ID code: '4RBY' 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' --------------------------------------------------------------------------------- 10 C1' C A 101 beta 5 11 8 30 C1' G A 102 beta 25 31 28 53 C1' C A 103 beta 48 54 51 72 C1' 2SG A 104 beta 73 74 70 96 C1' A A 105 beta 91 97 94 118 C1' A A 106 beta 113 119 116 140 C1' U A 107 beta 135 141 138 160 C1' U A 108 beta 155 161 158 180 C1' A A 109 beta 175 181 178 202 C1' G A 110 beta 197 203 200 225 C1' C A 111 beta 220 226 223 245 C1' G A 112 beta 240 246 243 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8 C2' C A 101 OK 10 6 9 28 C2' G A 102 OK 30 26 29 51 C2' C A 103 OK 53 49 52 70 C2' 2SG A 104 OK 72 68 71 94 C2' A A 105 OK 96 92 95 116 C2' A A 106 OK 118 114 117 138 C2' U A 107 OK 140 136 139 158 C2' U A 108 OK 160 156 159 178 C2' A A 109 OK 180 176 179 200 C2' G A 110 OK 202 198 201 223 C2' C A 111 OK 225 221 224 243 C2' G A 112 OK 245 241 244 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6 C3' C A 101 OK 4 7 8 26 C3' G A 102 OK 24 27 28 49 C3' C A 103 OK 47 50 51 68 C3' 2SG A 104 OK 67 69 70 92 C3' A A 105 OK 90 93 94 114 C3' A A 106 OK 112 115 116 136 C3' U A 107 OK 134 137 138 156 C3' U A 108 OK 154 157 158 176 C3' A A 109 OK 174 177 178 198 C3' G A 110 OK 196 199 200 221 C3' C A 111 OK 219 222 223 241 C3' G A 112 OK 239 242 243 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4 C4' C A 101 OK 6 3 5 24 C4' G A 102 OK 26 23 25 47 C4' C A 103 OK 49 46 48 67 C4' 2SG A 104 OK 68 66 73 90 C4' A A 105 OK 92 89 91 112 C4' A A 106 OK 114 111 113 134 C4' U A 107 OK 136 133 135 154 C4' U A 108 OK 156 153 155 174 C4' A A 109 OK 176 173 175 196 C4' G A 110 OK 198 195 197 219 C4' C A 111 OK 221 218 220 239 C4' G A 112 OK 241 238 240 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3 C5' C A 101 4 23 C5' G A 102 22 24 46 C5' C A 103 45 47 66 C5' 2SG A 104 65 67 89 C5' A A 105 88 90 111 C5' A A 106 110 112 133 C5' U A 107 132 134 153 C5' U A 108 152 154 173 C5' A A 109 172 174 195 C5' G A 110 194 196 218 C5' C A 111 217 219 238 C5' G A 112 237 239 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P G A 102 distorted distorted 7 20 21 22 42 P C A 103 distorted distorted 27 43 44 45 62 P 2SG A 104 50 65 85 P A A 105 distorted distorted 69 86 87 88 107 P A A 106 distorted distorted 93 108 109 110 129 P U A 107 distorted distorted 115 130 131 132 149 P U A 108 distorted distorted 137 150 151 152 169 P A A 109 distorted distorted 157 170 171 172 191 P G A 110 distorted distorted 177 192 193 194 214 P C A 111 distorted distorted 199 215 216 217 234 P G A 112 distorted distorted 222 235 236 237 ---------------------------------------------------------------------------------