ID code: '1BF5' 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' --------------------------------------------------------------------------------- 4415 C1' C B1002 beta 4411 4416 4414 4434 C1' A B1003 beta 4430 4435 4433 4455 C1' G B1004 beta 4451 4456 4454 4477 C1' T B1005 beta 4473 4478 4476 4497 C1' T B1006 beta 4493 4498 4496 4517 C1' T B1007 beta 4513 4518 4516 4537 C1' C B1008 beta 4533 4538 4536 4556 C1' C B1009 beta 4552 4557 4555 4575 C1' C B1010 beta 4571 4576 4574 4594 C1' G B1011 beta 4590 4595 4593 4616 C1' T B1012 beta 4612 4617 4615 4636 C1' A B1013 beta 4632 4637 4635 4657 C1' A B1014 beta 4653 4658 4656 4678 C1' A B1015 beta 4674 4679 4677 4699 C1' T B1016 beta 4695 4700 4698 4719 C1' G B1017 beta 4715 4720 4718 4741 C1' C B1018 beta 4737 4742 4740 4778 C1' G C2002 beta 4774 4779 4777 4800 C1' C C2003 beta 4796 4801 4799 4819 C1' A C2004 beta 4815 4820 4818 4840 C1' T C2005 beta 4836 4841 4839 4860 C1' T C2006 beta 4856 4861 4859 4880 C1' T C2007 beta 4876 4881 4879 4900 C1' A C2008 beta 4896 4901 4899 4921 C1' C C2009 beta 4917 4922 4920 4940 C1' G C2010 beta 4936 4941 4939 4962 C1' G C2011 beta 4958 4963 4961 4984 C1' G C2012 beta 4980 4985 4983 5006 C1' A C2013 beta 5002 5007 5005 5027 C1' A C2014 beta 5023 5028 5026 5048 C1' A C2015 beta 5044 5049 5047 5069 C1' C C2016 beta 5065 5070 5068 5088 C1' T C2017 beta 5084 5089 5087 5108 C1' G C2018 beta 5104 5109 5107 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4414 C2' C B1002 4415 4412 4433 C2' A B1003 4434 4431 4454 C2' G B1004 4455 4452 4476 C2' T B1005 4477 4474 4496 C2' T B1006 4497 4494 4516 C2' T B1007 4517 4514 4536 C2' C B1008 4537 4534 4555 C2' C B1009 4556 4553 4574 C2' C B1010 4575 4572 4593 C2' G B1011 4594 4591 4615 C2' T B1012 4616 4613 4635 C2' A B1013 4636 4633 4656 C2' A B1014 4657 4654 4677 C2' A B1015 4678 4675 4698 C2' T B1016 4699 4696 4718 C2' G B1017 4719 4716 4740 C2' C B1018 4741 4738 4777 C2' G C2002 4778 4775 4799 C2' C C2003 4800 4797 4818 C2' A C2004 4819 4816 4839 C2' T C2005 4840 4837 4859 C2' T C2006 4860 4857 4879 C2' T C2007 4880 4877 4899 C2' A C2008 4900 4897 4920 C2' C C2009 4921 4918 4939 C2' G C2010 4940 4937 4961 C2' G C2011 4962 4959 4983 C2' G C2012 4984 4981 5005 C2' A C2013 5006 5003 5026 C2' A C2014 5027 5024 5047 C2' A C2015 5048 5045 5068 C2' C C2016 5069 5066 5087 C2' T C2017 5088 5085 5107 C2' G C2018 5108 5105 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4412 C3' C B1002 OK 4410 4413 4414 4431 C3' A B1003 OK 4429 4432 4433 4452 C3' G B1004 OK 4450 4453 4454 4474 C3' T B1005 OK 4472 4475 4476 4494 C3' T B1006 OK 4492 4495 4496 4514 C3' T B1007 OK 4512 4515 4516 4534 C3' C B1008 OK 4532 4535 4536 4553 C3' C B1009 OK 4551 4554 4555 4572 C3' C B1010 OK 4570 4573 4574 4591 C3' G B1011 OK 4589 4592 4593 4613 C3' T B1012 OK 4611 4614 4615 4633 C3' A B1013 OK 4631 4634 4635 4654 C3' A B1014 OK 4652 4655 4656 4675 C3' A B1015 OK 4673 4676 4677 4696 C3' T B1016 OK 4694 4697 4698 4716 C3' G B1017 OK 4714 4717 4718 4738 C3' C B1018 OK 4736 4739 4740 4775 C3' G C2002 OK 4773 4776 4777 4797 C3' C C2003 OK 4795 4798 4799 4816 C3' A C2004 OK 4814 4817 4818 4837 C3' T C2005 OK 4835 4838 4839 4857 C3' T C2006 OK 4855 4858 4859 4877 C3' T C2007 OK 4875 4878 4879 4897 C3' A C2008 OK 4895 4898 4899 4918 C3' C C2009 OK 4916 4919 4920 4937 C3' G C2010 OK 4935 4938 4939 4959 C3' G C2011 OK 4957 4960 4961 4981 C3' G C2012 OK 4979 4982 4983 5003 C3' A C2013 OK 5001 5004 5005 5024 C3' A C2014 OK 5022 5025 5026 5045 C3' A C2015 OK 5043 5046 5047 5066 C3' C C2016 OK 5064 5067 5068 5085 C3' T C2017 OK 5083 5086 5087 5105 C3' G C2018 OK 5103 5106 5107 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4410 C4' C B1002 OK 4412 4409 4411 4429 C4' A B1003 OK 4431 4428 4430 4450 C4' G B1004 OK 4452 4449 4451 4472 C4' T B1005 OK 4474 4471 4473 4492 C4' T B1006 OK 4494 4491 