ID code: '4WTK' 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' G T 2 beta 8 14 11 36 C1' C T 3 beta 31 37 34 56 C1' C T 4 beta 51 57 54 78 C1' G P 1 beta 73 79 76 101 C1' G P 2 beta 96 102 99 4370 C1' CDP A 605 beta 4365 4371 4368 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G T 2 OK 13 9 12 34 C2' C T 3 OK 36 32 35 54 C2' C T 4 OK 56 52 55 76 C2' G P 1 OK 78 74 77 99 C2' G P 2 OK 101 97 100 4368 C2' CDP A 605 OK 4370 4366 4369 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G T 2 OK 7 10 11 32 C3' C T 3 OK 30 33 34 52 C3' C T 4 OK 50 53 54 74 C3' G P 1 OK 72 75 76 97 C3' G P 2 OK 95 98 99 4366 C3' CDP A 605 OK 4364 4367 4368 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G T 2 OK 9 6 8 30 C4' C T 3 OK 32 29 31 50 C4' C T 4 OK 52 49 51 72 C4' G P 1 OK 74 71 73 95 C4' G P 2 OK 97 94 96 4364 C4' CDP A 605 OK 4366 4363 4365 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G T 2 5 7 29 C5' C T 3 28 30 49 C5' C T 4 48 50 71 C5' G P 1 70 72 94 C5' G P 2 93 95 4363 C5' CDP A 605 4362 4364 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G T 2 distorted distorted 1 3 4 5 25 P C T 3 distorted distorted 10 26 27 28 45 P C T 4 distorted distorted 33 46 47 48 67 P G P 1 distorted distorted 68 69 70 90 P G P 2 distorted distorted 75 91 92 93 ---------------------------------------------------------------------------------