ID code: '1U1L' 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' --------------------------------------------------------------------------------- 8 C1' DT B 202 beta 4 9 7 28 C1' DA B 203 beta 24 29 27 49 C1' DG B 204 beta 45 50 48 71 C1' DG B 205 beta 67 72 70 93 C1' DG B 206 beta 89 94 92 115 C1' DT B 207 beta 111 116 114 135 C1' DT B 208 beta 131 136 134 154 C1' PRN B 209 beta 159 153 155 175 C1' DG B 210 beta 171 176 174 197 C1' DG B 211 beta 193 198 196 219 C1' DG B 212 beta 215 220 218 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DT B 202 8 5 27 C2' DA B 203 28 25 48 C2' DG B 204 49 46 70 C2' DG B 205 71 68 92 C2' DG B 206 93 90 114 C2' DT B 207 115 112 134 C2' DT B 208 135 132 155 C2' PRN B 209 154 156 174 C2' DG B 210 175 172 196 C2' DG B 211 197 194 218 C2' DG B 212 219 216 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DT B 202 OK 3 6 7 25 C3' DA B 203 OK 23 26 27 46 C3' DG B 204 OK 44 47 48 68 C3' DG B 205 OK 66 69 70 90 C3' DG B 206 OK 88 91 92 112 C3' DT B 207 OK 110 113 114 132 C3' DT B 208 OK 130 133 134 156 C3' PRN B 209 OK 158 157 155 172 C3' DG B 210 OK 170 173 174 194 C3' DG B 211 OK 192 195 196 216 C3' DG B 212 OK 214 217 218 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DT B 202 OK 5 2 4 23 C4' DA B 203 OK 25 22 24 44 C4' DG B 204 OK 46 43 45 66 C4' DG B 205 OK 68 65 67 88 C4' DG B 206 OK 90 87 89 110 C4' DT B 207 OK 112 109 111 130 C4' DT B 208 OK 132 129 131 158 C4' PRN B 209 OK 156 160 159 170 C4' DG B 210 OK 172 169 171 192 C4' DG B 211 OK 194 191 193 214 C4' DG B 212 OK 216 213 215 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DT B 202 1 3 22 C5' DA B 203 21 23 43 C5' DG B 204 42 44 65 C5' DG B 205 64 66 87 C5' DG B 206 86 88 109 C5' DT B 207 108 110 129 C5' DT B 208 128 130 160 C5' PRN B 209 161 158 169 C5' DG B 210 168 170 191 C5' DG B 211 190 192 213 C5' DG B 212 212 214 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P DA B 203 distorted distorted 6 19 20 21 39 P DG B 204 distorted distorted 26 40 41 42 61 P DG B 205 distorted distorted 47 62 63 64 83 P DG B 206 distorted distorted 69 84 85 86 105 P DT B 207 distorted distorted 91 106 107 108 125 P DT B 208 distorted distorted 113 126 127 128 162 P PRN B 209 distorted distorted 133 163 164 161 165 P DG B 210 distorted distorted 157 166 167 168 187 P DG B 211 distorted distorted 173 188 189 190 209 P DG B 212 distorted distorted 195 210 211 212 ---------------------------------------------------------------------------------