ID code: '1HUO' 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' G T 5 beta 7 12 10 33 C1' G T 6 beta 29 34 32 55 C1' C T 7 beta 51 56 54 74 C1' G T 8 beta 70 75 73 96 C1' T T 9 beta 92 97 95 116 C1' C T 10 beta 112 117 115 135 C1' G T 11 beta 131 136 134 158 C1' C P 1 beta 154 159 157 177 C1' G P 2 beta 173 178 176 199 C1' A P 3 beta 195 200 198 220 C1' C P 4 beta 216 221 219 239 C1' G P 5 beta 235 240 238 261 C1' C P 6 beta 257 262 260 280 C1' C P 7 beta 276 281 279 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G T 5 11 8 32 C2' G T 6 33 30 54 C2' C T 7 55 52 73 C2' G T 8 74 71 95 C2' T T 9 96 93 115 C2' C T 10 116 113 134 C2' G T 11 135 132 157 C2' C P 1 158 155 176 C2' G P 2 177 174 198 C2' A P 3 199 196 219 C2' C P 4 220 217 238 C2' G P 5 239 236 260 C2' C P 6 261 258 279 C2' C P 7 280 277 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G T 5 OK 6 9 10 30 C3' G T 6 OK 28 31 32 52 C3' C T 7 OK 50 53 54 71 C3' G T 8 OK 69 72 73 93 C3' T T 9 OK 91 94 95 113 C3' C T 10 OK 111 114 115 132 C3' G T 11 OK 130 133 134 155 C3' C P 1 OK 153 156 157 174 C3' G P 2 OK 172 175 176 196 C3' A P 3 OK 194 197 198 217 C3' C P 4 OK 215 218 219 236 C3' G P 5 OK 234 237 238 258 C3' C P 6 OK 256 259 260 277 C3' C P 7 OK 275 278 279 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G T 5 OK 8 5 7 28 C4' G T 6 OK 30 27 29 50 C4' C T 7 OK 52 49 51 69 C4' G T 8 OK 71 68 70 91 C4' T T 9 OK 93 90 92 111 C4' C T 10 OK 113 110 112 130 C4' G T 11 OK 132 129 131 153 C4' C P 1 OK 155 152 154 172 C4' G P 2 OK 174 171 173 194 C4' A P 3 OK 196 193 195 215 C4' C P 4 OK 217 214 216 234 C4' G P 5 OK 236 233 235 256 C4' C P 6 OK 258 255 257 275 C4' C P 7 OK 277 274 276 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G T 5 4 6 27 C5' G T 6 26 28 49 C5' C T 7 48 50 68 C5' G T 8 67 69 90 C5' T T 9 89 91 110 C5' C T 10 109 111 129 C5' G T 11 128 130 152 C5' C P 1 151 153 171 C5' G P 2 170 172 193 C5' A P 3 192 194 214 C5' C P 4 213 215 233 C5' G P 5 232 234 255 C5' C P 6 254 256 274 C5' C P 7 273 275 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G T 5 distorted distorted 2 3 4 23 P G T 6 distorted distorted 9 24 25 26 45 P C T 7 distorted distorted 31 46 47 48 64 P G T 8 distorted distorted 53 65 66 67 86 P T T 9 distorted distorted 72 87 88 89 106 P C T 10 distorted distorted 94 107 108 109 125 P G T 11 distorted distorted 114 126 127 128 148 P C P 1 distorted distorted 149 150 151 167 P G P 2 distorted distorted 156 168 169 170 189 P A P 3 distorted distorted 175 190 191 192 210 P C P 4 distorted distorted 197 211 212 213 229 P G P 5 distorted distorted 218 230 231 232 251 P C P 6 distorted distorted 237 252 253 254 270 P C P 7 distorted distorted 259 271 272 273 ---------------------------------------------------------------------------------