ID code: '3HGA' 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' --------------------------------------------------------------------------------- 9 C1' U X 1 beta 4 10 7 27 C1' US5 X 2 beta 34 19 28 49 C1' C X 3 beta 44 50 47 69 C1' G X 4 beta 64 70 67 92 C1' C X 5 beta 87 93 90 112 C1' G X 6 beta 107 113 110 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U X 1 OK 9 5 8 28 C2' US5 X 2 OK 27 31 29 47 C2' C X 3 OK 49 45 48 67 C2' G X 4 OK 69 65 68 90 C2' C X 5 OK 92 88 91 110 C2' G X 6 OK 112 108 111 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U X 1 OK 3 6 7 31 C3' US5 X 2 OK 33 32 28 45 C3' C X 3 OK 43 46 47 65 C3' G X 4 OK 63 66 67 88 C3' C X 5 OK 86 89 90 108 C3' G X 6 OK 106 109 110 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U X 1 OK 5 2 4 33 C4' US5 X 2 OK 31 35 34 43 C4' C X 3 OK 45 42 44 63 C4' G X 4 OK 65 62 64 86 C4' C X 5 OK 88 85 87 106 C4' G X 6 OK 108 105 107 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U X 1 1 3 35 C5' US5 X 2 36 33 42 C5' C X 3 41 43 62 C5' G X 4 61 63 85 C5' C X 5 84 86 105 C5' G X 6 104 106 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P US5 X 2 distorted distorted 6 37 30 36 38 P C X 3 distorted distorted 32 39 40 41 58 P G X 4 distorted distorted 46 59 60 61 81 P C X 5 distorted distorted 66 82 83 84 101 P G X 6 distorted distorted 89 102 103 104 ---------------------------------------------------------------------------------