ID code: '1R4H' 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' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' G A 3 alpha beta 73 96 79 76 112 C1' C A 4 alpha beta 107 127 113 110 143 C1' A A 5 alpha beta 138 160 144 141 176 C1' A A 6 alpha beta 171 193 177 174 209 C1' G A 7 alpha beta 204 227 210 207 243 C1' C A 8 alpha beta 238 258 244 241 274 C1' C A 9 alpha beta 269 289 275 272 305 C1' C A 10 alpha beta 300 321 306 303 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' G A 3 OK OK 78 74 94 77 110 C2' C A 4 OK OK 112 108 125 111 141 C2' A A 5 OK OK 143 139 158 142 174 C2' A A 6 OK OK 176 172 191 175 207 C2' G A 7 OK OK 209 205 225 208 241 C2' C A 8 OK OK 243 239 256 242 272 C2' C A 9 OK OK 274 270 287 273 303 C2' C A 10 OK OK 305 301 319 304 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' G A 3 OK OK 72 93 75 76 108 C3' C A 4 OK OK 106 124 109 110 139 C3' A A 5 OK OK 137 157 140 141 172 C3' A A 6 OK OK 170 190 173 174 205 C3' G A 7 OK OK 203 224 206 207 239 C3' C A 8 OK OK 237 255 240 241 270 C3' C A 9 OK OK 268 286 271 272 301 C3' C A 10 OK OK 299 317 302 303 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' G A 3 OK OK 74 92 71 73 106 C4' C A 4 OK OK 108 123 105 107 137 C4' A A 5 OK OK 139 156 136 138 170 C4' A A 6 OK OK 172 189 169 171 203 C4' G A 7 OK OK 205 223 202 204 237 C4' C A 8 OK OK 239 254 236 238 268 C4' C A 9 OK OK 270 285 267 269 299 C4' C A 10 OK OK 301 316 298 300 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' G A 3 OK OK 70 90 91 72 105 C5' C A 4 OK OK 104 121 122 106 136 C5' A A 5 OK OK 135 154 155 137 169 C5' A A 6 OK OK 168 187 188 170 202 C5' G A 7 OK OK 201 221 222 203 236 C5' C A 8 OK OK 235 252 253 237 267 C5' C A 9 OK OK 266 283 284 268 298 C5' C A 10 OK OK 297 314 315 299 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P C A 4 distorted distorted 75 102 103 104 132 P A A 5 distorted distorted 109 133 134 135 165 P A A 6 distorted distorted 140 166 167 168 198 P G A 7 distorted distorted 173 199 200 201 232 P C A 8 distorted distorted 206 233 234 235 263 P C A 9 distorted distorted 240 264 265 266 294 P C A 10 distorted distorted 271 295 296 297 ---------------------------------------------------------------------------------