4632 C2' U D 52 OK OK 4634 4630 4647 4633 4662 C2' C D 53 OK OK 4664 4660 4677 4663 4693 C2' U D 54 OK OK 4695 4691 4708 4694 4723 C2' C D 55 OK OK 4725 4721 4738 4724 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3339 C3' G C 8 OK OK 3337 3358 3340 3341 3374 C3' A C 9 OK OK 3372 3392 3375 3376 3407 C3' G C 10 OK OK 3405 3426 3408 3409 3441 C3' A C 11 OK OK 3439 3459 3442 3443 3474 C3' C C 12 OK OK 3472 3490 3475 3476 3505 C3' A C 13 OK OK 3503 3523 3506 3507 3538 C3' U C 14 OK OK 3536 3554 3539 3540 3568 C3' U C 15 OK OK 3566 3584 3569 3570 3598 C3' G C 16 OK OK 3596 3617 3599 3600 3632 C3' C C 17 OK OK 3630 3648 3633 3634 3663 C3' A C 18 OK OK 3661 3681 3664 3665 3696 C3' C C 19 OK OK 3694 3712 3697 3698 3727 C3' C C 20 OK OK 3725 3743 3728 3729 3758 C3' C C 21 OK OK 3756 3774 3759 3760 3789 C3' G C 22 OK OK 3787 3808 3790 3791 3823 C3' G C 23 OK OK 3821 3842 3824 3825 3857 C3' A C 24 OK OK 3855 3875 3858 3859 3890 C3' G C 25 OK OK 3888 3909 3891 3892 3924 C3' U C 26 OK OK 3922 3940 3925 3926 3954 C3' C C 27 OK OK 3952 3970 3955 3956 3985 C3' U C 28 OK OK 3983 4001 3986 3987 4015 C3' C C 29 OK OK 4013 4031 4016 4017 4045 C3' G D 34 OK OK 4043 4064 4046 4047 4080 C3' A D 35 OK OK 4078 4098 4081 4082 4113 C3' G D 36 OK OK 4111 4132 4114 4115 4147 C3' A D 37 OK OK 4145 4165 4148 4149 4180 C3' C D 38 OK OK 4178 4196 4181 4182 4211 C3' A D 39 OK OK 4209 4229 4212 4213 4244 C3' U D 40 OK OK 4242 4260 4245 4246 4274 C3' U D 41 OK OK 4272 4290 4275 4276 4304 C3' G D 42 OK OK 4302 4323 4305 4306 4338 C3' C D 43 OK OK 4336 4354 4339 4340 4369 C3' A D 44 OK OK 4367 4387 4370 4371 4402 C3' C D 45 OK OK 4400 4418 4403 4404 4433 C3' C D 46 OK OK 4431 4449 4434 4435 4464 C3' C D 47 OK OK 4462 4480 4465 4466 4495 C3' G D 48 OK OK 4493 4514 4496 4497 4529 C3' G D 49 OK OK 4527 4548 4530 4531 4563 C3' A D 50 OK OK 4561 4581 4564 4565 4596 C3' G D 51 OK OK 4594 4615 4597 4598 4630 C3' U D 52 OK OK 4628 4646 4631 4632 4660 C3' C D 53 OK OK 4658 4676 4661 4662 4691 C3' U D 54 OK OK 4689 4707 4692 4693 4721 C3' C D 55 OK OK 4719 4737 4722 4723 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3337 C4' G C 8 OK OK 3339 3357 3336 3338 3372 C4' A C 9 OK OK 3374 3391 3371 3373 3405 C4' G C 10 OK OK 3407 3425 3404 3406 3439 C4' A C 11 OK OK 3441 3458 3438 3440 3472 C4' C C 12 OK OK 3474 3489 3471 3473 3503 C4' A C 13 OK OK 3505 3522 3502 3504 3536 C4' U C 14 OK OK 3538 3553 3535 3537 3566 C4' U C 15 OK OK 3568 3583 3565 3567 3596 C4' G C 16 OK OK 3598 3616 3595 3597 3630 C4' C C 17 OK OK 3632 3647 3629 3631 3661 C4' A C 18 OK OK 3663 3680 3660 3662 3694 C4' C C 19 OK OK 3696 3711 3693 3695 3725 C4' C C 20 OK OK 3727 3742 3724 3726 3756 C4' C C 21 OK OK 3758 3773 3755 3757 3787 C4' G C 22 OK OK 3789 3807 3786 3788 3821 C4' G C 23 OK OK 3823 3841 3820 3822 3855 