ID code: '1CL8' 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' --------------------------------------------------------------------------------- 2079 C1' C B 2 beta 2075 2080 2078 2098 C1' G B 3 beta 2094 2099 2097 2120 C1' C B 4 beta 2116 2121 2119 2139 C1' G B 5 beta 2135 2140 2138 2161 C1' A B 6 beta 2157 2162 2160 2181 C1' AP B 7 beta 2186 2180 2182 2202 C1' T B 8 beta 2198 2203 2201 2222 C1' T B 9 beta 2218 2223 2221 2242 C1' C B 10 beta 2238 2243 2241 2261 C1' G B 11 beta 2257 2262 2260 2283 C1' C B 12 beta 2279 2284 2282 2302 C1' G B 13 beta 2298 2303 2301 4394 C1' C D 2 beta 4390 4395 4393 4413 C1' G D 3 beta 4409 4414 4412 4435 C1' C D 4 beta 4431 4436 4434 4454 C1' G D 5 beta 4450 4455 4453 4476 C1' A D 6 beta 4472 4477 4475 4496 C1' AP D 7 beta 4501 4495 4497 4517 C1' T D 8 beta 4513 4518 4516 4537 C1' T D 9 beta 4533 4538 4536 4557 C1' C D 10 beta 4553 4558 4556 4576 C1' G D 11 beta 4572 4577 4575 4598 C1' C D 12 beta 4594 4599 4597 4617 C1' G D 13 beta 4613 4618 4616 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2078 C2' C B 2 2079 2076 2097 C2' G B 3 2098 2095 2119 C2' C B 4 2120 2117 2138 C2' G B 5 2139 2136 2160 C2' A B 6 2161 2158 2182 C2' AP B 7 2181 2183 2201 C2' T B 8 2202 2199 2221 C2' T B 9 2222 2219 2241 C2' C B 10 2242 2239 2260 C2' G B 11 2261 2258 2282 C2' C B 12 2283 2280 2301 C2' G B 13 2302 2299 4393 C2' C D 2 4394 4391 4412 C2' G D 3 4413 4410 4434 C2' C D 4 4435 4432 4453 C2' G D 5 4454 4451 4475 C2' A D 6 4476 4473 4497 C2' AP D 7 4496 4498 4516 C2' T D 8 4517 4514 4536 C2' T D 9 4537 4534 4556 C2' C D 10 4557 4554 4575 C2' G D 11 4576 4573 4597 C2' C D 12 4598 4595 4616 C2' G D 13 4617 4614 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2076 C3' C B 2 OK 2074 2077 2078 2095 C3' G B 3 OK 2093 2096 2097 2117 C3' C B 4 OK 2115 2118 2119 2136 C3' G B 5 OK 2134 2137 2138 2158 C3' A B 6 OK 2156 2159 2160 2183 C3' AP B 7 OK 2185 2184 2182 2199 C3' T B 8 OK 2197 2200 2201 2219 C3' T B 9 OK 2217 2220 2221 2239 C3' C B 10 OK 2237 2240 2241 2258 C3' G B 11 OK 2256 2259 2260 2280 C3' C B 12 OK 2278 2281 2282 2299 C3' G B 13 OK 2297 2300 2301 4391 C3' C D 2 OK 4389 4392 4393 4410 C3' G D 3 OK 4408 4411 4412 4432 C3' C D 4 OK 4430 4433 4434 4451 C3' G D 5 OK 4449 4452 4453 4473 C3' A D 6 OK 4471 4474 4475 4498 C3' AP D 7 OK 4500 4499 4497 4514 C3' T D 8 OK 4512 4515 4516 4534 C3' T D 9 OK 4532 4535 4536 4554 C3' C D 10 OK 4552 4555 4556 4573 C3' G D 11 OK 4571 4574 4575 4595 C3' C D 12 OK 4593 4596 4597 4614 C3' G D 13 OK 4612 4615 4616 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2074 C4' C B 2 OK 2076 2073 2075 2093 C4' G B 3 OK 2095 2092 2094 2115 C4' C B 4 OK 