4493 4512 C4' T B1007 OK 4514 4511 4513 4532 C4' C B1008 OK 4534 4531 4533 4551 C4' C B1009 OK 4553 4550 4552 4570 C4' C B1010 OK 4572 4569 4571 4589 C4' G B1011 OK 4591 4588 4590 4611 C4' T B1012 OK 4613 4610 4612 4631 C4' A B1013 OK 4633 4630 4632 4652 C4' A B1014 OK 4654 4651 4653 4673 C4' A B1015 OK 4675 4672 4674 4694 C4' T B1016 OK 4696 4693 4695 4714 C4' G B1017 OK 4716 4713 4715 4736 C4' C B1018 OK 4738 4735 4737 4773 C4' G C2002 OK 4775 4772 4774 4795 C4' C C2003 OK 4797 4794 4796 4814 C4' A C2004 OK 4816 4813 4815 4835 C4' T C2005 OK 4837 4834 4836 4855 C4' T C2006 OK 4857 4854 4856 4875 C4' T C2007 OK 4877 4874 4876 4895 C4' A C2008 OK 4897 4894 4896 4916 C4' C C2009 OK 4918 4915 4917 4935 C4' G C2010 OK 4937 4934 4936 4957 C4' G C2011 OK 4959 4956 4958 4979 C4' G C2012 OK 4981 4978 4980 5001 C4' A C2013 OK 5003 5000 5002 5022 C4' A C2014 OK 5024 5021 5023 5043 C4' A C2015 OK 5045 5042 5044 5064 C4' C C2016 OK 5066 5063 5065 5083 C4' T C2017 OK 5085 5082 5084 5103 C4' G C2018 OK 5105 5102 5104 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4409 C5' C B1002 4408 4410 4428 C5' A B1003 4427 4429 4449 C5' G B1004 4448 4450 4471 C5' T B1005 4470 4472 4491 C5' T B1006 4490 4492 4511 C5' T B1007 4510 4512 4531 C5' C B1008 4530 4532 4550 C5' C B1009 4549 4551 4569 C5' C B1010 4568 4570 4588 C5' G B1011 4587 4589 4610 C5' T B1012 4609 4611 4630 C5' A B1013 4629 4631 4651 C5' A B1014 4650 4652 4672 C5' A B1015 4671 4673 4693 C5' T B1016 4692 4694 4713 C5' G B1017 4712 4714 4735 C5' C B1018 4734 4736 4772 C5' G C2002 4771 4773 4794 C5' C C2003 4793 4795 4813 C5' A C2004 4812 4814 4834 C5' T C2005 4833 4835 4854 C5' T C2006 4853 4855 4874 C5' T C2007 4873 4875 4894 C5' A C2008 4893 4895 4915 C5' C C2009 4914 4916 4934 C5' G C2010 4933 4935 4956 C5' G C2011 4955 4957 4978 C5' G C2012 4977 4979 5000 C5' A C2013 4999 5001 5021 C5' A C2014 5020 5022 5042 C5' A C2015 5041 5043 5063 C5' C C2016 5062 5064 5082 C5' T C2017 5081 5083 5102 C5' G C2018 5101 5103 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4424 P A B1003 distorted distorted 4413 4425 4426 4427 4445 P G B1004 distorted distorted 4432 4446 4447 4448 4467 P T B1005 distorted distorted 4453 4468 4469 4470 4487 P T B1006 distorted distorted 4475 4488 4489 4490 4507 P T B1007 distorted distorted 4495 4508 4509 4510 4527 P C B1008 distorted distorted 4515 4528 4529 4530 4546 P C B1009 distorted distorted 4535 4547 4548 4549 4565 P C B1010 distorted distorted 4554 4566 4567 4568 4584 P G B1011 distorted distorted 4585 4586 4587 4606 P T B1012 distorted distorted 4592 4607 4608 4609 4626 P A B1013 distorted distorted 4614 4627 4628 4629 4647 P A B1014 distorted distorted 4634 4648 4649 4650 4668 P A B1015 distorted distorted 4655 4669 4670 4671 4689 P T B1016 distorted distorted 4676 4690 4691 4692 4709 P G B1017 distorted distorted 4697 4710 4711 4712 4731 P C B1018 OK OK 4717 4732 4733 4734 4790 P C C2003 distorted distorted 4776 4791 4792 4793 4809 P A C2004 distorted distorted 4798 4810 4811 4812 4830 P T C2005 distorted distorted 4817 4831 4832 4833 4850 P T C2006 distorted distorted 4838 4851 4852 4853 4870 P T C2007 distorted distorted 4858 4871 4872 4873 4890 P A C2008 distorted distorted 4878 4891 4892 4893 4911 P C C2009 distorted distorted 4898 4912 4913 4914 4930 P G C2010 distorted distorted 4919 4931 4932 4933 4952 P G C2011 distorted distorted 4938 4953 4954 4955 4974 P G C2012 distorted distorted 4960 4975 4976 4977 4996 P A C2013 distorted distorted 4982 4997 4998 4999 5017 P A C2014 distorted distorted 5004 5018 5019 5020 5038 P A C2015 distorted distorted 5025 5039 5040 5041 5059 P C C2016 distorted distorted 5046 5060 5061 5062 5078 P T C2017 distorted distorted 5067 5079 5080 5081 5098 P G C2018 OK OK 5086 5099 5100 5101 ---------------------------------------------------------------------------------