ID code: '1LWW' 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' T D 9 beta 7 12 10 31 C1' G D 10 beta 27 32 30 53 C1' G D 11 beta 49 54 52 75 C1' A D 12 beta 71 76 74 96 C1' C D 13 beta 92 97 95 115 C1' G D 14 beta 111 116 114 137 C1' C D 15 beta 133 138 136 154 C1' G E 16 beta 150 155 153 176 C1' C E 17 beta 172 177 175 195 C1' G E 18 beta 191 196 194 217 C1' T E 19 beta 213 218 216 237 C1' C E 20 beta 233 238 236 256 C1' C E 21 beta 252 257 255 275 C1' A E 22 beta 271 276 274 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' T D 9 11 8 30 C2' G D 10 31 28 52 C2' G D 11 53 50 74 C2' A D 12 75 72 95 C2' C D 13 96 93 114 C2' G D 14 115 112 136 C2' C D 15 137 134 153 C2' G E 16 154 151 175 C2' C E 17 176 173 194 C2' G E 18 195 192 216 C2' T E 19 217 214 236 C2' C E 20 237 234 255 C2' C E 21 256 253 274 C2' A E 22 275 272 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' T D 9 OK 6 9 10 28 C3' G D 10 OK 26 29 30 50 C3' G D 11 OK 48 51 52 72 C3' A D 12 OK 70 73 74 93 C3' C D 13 OK 91 94 95 112 C3' G D 14 OK 110 113 114 134 C3' C D 15 OK 132 135 136 151 C3' G E 16 OK 149 152 153 173 C3' C E 17 OK 171 174 175 192 C3' G E 18 OK 190 193 194 214 C3' T E 19 OK 212 215 216 234 C3' C E 20 OK 232 235 236 253 C3' C E 21 OK 251 254 255 272 C3' A E 22 OK 270 273 274 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' T D 9 OK 8 5 7 26 C4' G D 10 OK 28 25 27 48 C4' G D 11 OK 50 47 49 70 C4' A D 12 OK 72 69 71 91 C4' C D 13 OK 93 90 92 110 C4' G D 14 OK 112 109 111 132 C4' C D 15 OK 134 131 133 149 C4' G E 16 OK 151 148 150 171 C4' C E 17 OK 173 170 172 190 C4' G E 18 OK 192 189 191 212 C4' T E 19 OK 214 211 213 232 C4' C E 20 OK 234 231 233 251 C4' C E 21 OK 253 250 252 270 C4' A E 22 OK 272 269 271 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' T D 9 4 6 25 C5' G D 10 24 26 47 C5' G D 11 46 48 69 C5' A D 12 68 70 90 C5' C D 13 89 91 109 C5' G D 14 108 110 131 C5' C D 15 130 132 148 C5' G E 16 147 149 170 C5' C E 17 169 171 189 C5' G E 18 188 190 211 C5' T E 19 210 212 231 C5' C E 20 230 232 250 C5' C E 21 249 251 269 C5' A E 22 268 270 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P T D 9 distorted distorted 2 3 4 21 P G D 10 distorted distorted 9 22 23 24 43 P G D 11 distorted distorted 29 44 45 46 65 P A D 12 distorted distorted 51 66 67 68 86 P C D 13 distorted distorted 73 87 88 89 105 P G D 14 distorted distorted 94 106 107 108 127 P C D 15 distorted distorted 113 128 129 130 166 P C E 17 distorted distorted 152 167 168 169 185 P G E 18 distorted distorted 174 186 187 188 207 P T E 19 distorted distorted 193 208 209 210 227 P C E 20 distorted distorted 215 228 229 230 246 P C E 21 distorted distorted 235 247 248 249 265 P A E 22 distorted distorted 254 266 267 268 ---------------------------------------------------------------------------------