📄 residue
字号:
#
# This table contains the parameters applied to the target protein.
# Twenty amino acids as well as several specific residues are presented.
# The lines headed by "ATOM" are organized as following:
# The 1st column: heading
# The 2nd column: name of the atom used in PDB file
# The 3rd column: atom type used in AMBER force field
# The 4th column: atomic hydrophobic scale, derived from XLOGP2
# The 5th column: hydrogen bonding character
# The 6th column: VDW radius from AMBER force field
# The 7th column: atom type used in Tripos force field
#
#----------------------------------------------------------------------------
# XlogP HB Charge r Type
#----------------------------------------------------------------------------
RESI ACE 7 0.00 ! Acetyl
ATOM C C -0.030 N 0.000 1.90 C.2
ATOM O O -0.399 A 0.000 1.66 O.2
ATOM CA CT 0.267 N 0.000 1.94 C.3
ATOM CH3 CT 0.267 N 0.000 1.94 C.3
ATOM HA1 HC 0.000 N 0.000 0.00 H
ATOM HA2 HC 0.000 N 0.000 0.00 H
ATOM HA3 HC 0.000 N 0.000 0.00 H
#
RESI ALA 11 0.00 ! Alanine
ATOM N N -0.096 D 0.000 1.83 N.am
ATOM H H 0.000 N 0.000 0.00 H
ATOM C C -0.030 N 0.000 1.90 C.2
ATOM O O -0.399 A 0.000 1.66 O.2
ATOM CA CT -0.305 N 0.000 1.94 C.3
ATOM HA H1 0.000 N 0.000 0.00 H
ATOM CB CT 0.528 N 0.000 1.94 C.3
ATOM HB1 HC 0.000 N 0.000 0.00 H
ATOM HB2 HC 0.000 N 0.000 0.00 H
ATOM HB3 HC 0.000 N 0.000 0.00 H
ATOM OXT O2 -0.880 A -0.500 1.66 O.co2
#
RESI ARG 25 1.00 ! Arginine
ATOM N N -0.096 D 0.000 1.83 N.am
ATOM H H 0.000 N 0.000 0.00 H
ATOM C C -0.030 N 0.000 1.90 C.2
ATOM O O -0.399 A 0.000 1.66 O.2
ATOM CA CT -0.305 N 0.000 1.94 C.3
ATOM HA H1 0.000 N 0.000 0.00 H
ATOM CB CT 0.358 N 0.000 1.94 C.3
ATOM HB1 HC 0.000 N 0.000 0.00 H
ATOM HB2 HC 0.000 N 0.000 0.00 H
ATOM CG CT 0.358 N 0.000 1.94 C.3
ATOM HG1 HC 0.000 N 0.000 0.00 H
ATOM HG2 HC 0.000 N 0.000 0.00 H
ATOM CD CT -0.137 N 0.000 1.94 C.3
ATOM HD1 H1 0.000 N 0.000 0.00 H
ATOM HD2 H1 0.000 N 0.000 0.00 H
ATOM NE N2 -0.096 D 0.000 1.83 N.am
ATOM HE H 0.000 N 0.000 0.00 H
ATOM CZ CA 0.005 N 1.000 1.90 C.cat
ATOM NH1 N2 -0.646 D 0.000 1.83 N.am
ATOM HH11 H 0.000 N 0.000 0.00 H
ATOM HH12 H 0.000 N 0.000 0.00 H
ATOM NH2 N2 -0.646 D 0.000 1.83 N.am