C4' A C 24 OK OK 3857 3874 3854 3856 3888 C4' G C 25 OK OK 3890 3908 3887 3889 3922 C4' U C 26 OK OK 3924 3939 3921 3923 3952 C4' C C 27 OK OK 3954 3969 3951 3953 3983 C4' U C 28 OK OK 3985 4000 3982 3984 4013 C4' C C 29 OK OK 4015 4030 4012 4014 4043 C4' G D 34 OK OK 4045 4063 4042 4044 4078 C4' A D 35 OK OK 4080 4097 4077 4079 4111 C4' G D 36 OK OK 4113 4131 4110 4112 4145 C4' A D 37 OK OK 4147 4164 4144 4146 4178 C4' C D 38 OK OK 4180 4195 4177 4179 4209 C4' A D 39 OK OK 4211 4228 4208 4210 4242 C4' U D 40 OK OK 4244 4259 4241 4243 4272 C4' U D 41 OK OK 4274 4289 4271 4273 4302 C4' G D 42 OK OK 4304 4322 4301 4303 4336 C4' C D 43 OK OK 4338 4353 4335 4337 4367 C4' A D 44 OK OK 4369 4386 4366 4368 4400 C4' C D 45 OK OK 4402 4417 4399 4401 4431 C4' C D 46 OK OK 4433 4448 4430 4432 4462 C4' C D 47 OK OK 4464 4479 4461 4463 4493 C4' G D 48 OK OK 4495 4513 4492 4494 4527 C4' G D 49 OK OK 4529 4547 4526 4528 4561 C4' A D 50 OK OK 4563 4580 4560 4562 4594 C4' G D 51 OK OK 4596 4614 4593 4595 4628 C4' U D 52 OK OK 4630 4645 4627 4629 4658 C4' C D 53 OK OK 4660 4675 4657 4659 4689 C4' U D 54 OK OK 4691 4706 4688 4690 4719 C4' C D 55 OK OK 4721 4736 4718 4720 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3336 C5' G C 8 OK OK 3335 3355 3356 3337 3371 C5' A C 9 OK OK 3370 3389 3390 3372 3404 C5' G C 10 OK OK 3403 3423 3424 3405 3438 C5' A C 11 OK OK 3437 3456 3457 3439 3471 C5' C C 12 OK OK 3470 3487 3488 3472 3502 C5' A C 13 distorted distorted 3501 3520 3521 3503 3535 C5' U C 14 OK OK 3534 3551 3552 3536 3565 C5' U C 15 distorted distorted 3564 3581 3582 3566 3595 C5' G C 16 OK OK 3594 3614 3615 3596 3629 C5' C C 17 distorted distorted 3628 3645 3646 3630 3660 C5' A C 18 OK OK 3659 3678 3679 3661 3693 C5' C C 19 OK OK 3692 3709 3710 3694 3724 C5' C C 20 OK OK 3723 3740 3741 3725 3755 C5' C C 21 OK OK 3754 3771 3772 3756 3786 C5' G C 22 distorted distorted 3785 3805 3806 3787 3820 C5' G C 23 OK OK 3819 3839 3840 3821 3854 C5' A C 24 OK OK 3853 3872 3873 3855 3887 C5' G C 25 OK OK 3886 3906 3907 3888 3921 C5' U C 26 OK OK 3920 3937 3938 3922 3951 C5' C C 27 OK OK 3950 3967 3968 3952 3982 C5' U C 28 OK OK 3981 3998 3999 3983 4012 C5' C C 29 OK OK 4011 4028 4029 4013 4042 C5' G D 34 OK OK 4041 4061 4062 4043 4077 C5' A D 35 OK OK 4076 4095 4096 4078 4110 C5' G D 36 distorted distorted 4109 4129 4130 4111 4144 C5' A D 37 OK OK 4143 4162 4163 4145 4177 C5' C D 38 OK OK 4176 4193 4194 4178 4208 C5' A D 39 distorted distorted 4207 4226 4227 4209 4241 C5' U D 40 OK OK 4240 4257 4258 4242 4271 C5' U D 41 distorted distorted 4270 4287 4288 4272 4301 C5' G D 42 OK OK 4300 4320 4321 4302 4335 C5' C D 43 distorted distorted 4334 4351 4352 4336 4366 C5' A D 44 distorted distorted 4365 4384 4385 4367 4399 C5' C D 45 OK OK 4398 4415 4416 4400 4430 C5' C D 46 OK OK 