# peptide_def.par -- This file Defines the Atoms and Residue of a ALL # Amino Acids Used by a variety of programs # Line begining with a # is a Comment line and ignored # Blank lines Separate one Record or List from the next # Spaces and Tabs separate entries within a record ATOM_NAMES N ND1 HZ1 HN ND2 HZ2 C HD1 HZ3 O HD2 OH CA HD21 HH HA HD22 HH2 CB HD1# HH11 HB1 CE HH12 HB2 CE1 HH21 HB# CE2 HH22 CG CE3 NH1 CG1 OE1 NH2 CG2 OE2 CH2 OG NE HE21 OG1 NE1 HE22 SG NE2 HA1 HG HE HA2 HG1 HE1 HD HG2 HE2 HB HG1# HE3 HG2# CD CZ HD2# CD1 CZ2 HG11 CD2 CZ3 HG12 OD1 NZ HE# OD2 HZ HA# HG# HD# HZ# HH1# HH2# HE2# HT# HB3 HG21 HG22 HG23 HD11 HD12 HD13 HT1 HT2 HT3 HD23 HG13 OT1 OT2 SD HG* HD* HAR HAR1 HAR2 HAR3 HAR4 HAR5 HAR6 HAR7 HAR8 HAR9 HAR10 HAR11 HAR12 HAR13 HAR14 HAR15 HAR16 HAR17 HAR18 HAR19 HAR20 HAR21 HAR22 HAR23 HAR24 HAR25 RESIDUE_NAMES BLNK GLY ALA VAL ILE LEU PHE PRO MET TRP CYS SER THR ASN GLN TYR HIS HIH ASP GLU LYS ARG RES ARO AA_DEFINITIONS AMINO_ACID BLNK CHAR_CODE 0 VALID_ATOMS EXCHANGEABLE SIDE_CHAIN BOND_ATOMS AMINO_ACID GLY CHAR_CODE G VALID_ATOMS N HN CA HA1 HA2 HA# C O EXCHANGEABLE HN SIDE_CHAIN BOND_ATOMS N HN N CA C O CA HA1 CA HA2 CA HA# AVRG_ATOM_TBL AVRG_ATOM Type True Names HA# FAST HA1 HA2 AMINO_ACID ALA CHAR_CODE A VALID_ATOMS N HN CA HA CB HB# HB1 HB2 HB3 C O EXCHANGEABLE HN SIDE_CHAIN CB HB# HB1 HB2 HB3 BOND_ATOMS N HN N CA C O CA HA CA CB CB HB# - CB HB1 CB HB2 CB HB3 AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 HB3 AMINO_ACID VAL CHAR_CODE V VALID_ATOMS N HN CA HA CB HB CG1 HG1# - CG2 HG2# C O HG11 HG12 HG13 - HG21 HG22 HG23 HG# EXCHANGEABLE HN SIDE_CHAIN CB HB CG1 HG1# CG2 HG2# HG11 HG12 HG13 - HG21 HG22 HG23 HG# BOND_ATOMS N HN N CA C O CA HA CA CB CB HB - CB CG1 CB CG2 CG1 HG1# CG2 HG2# - CG1 HG11 CG1 HG12 CG1 HG13 - CG2 HG21 CG2 HG22 CG2 HG23 AVRG_ATOM_TBL AVRG_ATOM Type True Names HG1# FAST HG11 HG12 HG13 HG2# FAST HG21 HG22 HG23 HG# SLOW HG2# HG1# AMINO_ACID ILE CHAR_CODE I VALID_ATOMS N HN CA HA CB HB CG1 HG11 - HG12 HG1# CG2 HG2# CD HD# CD1 HD1# C O - HG21 HG22 HG23 HD11 HD12 HD13 EXCHANGEABLE HN SIDE_CHAIN CB HB CG1 HG11 HG12 HG1# CG2 - HG2# CD HD# CD1 HD1# - HG21 HG22 HG23 HD11 HD12 HD13 BOND_ATOMS N HN N CA C O CA HA CA CB CB HB - CB CG1 CB CG2 CG1 HG11 CG1 HG12 CG1 HG1#- CG2 HG2# CG1 CD CD HD# CG1 CD1 CD1 HD1# - CG HG21 CG HG22 CG HG23 - CD HD11 CD HD12 CD HD13 AVRG_ATOM_TBL AVRG_ATOM Type True Names HG1# FAST HG11 HG12 HD1# ALIAS HD# HD# ALIAS HD1# HG2# FAST HG21 HG22 HG23 HD1# FAST HD11 HD12 HD13 # IUPAC name is HD1# but this atom has previously been called HD# AMINO_ACID LEU CHAR_CODE L VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - HG CD1 HD1# CD2 HD2# HD# C O - HD11 HD12 HD13 HD21 HD22 HD23 EXCHANGEABLE HN SIDE_CHAIN CB HB1 HB2 