ATOM HH21 H 0.000 N 0.000 0.00 H
ATOM HH22 H 0.000 N 0.000 0.00 H
ATOM OXT O2 -0.880 A -0.500 1.66 O.co2
#
RESI ASN 17 0.00 ! Asparagine
ATOM N N -0.096 D 0.000 1.83 N.am
ATOM H H 0.000 N 0.000 0.00 H
ATOM C C -0.030 N 0.000 1.90 C.2
ATOM O O -0.399 A 0.000 1.66 O.2
ATOM CA CT -0.305 N 0.000 1.94 C.3
ATOM HA H1 0.000 N 0.000 0.00 H
ATOM CB CT -0.008 N 0.000 1.94 C.3
ATOM HB1 HC 0.000 N 0.000 0.00 H
ATOM HB2 HC 0.000 N 0.000 0.00 H
ATOM CG C -0.030 N 0.000 1.90 C.2
ATOM OD1 O -0.399 A 0.000 1.66 O.2
ATOM AD1 O -0.399 A 0.000 1.66 O.2
ATOM ND2 N -0.646 D 0.000 1.83 N.am
ATOM AD2 N -0.646 D 0.000 1.83 N.am
ATOM HD21 H 0.000 N 0.000 0.00 H
ATOM HD22 H 0.000 N 0.000 0.00 H
ATOM OXT O2 -0.880 A -0.500 1.66 O.co2
#
RESI ASP 13 -1.00 ! Aspartic acid
ATOM N N -0.096 D 0.000 1.83 N.am
ATOM H H 0.000 N 0.000 0.00 H
ATOM C C -0.030 N 0.000 1.90 C.2
ATOM O O -0.399 A 0.000 1.66 O.2
ATOM CA CT -0.305 N 0.000 1.94 C.3
ATOM HA H1 0.000 N 0.000 0.00 H
ATOM CB CT 0.008 N 0.000 1.94 C.3
ATOM HB1 HC 0.000 N 0.000 0.00 H
ATOM HB2 HC 0.000 N 0.000 0.00 H
ATOM CG C -0.030 N 0.000 1.90 C.2
ATOM OD1 O2 -0.880 A -0.500 1.66 O.co2
ATOM OD2 O2 -0.880 A -0.500 1.66 O.co2
ATOM OXT O2 -0.880 A -0.500 1.66 O.co2
#
RESI CYS 12 0.00 ! Cysteine
ATOM N N -0.096 D 0.000 1.83 N.am
ATOM H H 0.000 N 0.000 0.00 H
ATOM C C -0.030 N 0.000 1.90 C.2
ATOM O O -0.399 A 0.000 1.66 O.2
ATOM CA CT -0.305 N 0.000 1.94 C.3
ATOM HA H1 0.000 N 0.000 0.00 H
ATOM CB CT 0.358 N 0.000 1.94 C.3
ATOM HB1 H1 0.000 N 0.000 0.00 H
ATOM HB2 H1 0.000 N 0.000 0.00 H
ATOM SG SH 0.419 N 0.000 2.09 S.3
ATOM HG HS 0.000 N 0.000 0.00 H
ATOM OXT O2 -0.880 A -0.500 1.66 O.co2
#
RESI GLN 20 0.00 ! Glutamine
ATOM N N -0.096 D 0.000 1.83 N.am
ATOM H H 0.000 N 0.000 0.00 H
ATOM C C -0.030 N 0.000 1.90 C.2
ATOM O O -0.399 A 0.000 1.66 O.2
ATOM CA CT -0.305 N 0.000 1.94 C.3
ATOM HA H1 0.000 N 0.000 0.00 H
ATOM CB CT 0.358 N 0.000 1.94 C.3
ATOM HB1 HC 0.000 N 0.000 0.00 H
ATOM HB2 HC 0.000 N 0.000 0.00 H
ATOM CG CT -0.008 N 0.000 1.94 C.3
ATOM HG1 HC 0.000 N 0.000 0.00 H
ATOM HG2 HC 0.000 N 0.000 0.00 H
ATOM CD C -0.030 N 0.000 1.90 C.2
ATOM OE1 O -0.399 A 0.000 1.66 O.2
ATOM AE1 O -0.399 A 0.000 1.66 O.2
