ID code: '4WTM' 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' --------------------------------------------------------------------------------- 13 C1' A T 2 beta 8 14 11 35 C1' G T 3 beta 30 36 33 58 C1' G T 4 beta 53 59 56 83 C1' C P 1 beta 78 84 81 103 C1' C P 2 beta 98 104 101 4374 C1' UDP A 605 beta 4379 4366 4375 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' A T 2 OK 13 9 12 33 C2' G T 3 OK 35 31 34 56 C2' G T 4 OK 58 54 57 81 C2' C P 1 OK 83 79 82 101 C2' C P 2 OK 103 99 102 4375 C2' UDP A 605 OK 4374 4377 4376 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' A T 2 OK 7 10 11 31 C3' G T 3 OK 29 32 33 54 C3' G T 4 OK 52 55 56 79 C3' C P 1 OK 77 80 81 99 C3' C P 2 OK 97 100 101 4377 C3' UDP A 605 OK 4378 4380 4375 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' A T 2 OK 9 6 8 29 C4' G T 3 OK 31 28 30 52 C4' G T 4 OK 54 51 53 77 C4' C P 1 OK 79 76 78 97 C4' C P 2 OK 99 96 98 4378 C4' UDP A 605 OK 4377 4381 4379 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' A T 2 5 7 28 C5' G T 3 27 29 51 C5' G T 4 50 52 76 C5' C P 1 75 77 96 C5' C P 2 95 97 4381 C5' UDP A 605 4382 4378 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P A T 2 distorted distorted 1 3 4 5 24 P G T 3 distorted distorted 10 25 26 27 47 P G T 4 distorted distorted 32 48 49 50 72 P C P 1 distorted distorted 73 74 75 92 P C P 2 distorted distorted 80 93 94 95 ---------------------------------------------------------------------------------