ID code: '4TYY' 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' --------------------------------------------------------------------------------- 12 C1' A B 0 alpha beta 7 29 13 10 45 C1' A B 1 alpha beta 40 62 46 43 78 C1' A B 2 alpha beta 73 95 79 76 111 C1' A B 3 alpha beta 106 128 112 109 144 C1' A B 4 alpha beta 139 161 145 142 177 C1' A B 5 alpha beta 172 194 178 175 210 C1' A B 6 alpha beta 205 227 211 208 243 C1' A B 7 alpha beta 238 260 244 241 276 C1' A B 8 alpha beta 271 294 277 274 7840 C1' CDP A 602 alpha beta 7835 7856 7841 7838 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A B 0 OK OK 12 8 27 11 43 C2' A B 1 OK OK 45 41 60 44 76 C2' A B 2 OK OK 78 74 93 77 109 C2' A B 3 OK OK 111 107 126 110 142 C2' A B 4 OK OK 144 140 159 143 175 C2' A B 5 OK OK 177 173 192 176 208 C2' A B 6 OK OK 210 206 225 209 241 C2' A B 7 OK OK 243 239 258 242 274 C2' A B 8 OK OK 276 272 292 275 7838 C2' CDP A 602 OK OK 7840 7836 7854 7839 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A B 0 OK OK 6 26 9 10 41 C3' A B 1 OK OK 39 59 42 43 74 C3' A B 2 OK OK 72 92 75 76 107 C3' A B 3 OK OK 105 125 108 109 140 C3' A B 4 OK OK 138 158 141 142 173 C3' A B 5 OK OK 171 191 174 175 206 C3' A B 6 OK OK 204 224 207 208 239 C3' A B 7 OK OK 237 257 240 241 272 C3' A B 8 OK OK 270 290 273 274 7836 C3' CDP A 602 OK OK 7834 7852 7837 7838 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A B 0 OK OK 8 25 5 7 39 C4' A B 1 OK OK 41 58 38 40 72 C4' A B 2 OK OK 74 91 71 73 105 C4' A B 3 OK OK 107 124 104 106 138 C4' A B 4 OK OK 140 157 137 139 171 C4' A B 5 OK OK 173 190 170 172 204 C4' A B 6 OK OK 206 223 203 205 237 C4' A B 7 OK OK 239 256 236 238 270 C4' A B 8 OK OK 272 289 269 271 7834 C4' CDP A 602 OK OK 7836 7851 7833 7835 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A B 0 OK OK 4 23 24 6 38 C5' A B 1 OK OK 37 56 57 39 71 C5' A B 2 OK OK 70 89 90 72 104 C5' A B 3 OK OK 103 122 123 105 137 C5' A B 4 OK OK 136 155 156 138 170 C5' A B 5 OK OK 169 188 189 171 203 C5' A B 6 OK OK 202 221 222 204 236 C5' A B 7 OK OK 235 254 255 237 269 C5' A B 8 OK OK 268 287 288 270 7833 C5' CDP A 602 OK OK 7832 7849 7850 7834 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A B 0 OK OK 2 3 4 34 P A B 1 distorted distorted 9 35 36 37 67 P A B 2 distorted distorted 42 68 69 70 100 P A B 3 distorted distorted 75 101 102 103 133 P A B 4 distorted distorted 108 134 135 136 166 P A B 5 distorted distorted 141 167 168 169 199 P A B 6 distorted distorted 174 200 201 202 232 P A B 7 distorted distorted 207 233 234 235 265 P A B 8 distorted distorted 240 266 267 268 ---------------------------------------------------------------------------------