HB# CG HG CD1 HD1# - CD2 HD2# HD11 HD12 HD13 HD21 HD22 HD23 HD# BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CB CG CG CD1 - CG CD2 CG HG CD1 HD1# CD2 HD2# - CD1 HD11 CD1 HD12 CD1 HD13 - CD2 HD21 CD2 HD22 CD2 HD23 AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 HD1# FAST HD11 HD12 HD13 HD2# FAST HD21 HD22 HD23 HD# SLOW HD1# HD2# AMINO_ACID PHE CHAR_CODE F VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - CD1 HD1 CD2 HD2 CE1 HE1 CE2 - HD# HE# HE2 CZ HZ C O EXCHANGEABLE HN SIDE_CHAIN CB HB1 HB2 HB# CG CD1 HD1 CD2 - HD2 CE1 HE1 CE2 HE2 CZ HZ HD# HE# BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CG CD1 CG CD2 - CD1 CE1 CD2 CE2 CD1 HD1 CD2 HD2 - CE1 CZ CE2 CZ CE1 HE1 CE2 HE2 CZ HZ AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 HD# SLOW HD1 HD2 HE# SLOW HE1 HE2 AMINO_ACID PRO CHAR_CODE P VALID_ATOMS N CA HA CB HB1 HB2 HB# CG HG1 - HG2 HG# CD HD1 HD2 HD# C O EXCHANGEABLE SIDE_CHAIN CB HB1 HB2 HB# CG HG1 HG2 CD - HD1 HD2 HD# BOND_ATOMS N CD N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CG CD CG HG1 - CG HG2 CG HG# CD HD1 CD HD2 CD HD# AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 HG# FAST HG1 HG2 HD# FAST HD1 HD2 AMINO_ACID MET CHAR_CODE M VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - HG1 HG2 HG# CE HE# C O SD HE1 HE2 HE3 EXCHANGEABLE HN SIDE_CHAIN CB HB1 HB2 HB# CG HG1 HG2 HG# - CE HE# SD HE1 HE2 HE3 BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CG HG1 CG HG2 CG HG# - CB HB# CE HE# CE HE1 CE HE2 CE HE3 AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 HG# FAST HG1 HG2 HE# FAST HE1 HE2 HE3 AMINO_ACID TRP CHAR_CODE W VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - CD1 HD1 CD2 NE1 HE1 CE2 CE3 HE3- CZ2 HZ2 CZ3 HZ3 CH2 HH2 C O EXCHANGEABLE HN HE1 SIDE_CHAIN CB HB1 HB2 HB# CG CD1 HD1 CD2 - NE1 HE1 CE2 CE3 HE3 CZ2 HZ2 - CZ3 HZ3 CH2 HH2 BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CG CD1 CG CD2 - CD1 NE1 CD2 CE2 CD2 CE3 CD1 HD1 - NE1 CE2 CE2 CZ2 CE3 CZ3 CE3 HE3 - NE1 HE1 CZ2 CH2 CZ3 CH2 CZ2 HZ2 - CZ3 HZ3 CH2 HH2 AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 AMINO_ACID CYS CHAR_CODE C VALID_ATOMS N HN CA HA CB HB1 HB2 HB# SG HG C O EXCHANGEABLE HN SIDE_CHAIN CB HB1 HB2 HB# HG BOND_ATOMS N HN N CA C O CA HA CA CB CB HB1 - CB HB2 CB HB# SG HG AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 AMINO_ACID SER CHAR_CODE S VALID_ATOMS N HN CA HA CB HB1 HB2 HB# OG - HG1 HG C O OT1 OT2 EXCHANGEABLE HN SIDE_CHAIN CB HB1 HB2 HB# OG HG1 HG OT1 OT2 BOND_ATOMS N HN N CA C O CA HA CA CB CB HB1 - CB HB2 CB HB# CB OG HG1 OG HG OG AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 HG ALIAS HG1 HG1 ALIAS HG # IUPAC name is HG but this atom has previously been called HG1 AMINO_ACID THR CHAR_CODE T VALID_ATOMS