ID code: '1H38' 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' --------------------------------------------------------------------------------- 11 C1' A H 11 beta 7 12 10 32 C1' T H 12 beta 28 33 31 52 C1' C H 13 beta 48 53 51 71 C1' G H 14 beta 67 72 70 93 C1' C H 15 beta 89 94 92 112 C1' C H 16 beta 108 113 111 131 C1' G H 17 beta 127 132 130 153 C1' C H 18 beta 149 154 152 171 C1' G I 1 beta 166 172 169 194 C1' C I 2 beta 189 195 192 214 C1' G I 3 beta 209 215 212 237 C1' G I 4 beta 232 238 235 260 C1' C I 5 beta 255 261 258 280 C1' G I 6 beta 275 281 278 303 C1' A I 7 beta 298 304 301 325 C1' U I 8 beta 320 326 323 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A H 11 11 8 31 C2' T H 12 32 29 51 C2' C H 13 52 49 70 C2' G H 14 71 68 92 C2' C H 15 93 90 111 C2' C H 16 112 109 130 C2' G H 17 131 128 152 C2' C H 18 153 150 169 C2' G I 1 OK 171 167 170 192 C2' C I 2 OK 194 190 193 212 C2' G I 3 OK 214 210 213 235 C2' G I 4 OK 237 233 236 258 C2' C I 5 OK 260 256 259 278 C2' G I 6 OK 280 276 279 301 C2' A I 7 OK 303 299 302 323 C2' U I 8 OK 325 321 324 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A H 11 OK 6 9 10 29 C3' T H 12 OK 27 30 31 49 C3' C H 13 OK 47 50 51 68 C3' G H 14 OK 66 69 70 90 C3' C H 15 OK 88 91 92 109 C3' C H 16 OK 107 110 111 128 C3' G H 17 OK 126 129 130 150 C3' C H 18 OK 148 151 152 167 C3' G I 1 OK 165 168 169 190 C3' C I 2 OK 188 191 192 210 C3' G I 3 OK 208 211 212 233 C3' G I 4 OK 231 234 235 256 C3' C I 5 OK 254 257 258 276 C3' G I 6 OK 274 277 278 299 C3' A I 7 OK 297 300 301 321 C3' U I 8 OK 319 322 323 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A H 11 OK 8 5 7 27 C4' T H 12 OK 29 26 28 47 C4' C H 13 OK 49 46 48 66 C4' G H 14 OK 68 65 67 88 C4' C H 15 OK 90 87 89 107 C4' C H 16 OK 109 106 108 126 C4' G H 17 OK 128 125 127 148 C4' C H 18 OK 150 147 149 165 C4' G I 1 OK 167 164 166 188 C4' C I 2 OK 190 187 189 208 C4' G I 3 OK 210 207 209 231 C4' G I 4 OK 233 230 232 254 C4' C I 5 OK 256 253 255 274 C4' G I 6 OK 276 273 275 297 C4' A I 7 OK 299 296 298 319 C4' U I 8 OK 321 318 320 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A H 11 4 6 26 C5' T H 12 25 27 46 C5' C H 13 45 47 65 C5' G H 14 64 66 87 C5' C H 15 86 88 106 C5' C H 16 105 107 125 C5' G H 17 124 126 147 C5' C H 18 146 148 164 C5' G I 1 163 165 187 C5' C I 2 186 188 207 C5' G I 3 206 208 230 C5' G I 4 229 231 253 C5' C I 5 252 254 273 C5' G I 6 272 274 296 C5' A I 7 295 297 318 C5' U I 8 317 319 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A H 11 distorted distorted 2 3 4 22 P T H 12 distorted distorted 9 23 24 25 42 P C H 13 distorted distorted 30 43 44 45 61 P G H 14 distorted distorted 50 62 63 64 83 P C H 15 distorted distorted 69 84 85 86 102 P C H 16 distorted distorted 91 103 104 105 121 P G H 17 distorted distorted 110 122 123 124 143 P C H 18 distorted distorted 129 144 145 146 183 P C I 2 distorted distorted 168 184 185 186 203 P G I 3 distorted distorted 191 204 205 206 226 P G I 4 distorted distorted 211 227 228 229 249 P C I 5 distorted distorted 234 250 251 252 269 P G I 6 distorted distorted 257 270 271 272 292 P A I 7 distorted distorted 277 293 294 295 314 P U I 8 OK OK 300 315 316 317 ---------------------------------------------------------------------------------