ID code: '4KTQ' 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' --------------------------------------------------------------------------------- 3958 C1' G B 101 beta 3954 3959 3957 3980 C1' A B 102 beta 3976 3981 3979 4001 C1' C B 103 beta 3997 4002 4000 4020 C1' C B 104 beta 4016 4021 4019 4039 C1' A B 105 beta 4035 4040 4038 4060 C1' C B 106 beta 4056 4061 4059 4079 C1' G B 107 beta 4075 4080 4078 4101 C1' G B 108 beta 4097 4102 4100 4123 C1' C B 109 beta 4119 4124 4122 4142 C1' G B 110 beta 4138 4143 4141 4164 C1' C B 111 beta 4160 4165 4163 4181 C1' DDC B 112 beta 4180 4182 4190 4248 C1' G D 205 beta 4244 4249 4247 4270 C1' G D 206 beta 4266 4271 4269 4292 C1' C D 207 beta 4288 4293 4291 4311 C1' G D 208 beta 4307 4312 4310 4333 C1' C D 209 beta 4329 4334 4332 4352 C1' C D 210 beta 4348 4353 4351 4371 C1' G D 211 beta 4367 4372 4370 4393 C1' T D 212 beta 4389 4394 4392 4413 C1' G D 213 beta 4409 4414 4412 4435 C1' G D 214 beta 4431 4436 4434 4457 C1' T D 215 beta 4453 4458 4456 4477 C1' C D 216 beta 4473 4478 4476 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3957 C2' G B 101 3958 3955 3979 C2' A B 102 3980 3977 4000 C2' C B 103 4001 3998 4019 C2' C B 104 4020 4017 4038 C2' A B 105 4039 4036 4059 C2' C B 106 4060 4057 4078 C2' G B 107 4079 4076 4100 C2' G B 108 4101 4098 4122 C2' C B 109 4123 4120 4141 C2' G B 110 4142 4139 4163 C2' C B 111 4164 4161 4190 C2' DDC B 112 4181 4191 4247 C2' G D 205 4248 4245 4269 C2' G D 206 4270 4267 4291 C2' C D 207 4292 4289 4310 C2' G D 208 4311 4308 4332 C2' C D 209 4333 4330 4351 C2' C D 210 4352 4349 4370 C2' G D 211 4371 4368 4392 C2' T D 212 4393 4390 4412 C2' G D 213 4413 4410 4434 C2' G D 214 4435 4432 4456 C2' T D 215 4457 4454 4476 C2' C D 216 4477 4474 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3955 C3' G B 101 OK 3953 3956 3957 3977 C3' A B 102 OK 3975 3978 3979 3998 C3' C B 103 OK 3996 3999 4000 4017 C3' C B 104 OK 4015 4018 4019 4036 C3' A B 105 OK 4034 4037 4038 4057 C3' C B 106 OK 4055 4058 4059 4076 C3' G B 107 OK 4074 4077 4078 4098 C3' G B 108 OK 4096 4099 4100 4120 C3' C B 109 OK 4118 4121 4122 4139 C3' G B 110 OK 4137 4140 4141 4161 C3' C B 111 OK 4159 4162 4163 4191 C3' DDC B 112 4179 4190 4245 C3' G D 205 OK 4243 4246 4247 4267 C3' G D 206 OK 4265 4268 4269 4289 C3' C D 207 OK 4287 4290 4291 4308 C3' G D 208 OK 4306 4309 4310 4330 C3' C D 209 OK 4328 4331 4332 4349 C3' C D 210 OK 4347 4350 4351 4368 C3' G D 211 OK 4366 4369 4370 4390 C3' T D 212 OK 4388 4391 4392 4410 C3' G D 213 OK 4408 4411 4412 4432 C3' G D 214 OK 4430 4433 4434 4454 C3' T D 215 OK 4452 4455 4456 4474 C3' C D 216 OK 4472 4475 4476 