ID code: '1S9B' 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' --------------------------------------------------------------------------------- 8 C1' G A 1 beta 4 9 7 30 C1' A A 2 beta 26 31 29 51 C1' A A 3 beta 47 52 50 72 C1' T A 4 beta 68 73 71 92 C1' T A 5 beta 88 93 91 112 C1' C A 6 beta 108 113 111 129 C1' G B 1 beta 125 130 128 151 C1' A B 2 beta 147 152 150 172 C1' A B 3 beta 168 173 171 193 C1' T B 4 beta 189 194 192 213 C1' T B 5 beta 209 214 212 233 C1' C B 6 beta 229 234 232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 8 5 29 C2' A A 2 30 27 50 C2' A A 3 51 48 71 C2' T A 4 72 69 91 C2' T A 5 92 89 111 C2' C A 6 112 109 128 C2' G B 1 129 126 150 C2' A B 2 151 148 171 C2' A B 3 172 169 192 C2' T B 4 193 190 212 C2' T B 5 213 210 232 C2' C B 6 233 230 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 27 C3' A A 2 OK 25 28 29 48 C3' A A 3 OK 46 49 50 69 C3' T A 4 OK 67 70 71 89 C3' T A 5 OK 87 90 91 109 C3' C A 6 OK 107 110 111 126 C3' G B 1 OK 124 127 128 148 C3' A B 2 OK 146 149 150 169 C3' A B 3 OK 167 170 171 190 C3' T B 4 OK 188 191 192 210 C3' T B 5 OK 208 211 212 230 C3' C B 6 OK 228 231 232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 25 C4' A A 2 OK 27 24 26 46 C4' A A 3 OK 48 45 47 67 C4' T A 4 OK 69 66 68 87 C4' T A 5 OK 89 86 88 107 C4' C A 6 OK 109 106 108 124 C4' G B 1 OK 126 123 125 146 C4' A B 2 OK 148 145 147 167 C4' A B 3 OK 169 166 168 188 C4' T B 4 OK 190 187 189 208 C4' T B 5 OK 210 207 209 228 C4' C B 6 OK 230 227 229 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 24 C5' A A 2 23 25 45 C5' A A 3 44 46 66 C5' T A 4 65 67 86 C5' T A 5 85 87 106 C5' C A 6 105 107 123 C5' G B 1 122 124 145 C5' A B 2 144 146 166 C5' A B 3 165 167 187 C5' T B 4 186 188 207 C5' T B 5 206 208 227 C5' C B 6 226 228 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P A A 2 distorted distorted 6 21 22 23 41 P A A 3 distorted distorted 28 42 43 44 62 P T A 4 distorted distorted 49 63 64 65 82 P T A 5 distorted distorted 70 83 84 85 102 P C A 6 distorted distorted 90 103 104 105 141 P A B 2 distorted distorted 127 142 143 144 162 P A B 3 distorted distorted 149 163 164 165 183 P T B 4 distorted distorted 170 184 185 186 203 P T B 5 distorted distorted 191 204 205 206 223 P C B 6 distorted distorted 211 224 225 226 ---------------------------------------------------------------------------------