ID code: '5HBW' 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' --------------------------------------------------------------------------------- 5 C1' LCC A 1 beta 4 6 16 27 C1' TLN A 2 beta 26 28 38 57 C1' LCG A 3 beta 60 48 54 77 C1' U A 4 beta 72 78 75 97 C1' A A 5 beta 92 98 95 119 C1' C A 6 beta 114 120 117 139 C1' A A 7 beta 134 140 137 155 C1' LCC B 1 beta 154 156 166 177 C1' TLN B 2 beta 176 178 188 207 C1' LCG B 3 beta 210 198 204 227 C1' U B 4 beta 222 228 225 247 C1' A B 5 beta 242 248 245 269 C1' C B 6 beta 264 270 267 289 C1' A B 7 beta 284 290 287 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 16 C2' LCC A 1 OK 5 15 17 38 C2' TLN A 2 OK 27 37 39 54 C2' LCG A 3 OK 57 46 64 75 C2' U A 4 OK 77 73 76 95 C2' A A 5 OK 97 93 96 117 C2' C A 6 OK 119 115 118 137 C2' A A 7 OK 139 135 138 166 C2' LCC B 1 OK 155 165 167 188 C2' TLN B 2 OK 177 187 189 204 C2' LCG B 3 OK 207 196 214 225 C2' U B 4 OK 227 223 226 245 C2' A B 5 OK 247 243 246 267 C2' C B 6 OK 269 265 268 287 C2' A B 7 OK 289 285 288 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 15 C3' LCC A 1 OK 3 18 16 37 C3' TLN A 2 OK 25 40 38 46 C3' LCG A 3 OK 56 65 54 73 C3' U A 4 OK 71 74 75 93 C3' A A 5 OK 91 94 95 115 C3' C A 6 OK 113 116 117 135 C3' A A 7 OK 133 136 137 165 C3' LCC B 1 OK 153 168 166 187 C3' TLN B 2 OK 175 190 188 196 C3' LCG B 3 OK 206 215 204 223 C3' U B 4 OK 221 224 225 243 C3' A B 5 OK 241 244 245 265 C3' C B 6 OK 263 266 267 285 C3' A B 7 OK 283 286 287 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' LCC A 1 OK 15 2 4 25 C4' TLN A 2 OK 37 24 26 56 C4' LCG A 3 OK 46 45 60 71 C4' U A 4 OK 73 70 72 91 C4' A A 5 OK 93 90 92 113 C4' C A 6 OK 115 112 114 133 C4' A A 7 OK 135 132 134 153 C4' LCC B 1 OK 165 152 154 175 C4' TLN B 2 OK 187 174 176 206 C4' LCG B 3 OK 196 195 210 221 C4' U B 4 OK 223 220 222 241 C4' A B 5 OK 243 240 242 263 C4' C B 6 OK 265 262 264 283 C4' A B 7 OK 285 282 284 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' LCC A 1 1 3 24 C5' TLN A 2 23 25 45 C5' LCG A 3 44 56 70 C5' U A 4 69 71 90 C5' A A 5 89 91 112 C5' C A 6 111 113 132 C5' A A 7 131 133 152 C5' LCC B 1 151 153 174 C5' TLN B 2 173 175 195 C5' LCG B 3 194 206 220 C5' U B 4 219 221 240 C5' A B 5 239 241 262 C5' C B 6 261 263 282 C5' A B 7 281 283 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P TLN A 2 distorted distorted 18 21 22 23 42 P LCG A 3 distorted distorted 40 43 61 44 66 P U A 4 distorted distorted 65 67 68 69 86 P A A 5 distorted distorted 74 87 88 89 108 P C A 6 distorted distorted 94 109 110 111 128 P A A 7 distorted distorted 116 129 130 131 170 P TLN B 2 distorted distorted 168 171 172 173 192 P LCG B 3 distorted distorted 190 193 211 194 216 P U B 4 distorted distorted 215 217 218 219 236 P A B 5 distorted distorted 224 237 238 239 258 P C B 6 distorted distorted 244 259 260 261 278 P A B 7 distorted distorted 266 279 280 281 ---------------------------------------------------------------------------------