#
# This file describes the connectivity of amino acid sidechains.
# The format uses commas to separate 4-character, PDB-style atom names
# and semi-colons to separate different polylines (like P in kinemage format)
#
aminoacid.mc = " N  , CA , C  , O  "
aminoacid.hy = " N  , H  ; CA , HA "

gly.sc = ""
gly.hy = " CA ,1HA ; CA ,2HA ; CA , HA2; CA , HA3"
ala.sc = " CA , CB "
ala.hy = " CB ,1HB ; CB ,2HB ; CB ,3HB ; CB , HB1; CB , HB2; CB , HB3"
val.sc = " CA , CB , CG1; CB , CG2"
val.hy = " CB , HB ; CG1,1HG1; CG1,2HG1; CG1,3HG1; CG2,1HG2; CG2,2HG2; CG2,3HG2; CG1,HG11; CG1,HG12; CG1,HG13; CG2,HG21; CG2,HG22; CG2,HG23"
leu.sc = " CA , CB , CG , CD1; CG , CD2"
leu.hy = " CB ,1HB ; CB ,2HB ; CG , HG ; CD1,1HD1; CD1,2HD1; CD1,3HD1; CD2,1HD2; CD2,2HD2; CD2,3HD2; CB , HB2; CB , HB3; CD1,HD11; CD1,HD12; CD1,HD13; CD2,HD21; CD2,HD22; CD2,HD23"
ile.sc = " CA , CB , CG1, CD1; CB , CG2"
ile.hy = " CB , HB ; CG1,1HG1; CG1,2HG1; CG2,1HG2; CG2,2HG2; CG2,3HG2; CD1,1HD1; CD1,2HD1; CD1,3HD1; CG1,HG12; CG1,HG13; CG2,HG21; CG2,HG22; CG2,HG23; CD1,HD11; CD1,HD12; CD1,HD13"
pro.sc = " CA , CB , CG , CD , N  "
pro.hy = " CB ,1HB ; CB ,2HB ; CG ,1HG ; CG ,2HG ; CD ,1HD ; CD ,2HD ; CB , HB2; CB , HB3; CG , HG2; CG , HG3; CD , HD2; CD , HD3"

phe.sc = " CA , CB , CG , CD1, CE1, CZ , CE2, CD2, CG "
phe.hy = " CB ,1HB ; CB ,2HB ; CD1, HD1; CD2, HD2; CE1, HE1; CE2, HE2; CZ , HZ ; CB , HB2; CB , HB3"
tyr.sc = " CA , CB , CG , CD1, CE1, CZ , CE2, CD2, CG ; CZ , OH "
tyr.hy = " CB ,1HB ; CB ,2HB ; CD1, HD1; CD2, HD2; CE1, HE1; CE2, HE2; OH , HH ; CB , HB2; CB , HB3"
trp.sc = " CA , CB , CG , CD1, NE1, CE2, CD2, CG ; CD2, CE3, CZ3, CH2, CZ2, CE2"
trp.hy = " CB ,1HB ; CB ,2HB ; CD1, HD1; NE1, HE1; CZ2, HZ2; CH2, HH2; CE3, HE3; CZ3, HZ3; CB , HB2; CB , HB3"

ser.sc = " CA , CB , OG "
ser.hy = " CB ,1HB ; CB ,2HB ; OG , HG ; CB , HB2; CB , HB3"
thr.sc = " CA , CB , OG1; CB , CG2"
thr.hy = " CB , HB ; OG1, HG1; CG2,1HG2; CG2,2HG2; CG2,3HG2; CG2,HG21; CG2,HG22; CG2,HG23"
cys.sc = " CA , CB , SG "
cys.hy = " CB ,1HB ; CB ,2HB ; SG , HG ; CB , HB2; CB , HB3; SG , HG "
met.sc = " CA , CB , CG , SD , CE "
met.hy = " CB ,1HB ; CB ,2HB ; CG ,1HG ; CG ,2HG ; CE ,1HE ; CE ,2HE ; CE ,3HE ; CB , HB2; CB , HB3; CG , HG2; CG , HG3; CE , HE1; CE , HE2; CE , HE3"
mse.sc = " CA , CB , CG ,SED , CE ; CG ,SE  , CE "
mse.hy = " CB ,1HB ; CB ,2HB ; CG ,1HG ; CG ,2HG ; CE ,1HE ; CE ,2HE ; CE ,3HE ; CB , HB2; CB , HB3; CG , HG2; CG , HG3; CE , HE1; CE , HE2; CE , HE3"

lys.sc = " CA , CB , CG , CD , CE , NZ "
lys.hy = " CB ,1HB ; CB ,2HB ; CG ,1HG ; CG ,2HG ; CD ,1HD ; CD ,2HD ; CE ,1HE ; CE ,2HE ; NZ ,1HZ ; NZ ,2HZ ; NZ ,3HZ ; CB , HB2; CB , HB3; CG , HG2; CG , HG3; CD , HD2; CD , HD3; CE , HE2; CE , HE3; NZ , HZ1; NZ , HZ2; NZ , HZ3"
his.sc = " CA , CB , CG , ND1, CE1, NE2, CD2, CG "
his.hy = " CB ,1HB ; CB ,2HB ; ND1, HD1; CE1, HE1; NE2, HE2; CD2, HD2; CB , HB2; CB , HB3"
arg.sc = " CA , CB , CG , CD , NE , CZ , NH1; CZ , NH2"
arg.hy = " CB ,1HB ; CB ,2HB ; CG ,1HG ; CG ,2HG ; CD ,1HD ; CD ,2HD ; NE , HE ; NH1,1HH1; NH1,2HH1; NH2,1HH2; NH2,2HH2; CB , HB2; CB , HB3; CG , HG2; CG , HG3; CD , HD2; CD , HD3; NH1,HH11; NH1,HH12; NH2,HH21; NH2,HH22"

asp.sc = " CA , CB , CG , OD1; CG , OD2"
asp.hy = " CB ,1HB ; CB ,2HB ; CB , HB2; CB , HB3"
asn.sc = " CA , CB , CG , OD1; CG , ND2"
asn.hy = " CB ,1HB ; CB ,2HB ; ND2,1HD2; ND2,2HD2; CB , HB2; CB , HB3; ND2,HD21; ND2,HD22"
gln.sc = " CA , CB , CG , CD , OE1; CD , NE2"
gln.hy = " CB ,1HB ; CB ,2HB ; CG ,1HG ; CG ,2HG ; NE2,1HE2; NE2,2HE2; CB , HB2; CB , HB3; CG , HG2; CG , HG3; NE2,HE21; NE2,HE22"
glu.sc = " CA , CB , CG , CD , OE1; CD , OE2"
glu.hy = " CB ,1HB ; CB ,2HB ; CG ,1HG ; CG ,2HG ; CB , HB2; CB , HB3; CG , HG2; CG , HG3"