2117 2114 2116 2134 C4' G B 5 OK 2136 2133 2135 2156 C4' A B 6 OK 2158 2155 2157 2185 C4' AP B 7 OK 2183 2187 2186 2197 C4' T B 8 OK 2199 2196 2198 2217 C4' T B 9 OK 2219 2216 2218 2237 C4' C B 10 OK 2239 2236 2238 2256 C4' G B 11 OK 2258 2255 2257 2278 C4' C B 12 OK 2280 2277 2279 2297 C4' G B 13 OK 2299 2296 2298 4389 C4' C D 2 OK 4391 4388 4390 4408 C4' G D 3 OK 4410 4407 4409 4430 C4' C D 4 OK 4432 4429 4431 4449 C4' G D 5 OK 4451 4448 4450 4471 C4' A D 6 OK 4473 4470 4472 4500 C4' AP D 7 OK 4498 4502 4501 4512 C4' T D 8 OK 4514 4511 4513 4532 C4' T D 9 OK 4534 4531 4533 4552 C4' C D 10 OK 4554 4551 4553 4571 C4' G D 11 OK 4573 4570 4572 4593 C4' C D 12 OK 4595 4592 4594 4612 C4' G D 13 OK 4614 4611 4613 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2073 C5' C B 2 2072 2074 2092 C5' G B 3 2091 2093 2114 C5' C B 4 2113 2115 2133 C5' G B 5 2132 2134 2155 C5' A B 6 2154 2156 2187 C5' AP B 7 2188 2185 2196 C5' T B 8 2195 2197 2216 C5' T B 9 2215 2217 2236 C5' C B 10 2235 2237 2255 C5' G B 11 2254 2256 2277 C5' C B 12 2276 2278 2296 C5' G B 13 2295 2297 4388 C5' C D 2 4387 4389 4407 C5' G D 3 4406 4408 4429 C5' C D 4 4428 4430 4448 C5' G D 5 4447 4449 4470 C5' A D 6 4469 4471 4502 C5' AP D 7 4503 4500 4511 C5' T D 8 4510 4512 4531 C5' T D 9 4530 4532 4551 C5' C D 10 4550 4552 4570 C5' G D 11 4569 4571 4592 C5' C D 12 4591 4593 4611 C5' G D 13 4610 4612 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2088 P G B 3 distorted distorted 2077 2089 2090 2091 2110 P C B 4 distorted distorted 2096 2111 2112 2113 2129 P G B 5 distorted distorted 2118 2130 2131 2132 2151 P A B 6 distorted distorted 2137 2152 2153 2154 2189 P AP B 7 OK OK 2159 2190 2191 2188 2192 P T B 8 distorted distorted 2184 2193 2194 2195 2212 P T B 9 distorted distorted 2200 2213 2214 2215 2232 P C B 10 distorted distorted 2220 2233 2234 2235 2251 P G B 11 distorted distorted 2240 2252 2253 2254 2273 P C B 12 distorted distorted 2259 2274 2275 2276 2292 P G B 13 distorted distorted 2281 2293 2294 2295 4403 P G D 3 distorted distorted 4392 4404 4405 4406 4425 P C D 4 distorted distorted 4411 4426 4427 4428 4444 P G D 5 distorted distorted 4433 4445 4446 4447 4466 P A D 6 distorted distorted 4452 4467 4468 4469 4504 P AP D 7 OK OK 4474 4505 4506 4503 4507 P T D 8 distorted distorted 4499 4508 4509 4510 4527 P T D 9 distorted distorted 4515 4528 4529 4530 4547 P C D 10 distorted distorted 4535 4548 4549 4550 4566 P G D 11 distorted distorted 4555 4567 4568 4569 4588 P C D 12 distorted distorted 4574 4589 4590 4591 4607 P G D 13 distorted distorted 4596 4608 4609 4610 ---------------------------------------------------------------------------------