ID code: '1J75' 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' C B 201 beta 7 12 10 30 C1' G B 202 beta 26 31 29 52 C1' C B 203 beta 48 53 51 71 C1' G B 204 beta 67 72 70 93 C1' C B 205 beta 89 94 92 112 C1' G B 206 beta 108 113 111 135 C1' C D 201 beta 131 136 134 154 C1' G D 202 beta 150 155 153 176 C1' C D 203 beta 172 177 175 195 C1' G D 204 beta 191 196 194 217 C1' C D 205 beta 213 218 216 236 C1' G D 206 beta 232 237 235 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C B 201 11 8 29 C2' G B 202 30 27 51 C2' C B 203 52 49 70 C2' G B 204 71 68 92 C2' C B 205 93 90 111 C2' G B 206 112 109 134 C2' C D 201 135 132 153 C2' G D 202 154 151 175 C2' C D 203 176 173 194 C2' G D 204 195 192 216 C2' C D 205 217 214 235 C2' G D 206 236 233 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C B 201 OK 6 9 10 27 C3' G B 202 OK 25 28 29 49 C3' C B 203 OK 47 50 51 68 C3' G B 204 OK 66 69 70 90 C3' C B 205 OK 88 91 92 109 C3' G B 206 OK 107 110 111 132 C3' C D 201 OK 130 133 134 151 C3' G D 202 OK 149 152 153 173 C3' C D 203 OK 171 174 175 192 C3' G D 204 OK 190 193 194 214 C3' C D 205 OK 212 215 216 233 C3' G D 206 OK 231 234 235 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C B 201 OK 8 5 7 25 C4' G B 202 OK 27 24 26 47 C4' C B 203 OK 49 46 48 66 C4' G B 204 OK 68 65 67 88 C4' C B 205 OK 90 87 89 107 C4' G B 206 OK 109 106 108 130 C4' C D 201 OK 132 129 131 149 C4' G D 202 OK 151 148 150 171 C4' C D 203 OK 173 170 172 190 C4' G D 204 OK 192 189 191 212 C4' C D 205 OK 214 211 213 231 C4' G D 206 OK 233 230 232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C B 201 4 6 24 C5' G B 202 23 25 46 C5' C B 203 45 47 65 C5' G B 204 64 66 87 C5' C B 205 86 88 106 C5' G B 206 105 107 129 C5' C D 201 128 130 148 C5' G D 202 147 149 170 C5' C D 203 169 171 189 C5' G D 204 188 190 211 C5' C D 205 210 212 230 C5' G D 206 229 231 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C B 201 distorted distorted 2 3 4 20 P G B 202 distorted distorted 9 21 22 23 42 P C B 203 distorted distorted 28 43 44 45 61 P G B 204 distorted distorted 50 62 63 64 83 P C B 205 distorted distorted 69 84 85 86 102 P G B 206 distorted distorted 91 103 104 105 125 P C D 201 distorted distorted 126 127 128 144 P G D 202 distorted distorted 133 145 146 147 166 P C D 203 distorted distorted 152 167 168 169 185 P G D 204 distorted distorted 174 186 187 188 207 P C D 205 distorted distorted 193 208 209 210 226 P G D 206 distorted distorted 215 227 228 229 ---------------------------------------------------------------------------------