#
# 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).
# It uses the old PDB v2.3 nomenclature.
#
aa.mc = " N  , CA , C  , O  , OXT"
aa.hy = " N  , H  ; CA , HA "

gly.sc = ""
gly.hy = " CA ,1HA ; CA ,2HA "
ala.sc = " CA , CB "
ala.hy = " CB ,1HB ; CB ,2HB ; CB ,3HB "
val.sc = " CA , CB , CG1; CB , CG2"
val.hy = " CB , HB ; CG1,1HG1; CG1,2HG1; CG1,3HG1; CG2,1HG2; CG2,2HG2; CG2,3HG2"
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"
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"
pro.sc = " CA , CB , CG , CD , N  "
pro.hy = " CB ,1HB ; CB ,2HB ; CG ,1HG ; CG ,2HG ; CD ,1HD ; CD ,2HD ;"

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 "
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 "
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"

ser.sc = " CA , CB , OG "
ser.hy = " CB ,1HB ; CB ,2HB ; OG , HG "
thr.sc = " CA , CB , OG1; CB , CG2"
thr.hy = " CB , HB ; OG1, HG1; CG2,1HG2; CG2,2HG2; CG2,3HG2"
cys.sc = " CA , CB , SG "
cys.hy = " CB ,1HB ; CB ,2HB ; 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 "
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 "

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 "
his.sc = " CA , CB , CG , ND1, CE1, NE2, CD2, CG "
his.hy = " CB ,1HB ; CB ,2HB ; ND1, HD1; CE1, HE1; NE2, HE2; CD2, HD2"
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"

asp.sc = " CA , CB , CG , OD1; CG , OD2"
asp.hy = " CB ,1HB ; CB ,2HB "
asn.sc = " CA , CB , CG , OD1; CG , ND2"
asn.hy = " CB ,1HB ; CB ,2HB ; ND2,1HD2; ND2,2HD2"
gln.sc = " CA , CB , CG , CD , OE1; CD , NE2"
gln.hy = " CB ,1HB ; CB ,2HB ; CG ,1HG ; CG ,2HG ; NE2,1HE2; NE2,2HE2"
glu.sc = " CA , CB , CG , CD , OE1; CD , OE2"
glu.hy = " CB ,1HB ; CB ,2HB ; CG ,1HG ; CG ,2HG "