N HN CA HA CB HB OG1 HG1 CG2- HG2# HG21 HG22 HG23 C O EXCHANGEABLE HN SIDE_CHAIN CB HB OG1 HG1 CG2 HG2# HG21 HG22 HG23 BOND_ATOMS N HN N CA C O CA HA CA CB CB OG1 - CB CG2 CB HB OG1 HG1 CG2 HG2# - CG2 HG21 CG2 HG22 CG2 HG23 AVRG_ATOM_TBL AVRG_ATOM Type True Names HG2# FAST HG21 HG22 HG23 AMINO_ACID RES CHAR_CODE X VALID_ATOMS N HN CA HA CB HB OG1 HG1 HG2 CG2- HG1# HG2# HG21 HG22 HG23 C O HA1 HA2 HB1 HB2 HB#- HG HG# HD1 HD2 HD1# HD2# HD# EXCHANGEABLE HN SIDE_CHAIN CB HB OG1 HG1 CG2 HG2# HG21 HG22 HG23 BOND_ATOMS N HN N CA C O CA HA CA CB CB OG1 - CB CG2 CB HB OG1 HG1 CG2 HG2# - CG2 HG21 CG2 HG22 CG2 HG23 AVRG_ATOM_TBL AVRG_ATOM Type True Names HG2# FAST HG21 HG22 HG23 AMINO_ACID ARO CHAR_CODE Z VALID_ATOMS HAR1 HAR2 HAR3 HAR4 HAR5 HAR6 HAR7 HAR8 HAR9 HAR10- HAR11 HAR12 HAR13 HAR14 HAR15 HAR16 HAR17 HAR18 HAR19- HAR20 HAR21 HAR22 HAR23 HAR24 HAR25- N HN CA HA CB HB OG1 HG1 HG2 CG2- HG1# HG2# HG21 HG22 HG23 C O HA1 HA2 HB1 HB2 HB#- HG HG# HD1 HD2 HD1# HD2# HD# EXCHANGEABLE HN SIDE_CHAIN CB HB OG1 HG1 CG2 HG2# HG21 HG22 HG23 BOND_ATOMS N HN N CA C O CA HA CA CB CB OG1 - CB CG2 CB HB OG1 HG1 CG2 HG2# - CG2 HG21 CG2 HG22 CG2 HG23 HAR1 HAR2 HAR2 HAR3 - HAR3 HAR4 HAR4 HAR5 HAR5 HAR6 HAR6 HAR7 HAR7 HAR8 - HAR8 HAR9 HAR9 HAR10 HAR10 HAR11 HAR11 HAR12 HAR12 HAR13 - HAR13 HAR14 HAR14 HAR15 HAR15 HAR16 HAR16 HAR17 HAR17 HAR18 - HAR18 HAR19 HAR19 HAR20 HAR20 HAR21 HAR21 HAR22 HAR22 HAR23 - HAR23 HAR24 HAR24 HAR25 AVRG_ATOM_TBL AVRG_ATOM Type True Names HG2# FAST HG21 HG22 HG23 AMINO_ACID ASN CHAR_CODE N VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - OD1 ND2 HD21 HD22 HD2# C O EXCHANGEABLE HN HD21 HD22 SIDE_CHAIN CB HB1 HB2 HB# CG OD1 ND2 HD21 HD22 BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CG ND2 CG OD1 - ND2 HD21 ND2 HD22 ND2 HD2# AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# SLOW HB1 HB2 HD2# FAST HD21 HD22 AMINO_ACID GLN CHAR_CODE Q VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - HG1 HG2 HG# CD OE1 NE2 HE21 HE22 - HE2# C O EXCHANGEABLE HN HE21 HE22 HE2# SIDE_CHAIN CB HB1 HB2 HB# CG HG1 HG2 HG# CD - OE1 NE2 HE21 HE22 HE2# BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CG CD CG HG1 - CG HG2 CG HG# CD OE1 CD NE2 NE2 HE21 - NE2 HE22 NE2 HE2# AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 HG# FAST HG1 HG2 HE2# FAST HE21 HE22 AMINO_ACID TYR CHAR_CODE Y VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - CD1 HD1 CD2 HD2 CE1 HE1 CE2 - HE2 HD# HE# CZ OH HH C O EXCHANGEABLE HN SIDE_CHAIN CB HB1 HB2 HB# CG CD1 HD1 CD2 - HD2 CE1 HE1 CE2 HE2 CZ - OH HH BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CG CD1 CG CD2 - CD1 CE1 CD2 CE2 CD1 HD1 CD2 HD2 - CE1 CZ CE2 CZ CE1 HE1 CE2 HE2 - CZ OH OH HH AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 