ID code: '2E9R' 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' C A 902 beta 4 10 7 29 C1' A A 903 beta 24 30 27 51 C1' U A 904 beta 46 52 49 71 C1' G A 905 beta 66 72 69 94 C1' G A 906 beta 89 95 92 117 C1' G A 907 beta 112 118 115 140 C1' C A 908 beta 135 141 138 160 C1' C A 909 beta 155 161 158 180 C1' C A 910 beta 175 181 178 198 C1' G B 915 beta 193 199 196 221 C1' G B 916 beta 216 222 219 244 C1' G B 917 beta 239 245 242 267 C1' C B 918 beta 262 268 265 287 C1' C B 919 beta 282 288 285 307 C1' C B 920 beta 302 308 305 4017 C1' RTP X3832 beta 4016 4018 4026 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 902 OK 9 5 8 27 C2' A A 903 OK 29 25 28 49 C2' U A 904 OK 51 47 50 69 C2' G A 905 OK 71 67 70 92 C2' G A 906 OK 94 90 93 115 C2' G A 907 OK 117 113 116 138 C2' C A 908 OK 140 136 139 158 C2' C A 909 OK 160 156 159 178 C2' C A 910 OK 180 176 179 196 C2' G B 915 OK 198 194 197 219 C2' G B 916 OK 221 217 220 242 C2' G B 917 OK 244 240 243 265 C2' C B 918 OK 267 263 266 285 C2' C B 919 OK 287 283 286 305 C2' C B 920 OK 307 303 306 4026 C2' RTP X3832 OK 4017 4028 4027 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 902 OK 3 6 7 25 C3' A A 903 OK 23 26 27 47 C3' U A 904 OK 45 48 49 67 C3' G A 905 OK 65 68 69 90 C3' G A 906 OK 88 91 92 113 C3' G A 907 OK 111 114 115 136 C3' C A 908 OK 134 137 138 156 C3' C A 909 OK 154 157 158 176 C3' C A 910 OK 174 177 178 194 C3' G B 915 OK 192 195 196 217 C3' G B 916 OK 215 218 219 240 C3' G B 917 OK 238 241 242 263 C3' C B 918 OK 261 264 265 283 C3' C B 919 OK 281 284 285 303 C3' C B 920 OK 301 304 305 4028 C3' RTP X3832 OK 4015 4029 4026 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 902 OK 5 2 4 23 C4' A A 903 OK 25 22 24 45 C4' U A 904 OK 47 44 46 65 C4' G A 905 OK 67 64 66 88 C4' G A 906 OK 90 87 89 111 C4' G A 907 OK 113 110 112 134 C4' C A 908 OK 136 133 135 154 C4' C A 909 OK 156 153 155 174 C4' C A 910 OK 176 173 175 192 C4' G B 915 OK 194 191 193 215 C4' G B 916 OK 217 214 216 238 C4' G B 917 OK 240 237 239 261 C4' C B 918 OK 263 260 262 281 C4' C B 919 OK 283 280 282 301 C4' C B 920 OK 303 300 302 4015 C4' RTP X3832 OK 4028 4014 4016 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 902 1 3 22 C5' A A 903 21 23 44 C5' U A 904 43 45 64 C5' G A 905 63 65 87 C5' G A 906 86 88 110 C5' G A 907 109 111 133 C5' C A 908 132 134 153 C5' C A 909 152 154 173 C5' C A 910 172 174 191 C5' G B 915 190 192 214 C5' G B 916 213 215 237 C5' G B 917 236 238 260 C5' C B 918 259 261 280 C5' C B 919 279 281 300 C5' C B 920 299 301 4014 C5' RTP X3832 4013 4015 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P A A 903 distorted distorted 6 19 20 21 40 P U A 904 distorted distorted 26 41 42 43 60 P G A 905 distorted distorted 48 61 62 63 83 P G A 906 distorted distorted 68 84 85 86 106 P G A 907 distorted distorted 91 107 108 109 129 P C A 908 distorted distorted 114 130 131 132 149 P C A 909 distorted distorted 137 150 151 152 169 P C A 910 distorted distorted 157 170 171 172 210 P G B 916 distorted distorted 195 211 212 213 233 P G B 917 distorted distorted 218 234 235 236 256 P C B 918 distorted distorted 241 257 258 259 276 P C B 919 distorted distorted 264 277 278 279 296 P C B 920 distorted distorted 284 297 298 299 ---------------------------------------------------------------------------------