ID code: '4WTL' 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' C T 3 beta 30 36 33 55 C1' C T 4 beta 50 56 53 77 C1' G P 1 beta 72 78 75 100 C1' G P 2 beta 95 101 98 4422 C1' UDP A 604 beta 4427 4414 4423 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C T 3 OK 35 31 34 53 C2' C T 4 OK 55 51 54 75 C2' G P 1 OK 77 73 76 98 C2' G P 2 OK 100 96 99 4423 C2' UDP A 604 OK 4422 4425 4424 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' A T 2 OK 7 10 11 31 C3' C T 3 OK 29 32 33 51 C3' C T 4 OK 49 52 53 73 C3' G P 1 OK 71 74 75 96 C3' G P 2 OK 94 97 98 4425 C3' UDP A 604 OK 4426 4428 4423 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' A T 2 OK 9 6 8 29 C4' C T 3 OK 31 28 30 49 C4' C T 4 OK 51 48 50 71 C4' G P 1 OK 73 70 72 94 C4' G P 2 OK 96 93 95 4426 C4' UDP A 604 OK 4425 4429 4427 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' A T 2 5 7 28 C5' C T 3 27 29 48 C5' C T 4 47 49 70 C5' G P 1 69 71 93 C5' G P 2 92 94 4429 C5' UDP A 604 4430 4426 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P A T 2 distorted distorted 1 3 4 5 24 P C T 3 distorted distorted 10 25 26 27 44 P C T 4 distorted distorted 32 45 46 47 66 P G P 1 distorted distorted 67 68 69 89 P G P 2 distorted distorted 74 90 91 92 ---------------------------------------------------------------------------------