ID code: '1MSW' 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' T T 126 beta 7 12 10 31 C1' G T 125 beta 27 32 30 53 C1' C T 124 beta 49 54 52 72 C1' G T 123 beta 68 73 71 94 C1' C T 122 beta 90 95 93 113 C1' A T 121 beta 109 114 112 135 C1' T N 21 beta 131 136 134 155 C1' G N 22 beta 151 156 154 177 C1' C N 23 beta 173 178 176 196 C1' G N 24 beta 192 197 195 218 C1' C N 25 beta 214 219 217 237 C1' A N 26 beta 233 238 236 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' T T 126 11 8 30 C2' G T 125 31 28 52 C2' C T 124 53 50 71 C2' G T 123 72 69 93 C2' C T 122 94 91 112 C2' A T 121 113 110 134 C2' T N 21 135 132 154 C2' G N 22 155 152 176 C2' C N 23 177 174 195 C2' G N 24 196 193 217 C2' C N 25 218 215 236 C2' A N 26 237 234 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' T T 126 OK 6 9 10 28 C3' G T 125 OK 26 29 30 50 C3' C T 124 OK 48 51 52 69 C3' G T 123 OK 67 70 71 91 C3' C T 122 OK 89 92 93 110 C3' A T 121 OK 108 111 112 132 C3' T N 21 OK 130 133 134 152 C3' G N 22 OK 150 153 154 174 C3' C N 23 OK 172 175 176 193 C3' G N 24 OK 191 194 195 215 C3' C N 25 OK 213 216 217 234 C3' A N 26 OK 232 235 236 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' T T 126 OK 8 5 7 26 C4' G T 125 OK 28 25 27 48 C4' C T 124 OK 50 47 49 67 C4' G T 123 OK 69 66 68 89 C4' C T 122 OK 91 88 90 108 C4' A T 121 OK 110 107 109 130 C4' T N 21 OK 132 129 131 150 C4' G N 22 OK 152 149 151 172 C4' C N 23 OK 174 171 173 191 C4' G N 24 OK 193 190 192 213 C4' C N 25 OK 215 212 214 232 C4' A N 26 OK 234 231 233 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' T T 126 4 6 25 C5' G T 125 24 26 47 C5' C T 124 46 48 66 C5' G T 123 65 67 88 C5' C T 122 87 89 107 C5' A T 121 106 108 129 C5' T N 21 128 130 149 C5' G N 22 148 150 171 C5' C N 23 170 172 190 C5' G N 24 189 191 212 C5' C N 25 211 213 231 C5' A N 26 230 232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P T T 126 distorted distorted 2 3 4 21 P G T 125 distorted distorted 9 22 23 24 43 P C T 124 distorted distorted 29 44 45 46 62 P G T 123 distorted distorted 51 63 64 65 84 P C T 122 distorted distorted 70 85 86 87 103 P A T 121 distorted distorted 92 104 105 106 125 P T N 21 distorted distorted 126 127 128 145 P G N 22 distorted distorted 133 146 147 148 167 P C N 23 distorted distorted 153 168 169 170 186 P G N 24 distorted distorted 175 187 188 189 208 P C N 25 distorted distorted 194 209 210 211 227 P A N 26 distorted distorted 216 228 229 230 ---------------------------------------------------------------------------------