ID code: '4ZLR' 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' --------------------------------------------------------------------------------- 4389 C1' U C 1 alpha beta 4384 4404 4390 4387 4420 C1' U C 2 alpha beta 4415 4435 4421 4418 4450 C1' G C 3 alpha beta 4445 4468 4451 4448 4484 C1' U C 4 alpha beta 4479 4499 4485 4482 4514 C1' U C 5 alpha beta 4509 4529 4515 4512 4544 C1' G C 6 alpha beta 4539 4562 4545 4542 4578 C1' U C 7 4573 4576 4596 C1' U C 8 alpha beta 4591 4611 4597 4594 4626 C1' U C 9 alpha beta 4621 4641 4627 4624 4656 C1' U C 10 alpha beta 4651 4671 4657 4654 4686 C1' U C 11 alpha beta 4681 4701 4687 4684 4716 C1' U C 12 alpha beta 4711 4731 4717 4714 4746 C1' U C 13 alpha beta 4741 4761 4747 4744 4776 C1' U C 14 alpha beta 4771 4791 4777 4774 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4387 C2' U C 1 OK OK 4389 4385 4402 4388 4418 C2' U C 2 OK OK 4420 4416 4433 4419 4448 C2' G C 3 OK OK 4450 4446 4466 4449 4482 C2' U C 4 OK OK 4484 4480 4497 4483 4512 C2' U C 5 OK OK 4514 4510 4527 4513 4542 C2' G C 6 OK OK 4544 4540 4560 4543 4576 C2' U C 7 OK OK 4578 4574 4583 4577 4594 C2' U C 8 OK OK 4596 4592 4609 4595 4624 C2' U C 9 OK OK 4626 4622 4639 4625 4654 C2' U C 10 OK OK 4656 4652 4669 4655 4684 C2' U C 11 OK OK 4686 4682 4699 4685 4714 C2' U C 12 OK OK 4716 4712 4729 4715 4744 C2' U C 13 OK OK 4746 4742 4759 4745 4774 C2' U C 14 OK OK 4776 4772 4789 4775 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4385 C3' U C 1 OK OK 4383 4401 4386 4387 4416 C3' U C 2 OK OK 4414 4432 4417 4418 4446 C3' G C 3 OK OK 4444 4465 4447 4448 4480 C3' U C 4 OK OK 4478 4496 4481 4482 4510 C3' U C 5 OK OK 4508 4526 4511 4512 4540 C3' G C 6 OK OK 4538 4559 4541 4542 4574 C3' U C 7 OK OK 4572 4582 4575 4576 4592 C3' U C 8 OK OK 4590 4608 4593 4594 4622 C3' U C 9 OK OK 4620 4638 4623 4624 4652 C3' U C 10 OK OK 4650 4668 4653 4654 4682 C3' U C 11 OK OK 4680 4698 4683 4684 4712 C3' U C 12 OK OK 4710 4728 4713 4714 4742 C3' U C 13 OK OK 4740 4758 4743 4744 4772 C3' U C 14 OK OK 4770 4788 4773 4774 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4383 C4' U C 1 OK OK 4385 4400 4382 4384 4414 C4' U C 2 OK OK 4416 4431 4413 4415 4444 C4' G C 3 OK OK 4446 4464 4443 4445 4478 C4' U C 4 OK OK 4480 4495 4477 4479 4508 C4' U C 5 OK OK 4510 4525 4507 4509 4538 C4' G C 6 OK OK 4540 4558 4537 4539 4572 C4' U C 7 OK OK 4574 4581 4571 4573 4590 C4' U C 8 OK OK 4592 4607 4589 4591 4620 C4' U C 9 OK OK 4622 4637 4619 4621 4650 C4' U C 10 OK OK 4652 4667 4649 4651 4680 C4' U C 11 OK OK 4682 4697 4679 4681 4710 C4' U C 12 OK OK 4712 4727 4709 4711 4740 C4' U C 13 OK OK 4742 4757 4739 4741 4770 C4' U C 14 OK OK 4772 4787 4769 4771 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4382 C5' U C 1 OK OK 4381 4398 4399 4383 4413 C5' U C 2 OK OK 4412 4429 4430 4414 4443 C5' G C 3 OK OK 4442 4462 4463 4444 4477 C5' U C 4 OK OK 4476 4493 4494 4478 4507 C5' U C 5 OK OK 4506 4523 4524 4508 4537 C5' G C 6 OK OK 4536 4556 4557 4538 4571 C5' U C 7 OK OK 4570 4579 4580 4572 4589 C5' U C 8 OK OK 4588 4605 4606 4590 4619 C5' U C 9 OK OK 4618 4635 4636 4620 4649 C5' U C 10 OK OK 4648 4665 4666 4650 4679 C5' U C 11 OK OK 4678 4695 4696 4680 4709 C5' U C 12 OK OK 4708 4725 4726 4710 4739 C5' U C 13 OK OK 4738 4755 4756 4740 4769 C5' U C 14 OK OK 4768 4785 4786 4770 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4409 P U C 2 distorted distorted 4386 4410 4411 4412 4439 P G C 3 distorted distorted 4417 4440 4441 4442 4473 P U C 4 distorted distorted 4447 4474 4475 4476 4503 P U C 5 distorted distorted 4481 4504 4505 4506 4533 P G C 6 distorted distorted 4511 4534 4535 4536 4567 P U C 7 distorted distorted 4541 4568 4569 4570 4585 P U C 8 distorted distorted 4575 4586 4587 4588 4615 P U C 9 distorted distorted 4593 4616 4617 4618 4645 P U C 10 distorted distorted 4623 4646 4647 4648 4675 P U C 11 distorted distorted 4653 4676 4677 4678 4705 P U C 12 distorted distorted 4683 4706 4707 4708 4735 P U C 13 distorted distorted 4713 4736 4737 4738 4765 P U C 14 distorted distorted 4743 4766 4767 4768 ---------------------------------------------------------------------------------