ID code: '2HT1' 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 J 1 beta 4 10 7 29 C1' C J 2 beta 24 30 27 47 C1' U K 1 beta 42 48 45 67 C1' C K 2 beta 62 68 65 85 C1' U M 1 beta 80 86 83 105 C1' C M 2 beta 100 106 103 125 C1' U M 3 beta 120 126 123 145 C1' C M 4 beta 140 146 143 165 C1' U M 5 beta 160 166 163 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U J 1 OK 9 5 8 27 C2' C J 2 OK 29 25 28 45 C2' U K 1 OK 47 43 46 65 C2' C K 2 OK 67 63 66 83 C2' U M 1 OK 85 81 84 103 C2' C M 2 OK 105 101 104 123 C2' U M 3 OK 125 121 124 143 C2' C M 4 OK 145 141 144 163 C2' U M 5 OK 165 161 164 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U J 1 OK 3 6 7 25 C3' C J 2 OK 23 26 27 43 C3' U K 1 OK 41 44 45 63 C3' C K 2 OK 61 64 65 81 C3' U M 1 OK 79 82 83 101 C3' C M 2 OK 99 102 103 121 C3' U M 3 OK 119 122 123 141 C3' C M 4 OK 139 142 143 161 C3' U M 5 OK 159 162 163 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U J 1 OK 5 2 4 23 C4' C J 2 OK 25 22 24 41 C4' U K 1 OK 43 40 42 61 C4' C K 2 OK 63 60 62 79 C4' U M 1 OK 81 78 80 99 C4' C M 2 OK 101 98 100 119 C4' U M 3 OK 121 118 120 139 C4' C M 4 OK 141 138 140 159 C4' U M 5 OK 161 158 160 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U J 1 1 3 22 C5' C J 2 21 23 40 C5' U K 1 39 41 60 C5' C K 2 59 61 78 C5' U M 1 77 79 98 C5' C M 2 97 99 118 C5' U M 3 117 119 138 C5' C M 4 137 139 158 C5' U M 5 157 159 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C J 2 distorted distorted 6 19 20 21 56 P C K 2 distorted distorted 44 57 58 59 94 P C M 2 distorted distorted 82 95 96 97 114 P U M 3 distorted distorted 102 115 116 117 134 P C M 4 distorted distorted 122 135 136 137 154 P U M 5 distorted distorted 142 155 156 157 ---------------------------------------------------------------------------------