ID code: '2A1R' 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' A C 501 beta 4 10 7 31 C1' A C 502 beta 26 32 29 53 C1' A C 503 beta 48 54 51 73 C1' A D 601 beta 68 74 71 95 C1' A D 602 beta 90 96 93 117 C1' A D 603 beta 112 118 115 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A C 501 OK 9 5 8 29 C2' A C 502 OK 31 27 30 51 C2' A C 503 OK 53 49 52 71 C2' A D 601 OK 73 69 72 93 C2' A D 602 OK 95 91 94 115 C2' A D 603 OK 117 113 116 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A C 501 OK 3 6 7 27 C3' A C 502 OK 25 28 29 49 C3' A C 503 OK 47 50 51 69 C3' A D 601 OK 67 70 71 91 C3' A D 602 OK 89 92 93 113 C3' A D 603 OK 111 114 115 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A C 501 OK 5 2 4 25 C4' A C 502 OK 27 24 26 47 C4' A C 503 OK 49 46 48 67 C4' A D 601 OK 69 66 68 89 C4' A D 602 OK 91 88 90 111 C4' A D 603 OK 113 110 112 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A C 501 1 3 24 C5' A C 502 23 25 46 C5' A C 503 45 47 66 C5' A D 601 65 67 88 C5' A D 602 87 89 110 C5' A D 603 109 111 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P A C 502 distorted distorted 6 21 22 23 42 P A C 503 distorted distorted 28 43 44 45 84 P A D 602 distorted distorted 70 85 86 87 106 P A D 603 distorted distorted 92 107 108 109 ---------------------------------------------------------------------------------