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3953 C4' G B 101 OK 3955 3952 3954 3975 C4' A B 102 OK 3977 3974 3976 3996 C4' C B 103 OK 3998 3995 3997 4015 C4' C B 104 OK 4017 4014 4016 4034 C4' A B 105 OK 4036 4033 4035 4055 C4' C B 106 OK 4057 4054 4056 4074 C4' G B 107 OK 4076 4073 4075 4096 C4' G B 108 OK 4098 4095 4097 4118 C4' C B 109 OK 4120 4117 4119 4137 C4' G B 110 OK 4139 4136 4138 4159 C4' C B 111 OK 4161 4158 4160 4179 C4' DDC B 112 OK 4191 4178 4180 4243 C4' G D 205 OK 4245 4242 4244 4265 C4' G D 206 OK 4267 4264 4266 4287 C4' C D 207 OK 4289 4286 4288 4306 C4' G D 208 OK 4308 4305 4307 4328 C4' C D 209 OK 4330 4327 4329 4347 C4' C D 210 OK 4349 4346 4348 4366 C4' G D 211 OK 4368 4365 4367 4388 C4' T D 212 OK 4390 4387 4389 4408 C4' G D 213 OK 4410 4407 4409 4430 C4' G D 214 OK 4432 4429 4431 4452 C4' T D 215 OK 4454 4451 4453 4472 C4' C D 216 OK 4474 4471 4473 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3952 C5' G B 101 3951 3953 3974 C5' A B 102 3973 3975 3995 C5' C B 103 3994 3996 4014 C5' C B 104 4013 4015 4033 C5' A B 105 4032 4034 4054 C5' C B 106 4053 4055 4073 C5' G B 107 4072 4074 4095 C5' G B 108 4094 4096 4117 C5' C B 109 4116 4118 4136 C5' G B 110 4135 4137 4158 C5' C B 111 4157 4159 4178 C5' DDC B 112 4177 4179 4242 C5' G D 205 4241 4243 4264 C5' G D 206 4263 4265 4286 C5' C D 207 4285 4287 4305 C5' G D 208 4304 4306 4327 C5' C D 209 4326 4328 4346 C5' C D 210 4345 4347 4365 C5' G D 211 4364 4366 4387 C5' T D 212 4386 4388 4407 C5' G D 213 4406 4408 4429 C5' G D 214 4428 4430 4451 C5' T D 215 4450 4452 4471 C5' C D 216 4470 4472 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3970 P A B 102 OK OK 3956 3971 3972 3973 3991 P C B 103 distorted distorted 3978 3992 3993 3994 4010 P C B 104 OK OK 3999 4011 4012 4013 4029 P A B 105 OK OK 4018 4030 4031 4032 4050 P C B 106 OK OK 4037 4051 4052 4053 4069 P G B 107 OK OK 4058 4070 4071 4072 4091 P G B 108 OK OK 4077 4092 4093 4094 4113 P C B 109 OK OK 4099 4114 4115 4116 4132 P G B 110 OK OK 4121 4133 4134 4135 4154 P C B 111 OK OK 4140 4155 4156 4157 4174 P DDC B 112 OK OK 4162 4175 4176 4177 4260 P G D 206 OK OK 4246 4261 4262 4263 4282 P C D 207 OK OK 4268 4283 4284 4285 4301 P G D 208 OK OK 4290 4302 4303 4304 4323 P C D 209 OK OK 4309 4324 4325 4326 4342 P C D 210 OK OK 4331 4343 4344 4345 4361 P G D 211 OK OK 4350 4362 4363 4364 4383 P T D 212 OK OK 4369 4384 4385 4386 4403 P G D 213 OK OK 4391 4404 4405 4406 4425 P G D 214 OK OK 4411 4426 4427 4428 4447 P T D 215 OK OK 4433 4448 4449 4450 4467 P C D 216 distorted distorted 4455 4468 4469 4470 ---------------------------------------------------------------------------------