HD# SLOW HD1 HD2 HE# SLOW HE1 HE2 AMINO_ACID HIH CHAR_CODE H VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - ND1 HD1 CD2 HD2 CE1 HE1 NE2 C O EXCHANGEABLE HN HD1 SIDE_CHAIN CB HB1 HB2 HB# CG ND1 HD1 CD2 - HD2 CE1 HE1 NE2 BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CG CD2 CG ND1 - ND1 CE1 CD2 NE2 ND1 HD1 CD2 HD2 - CE1 NE2 CE1 HE1 AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 AMINO_ACID HIS CHAR_CODE H VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - ND1 HD1 CD2 HD2 CE1 HE1 NE2 C O HE2 EXCHANGEABLE HN HD1 SIDE_CHAIN CB HB1 HB2 HB# CG ND1 HD1 CD2 - HD2 CE1 HE1 NE2 BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CG CD2 CG ND1 - ND1 CE1 CD2 NE2 ND1 HD1 CD2 HD2 - CE1 NE2 CE1 HE1 AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 AMINO_ACID ASP CHAR_CODE D VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - OD1 OD2 C O HD2 EXCHANGEABLE HN SIDE_CHAIN CB HB1 HB2 HB# CG OD1 OD2 BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CG OD1 CG OD2 AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 AMINO_ACID GLU CHAR_CODE E VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - HG1 HG2 HG# CD OE1 OE2 C O HT# - HT1 HT2 HT3 HE2 EXCHANGEABLE HN SIDE_CHAIN CB HB1 HB2 HB# CG HG1 HG2 HG# - CD OE1 OE2 HT# HT1 HT2 HT3 BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CG CD CG HG1 - CG HG2 CG HG# CD OE1 CD OE2 N HT# - N HT1 N HT2 N HT3 AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 HG# FAST HG1 HG2 HT# FAST HT1 HT2 HT3 AMINO_ACID LYS CHAR_CODE K VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - HG1 HG2 HG# CD HD1 HD2 HD# CE - HE1 HE2 HE# NZ HZ1 HZ2 HZ3 HZ# C O EXCHANGEABLE HN HZ1 HZ2 HZ3 HZ# SIDE_CHAIN CB HB1 HB2 HB# CG HG1 HG2 HG# - CD HD1 HD2 HD# CE HE1 HE2 HE# - NZ HZ1 HZ2 HZ3 HZ# BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CG CD CG HG1 - CG HG2 CG HG# CD CE CD HD1 CD HD2 - CD HD# CE NZ CE HE1 CE HE2 CE HE# - NZ HZ1 NZ HZ2 NZ HZ3 NZ HZ# AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 HG# FAST HG1 HG2 HD# FAST HD1 HD2 HE# FAST HE1 HE2 HZ# FAST HZ1 HZ2 HZ3 AMINO_ACID ARG CHAR_CODE R VALID_ATOMS N HN CA HA CB HB1 HB2 HB# CG - HG1 HG2 HG# CD HD1 HD2 HD# NE HE - CZ NH1 HH11 HH12 HH1# NH2 HH21 - HH22 HH2# HG1# C O EXCHANGEABLE HN HE HH11 HH12 HH1# HH21 HH22 HH2# SIDE_CHAIN CB HB1 HB2 HB# CG HG1 HG2 HG# CD - HD1 HD2 HD# NE HE CZ NH1 HH11 - HH12 HH1# NH2 HH21 HH22 HH2# BOND_ATOMS N HN N CA C O CA HA CA CB CB CG - CB HB1 CB HB2 CB HB# CG CD CG HG1 - CG HG2 CG HG# CD NE CD HD1 CD HD2 - CD HD# NE CZ NE HE CZ NH1 CZ NH2 - NH1 HH11 NH1 HH12 NH1 HH1# NH2 HH21 - NH2 HH22 NH2 HH2# AVRG_ATOM_TBL AVRG_ATOM Type True Names HB# FAST HB1 HB2 HG# FAST HG1 HG2 HD# FAST HD1 HD2 HH1# FAST HH11 HH12 HH2# FAST HH21 HH22 HG1# FAST HG1 HG2