ID code: '1NNJ' 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 D 8 beta 7 12 10 31 C1' T D 9 beta 27 32 30 51 C1' T D 10 beta 47 52 50 71 C1' C D 11 beta 67 72 70 90 C1' T D 12 beta 86 91 89 110 C1' C D 13 beta 106 111 109 129 C1' G D 14 beta 125 130 128 152 C1' C E 16 beta 148 153 151 171 C1' G E 17 beta 167 172 170 193 C1' A E 18 beta 189 194 192 214 C1' G E 19 beta 210 215 213 236 C1' A E 20 beta 232 237 235 257 C1' A E 21 beta 253 258 256 278 C1' A E 22 beta 274 279 277 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' T D 8 11 8 30 C2' T D 9 31 28 50 C2' T D 10 51 48 70 C2' C D 11 71 68 89 C2' T D 12 90 87 109 C2' C D 13 110 107 128 C2' G D 14 129 126 151 C2' C E 16 152 149 170 C2' G E 17 171 168 192 C2' A E 18 193 190 213 C2' G E 19 214 211 235 C2' A E 20 236 233 256 C2' A E 21 257 254 277 C2' A E 22 278 275 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' T D 8 OK 6 9 10 28 C3' T D 9 OK 26 29 30 48 C3' T D 10 OK 46 49 50 68 C3' C D 11 OK 66 69 70 87 C3' T D 12 OK 85 88 89 107 C3' C D 13 OK 105 108 109 126 C3' G D 14 OK 124 127 128 149 C3' C E 16 OK 147 150 151 168 C3' G E 17 OK 166 169 170 190 C3' A E 18 OK 188 191 192 211 C3' G E 19 OK 209 212 213 233 C3' A E 20 OK 231 234 235 254 C3' A E 21 OK 252 255 256 275 C3' A E 22 OK 273 276 277 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' T D 8 OK 8 5 7 26 C4' T D 9 OK 28 25 27 46 C4' T D 10 OK 48 45 47 66 C4' C D 11 OK 68 65 67 85 C4' T D 12 OK 87 84 86 105 C4' C D 13 OK 107 104 106 124 C4' G D 14 OK 126 123 125 147 C4' C E 16 OK 149 146 148 166 C4' G E 17 OK 168 165 167 188 C4' A E 18 OK 190 187 189 209 C4' G E 19 OK 211 208 210 231 C4' A E 20 OK 233 230 232 252 C4' A E 21 OK 254 251 253 273 C4' A E 22 OK 275 272 274 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' T D 8 4 6 25 C5' T D 9 24 26 45 C5' T D 10 44 46 65 C5' C D 11 64 66 84 C5' T D 12 83 85 104 C5' C D 13 103 105 123 C5' G D 14 122 124 146 C5' C E 16 145 147 165 C5' G E 17 164 166 187 C5' A E 18 186 188 208 C5' G E 19 207 209 230 C5' A E 20 229 231 251 C5' A E 21 250 252 272 C5' A E 22 271 273 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P T D 8 distorted distorted 2 3 4 21 P T D 9 distorted distorted 9 22 23 24 41 P T D 10 distorted distorted 29 42 43 44 61 P C D 11 distorted distorted 49 62 63 64 80 P T D 12 distorted distorted 69 81 82 83 100 P C D 13 distorted distorted 88 101 102 103 119 P G D 14 distorted distorted 108 120 121 122 142 P C E 16 distorted distorted 143 144 145 161 P G E 17 distorted distorted 150 162 163 164 183 P A E 18 distorted distorted 169 184 185 186 204 P G E 19 distorted distorted 191 205 206 207 226 P A E 20 distorted distorted 212 227 228 229 247 P A E 21 distorted distorted 234 248 249 250 268 P A E 22 distorted distorted 255 269 270 271 ---------------------------------------------------------------------------------