4429 4446 4447 4431 4461 C5' C D 47 OK OK 4460 4477 4478 4462 4492 C5' G D 48 OK OK 4491 4511 4512 4493 4526 C5' G D 49 OK OK 4525 4545 4546 4527 4560 C5' A D 50 OK OK 4559 4578 4579 4561 4593 C5' G D 51 OK OK 4592 4612 4613 4594 4627 C5' U D 52 OK OK 4626 4643 4644 4628 4657 C5' C D 53 distorted distorted 4656 4673 4674 4658 4688 C5' U D 54 distorted distorted 4687 4704 4705 4689 4718 C5' C D 55 OK OK 4717 4734 4735 4719 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3367 P A C 9 distorted distorted 3340 3368 3369 3370 3400 P G C 10 distorted distorted 3375 3401 3402 3403 3434 P A C 11 distorted distorted 3408 3435 3436 3437 3467 P C C 12 distorted distorted 3442 3468 3469 3470 3498 P A C 13 distorted distorted 3475 3499 3500 3501 3531 P U C 14 distorted distorted 3506 3532 3533 3534 3561 P U C 15 distorted distorted 3539 3562 3563 3564 3591 P G C 16 distorted distorted 3569 3592 3593 3594 3625 P C C 17 distorted distorted 3599 3626 3627 3628 3656 P A C 18 distorted distorted 3633 3657 3658 3659 3689 P C C 19 distorted distorted 3664 3690 3691 3692 3720 P C C 20 distorted distorted 3697 3721 3722 3723 3751 P C C 21 distorted distorted 3728 3752 3753 3754 3782 P G C 22 distorted distorted 3759 3783 3784 3785 3816 P G C 23 distorted distorted 3790 3817 3818 3819 3850 P A C 24 distorted distorted 3824 3851 3852 3853 3883 P G C 25 distorted distorted 3858 3884 3885 3886 3917 P U C 26 distorted distorted 3891 3918 3919 3920 3947 P C C 27 distorted distorted 3925 3948 3949 3950 3978 P U C 28 distorted distorted 3955 3979 3980 3981 4008 P C C 29 distorted distorted 3986 4009 4010 4011 4073 P A D 35 distorted distorted 4046 4074 4075 4076 4106 P G D 36 distorted distorted 4081 4107 4108 4109 4140 P A D 37 distorted distorted 4114 4141 4142 4143 4173 P C D 38 distorted distorted 4148 4174 4175 4176 4204 P A D 39 distorted distorted 4181 4205 4206 4207 4237 P U D 40 distorted distorted 4212 4238 4239 4240 4267 P U D 41 distorted distorted 4245 4268 4269 4270 4297 P G D 42 distorted distorted 4275 4298 4299 4300 4331 P C D 43 distorted distorted 4305 4332 4333 4334 4362 P A D 44 distorted distorted 4339 4363 4364 4365 4395 P C D 45 distorted distorted 4370 4396 4397 4398 4426 P C D 46 distorted distorted 4403 4427 4428 4429 4457 P C D 47 distorted distorted 4434 4458 4459 4460 4488 P G D 48 distorted distorted 4465 4489 4490 4491 4522 P G D 49 distorted distorted 4496 4523 4524 4525 4556 P A D 50 distorted distorted 4530 4557 4558 4559 4589 P G D 51 distorted distorted 4564 4590 4591 4592 4623 P U D 52 distorted distorted 4597 4624 4625 4626 4653 P C D 53 distorted distorted 4631 4654 4655 4656 4684 P U D 54 distorted distorted 4661 4685 4686 4687 4714 P C D 55 distorted distorted 4692 4715 4716 4717 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