ID code: '4U34' 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 A 1 beta 4 10 7 29 C1' A A 2 beta 24 30 27 51 C1' G A 3 beta 46 52 49 74 C1' C A 4 beta 69 75 72 91 C1' SUR A 5 beta 89 92 93 114 C1' C A 6 beta 109 115 112 134 C1' C A 7 beta 129 135 132 152 C1' G B 8 beta 147 153 150 175 C1' G B 9 beta 170 176 173 198 C1' A B 10 beta 193 199 196 220 C1' G B 11 beta 215 221 218 243 C1' C B 12 beta 238 244 241 263 C1' U B 13 beta 258 264 261 283 C1' A B 14 beta 278 284 281 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK 9 5 8 27 C2' A A 2 OK 29 25 28 49 C2' G A 3 OK 51 47 50 72 C2' C A 4 OK 74 70 73 93 C2' SUR A 5 OK 91 90 101 112 C2' C A 6 OK 114 110 113 132 C2' C A 7 OK 134 130 133 150 C2' G B 8 OK 152 148 151 173 C2' G B 9 OK 175 171 174 196 C2' A B 10 OK 198 194 197 218 C2' G B 11 OK 220 216 219 241 C2' C B 12 OK 243 239 242 261 C2' U B 13 OK 263 259 262 281 C2' A B 14 OK 283 279 282 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK 3 6 7 25 C3' A A 2 OK 23 26 27 47 C3' G A 3 OK 45 48 49 70 C3' C A 4 OK 68 71 72 90 C3' SUR A 5 OK 88 102 93 110 C3' C A 6 OK 108 111 112 130 C3' C A 7 OK 128 131 132 148 C3' G B 8 OK 146 149 150 171 C3' G B 9 OK 169 172 173 194 C3' A B 10 OK 192 195 196 216 C3' G B 11 OK 214 217 218 239 C3' C B 12 OK 237 240 241 259 C3' U B 13 OK 257 260 261 279 C3' A B 14 OK 277 280 281 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK 5 2 4 23 C4' A A 2 OK 25 22 24 45 C4' G A 3 OK 47 44 46 68 C4' C A 4 OK 70 67 69 88 C4' SUR A 5 OK 90 87 89 108 C4' C A 6 OK 110 107 109 128 C4' C A 7 OK 130 127 129 146 C4' G B 8 OK 148 145 147 169 C4' G B 9 OK 171 168 170 192 C4' A B 10 OK 194 191 193 214 C4' G B 11 OK 216 213 215 237 C4' C B 12 OK 239 236 238 257 C4' U B 13 OK 259 256 258 277 C4' A B 14 OK 279 276 278 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 1 3 22 C5' A A 2 21 23 44 C5' G A 3 43 45 67 C5' C A 4 66 68 87 C5' SUR A 5 86 88 107 C5' C A 6 106 108 127 C5' C A 7 126 128 145 C5' G B 8 144 146 168 C5' G B 9 167 169 191 C5' A B 10 190 192 213 C5' G B 11 212 214 236 C5' C B 12 235 237 256 C5' U B 13 255 257 276 C5' A B 14 275 277 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P A A 2 distorted distorted 6 19 20 21 40 P G A 3 distorted distorted 26 41 42 43 63 P C A 4 distorted distorted 48 64 65 66 83 P SUR A 5 OK OK 71 84 85 86 103 P C A 6 distorted distorted 102 104 105 106 123 P C A 7 distorted distorted 111 124 125 126 164 P G B 9 distorted distorted 149 165 166 167 187 P A B 10 distorted distorted 172 188 189 190 209 P G B 11 distorted distorted 195 210 211 212 232 P C B 12 distorted distorted 217 233 234 235 252 P U B 13 distorted distorted 240 253 254 255 272 P A B 14 distorted distorted 260 273 274 275 ---------------------------------------------------------------------------------