ATOM NE2 N -0.646 D 0.000 1.83 N.am
ATOM AE2 N -0.646 D 0.000 1.83 N.am
ATOM HE21 H 0.000 N 0.000 0.00 H
ATOM HE22 H 0.000 N 0.000 0.00 H
ATOM OXT O2 -0.880 A -0.500 1.66 O.co2
#
RESI GLU 16 -1.00 ! Glutamic acid
ATOM N N -0.096 D 0.000 1.83 N.am
ATOM H H 0.000 N 0.000 0.00 H
ATOM C C -0.030 N 0.000 1.90 C.2
ATOM O O -0.399 A 0.000 1.66 O.2
ATOM CA CT -0.305 N 0.000 1.94 C.3
ATOM HA H1 0.000 N 0.000 0.00 H
ATOM CB CT 0.358 N 0.000 1.94 C.3
ATOM HB1 HC 0.000 N 0.000 0.00 H
ATOM HB2 HC 0.000 N 0.000 0.00 H
ATOM CG CT -0.008 N 0.000 1.94 C.3
ATOM HG1 HC 0.000 N 0.000 0.00 H
ATOM HG2 HC 0.000 N 0.000 0.00 H
ATOM CD C -0.030 N 0.000 1.90 C.2
ATOM OE1 O2 -0.880 A -0.500 1.66 O.co2
ATOM OE2 O2 -0.880 A -0.500 1.66 O.co2
ATOM OXT O2 -0.880 A -0.500 1.66 O.co2
#
RESI GLY 8 0.00 ! Glycine
ATOM N N -0.096 D 0.000 1.83 N.am
ATOM H H 0.000 N 0.000 0.00 H
ATOM C C -0.030 N 0.000 1.90 C.2
ATOM O O -0.399 A 0.000 1.66 O.2
ATOM CA CT -0.303 N 0.000 1.94 C.3
ATOM HA1 H1 0.000 N 0.000 0.00 H
ATOM HA2 H1 0.000 N 0.000 0.00 H
ATOM OXT O2 -0.880 A -0.500 1.66 O.co2
#
RESI HIS 19 0.90 ! Histidine (uncharged with proton on nd1)
ATOM N N -0.096 D 0.000 1.83 N.am
ATOM H H 0.000 N 0.000 0.00 H
ATOM C C -0.030 N 0.000 1.90 C.2
ATOM O O -0.399 A 0.000 1.66 O.2
ATOM CA CT -0.305 N 0.000 1.94 C.3
ATOM HA H1 0.000 N 0.000 0.00 H
ATOM CB CT -0.008 N 0.000 1.94 C.3
ATOM HB1 HC 0.000 N 0.000 0.00 H
ATOM HB2 HC 0.000 N 0.000 0.00 H
ATOM CG CC -0.027 N 0.000 1.90 C.2
ATOM ND1 NA 0.135 DA 0.500 1.87 N.2
ATOM HD1 H 0.000 N 0.000 0.00 H
ATOM CD2 CV -0.310 N 0.000 1.90 C.2
ATOM HD2 H4 0.000 N 0.000 0.00 H
ATOM CE1 CR -0.310 N 0.000 1.90 C.2
ATOM HE1 H5 0.000 N 0.000 0.00 H
ATOM NE2 NB 0.135 DA 0.500 1.87 N.2
ATOM HE2 H5 0.000 N 0.000 0.00 H
ATOM OXT O2 -0.880 A -0.500 1.66 O.co2
#
RESI ILE 20 0.00 ! Isoleucine
ATOM N N -0.096 D 0.000 1.83 N.am
ATOM H H 0.000 N 0.000 0.00 H
ATOM C C -0.030 N 0.000 1.90 C.2
ATOM O O -0.399 A 0.000 1.66 O.2
ATOM CA CT -0.305 N 0.000 1.94 C.3
ATOM HA H1 0.000 N 0.000 0.00 H
ATOM CB CT 0.127 N 0.000 1.94 C.3
ATOM HB HC 0.000 N 0.000 0.00 H
ATOM CG2 CT 0.528 N 0.000 1.94 C.3
ATOM HG21 HC 0.000 N 0.000 0.00 H
ATOM HG22 HC 0.000 N 0.000 0.00 H
ATOM HG23 HC 0.000 N 0.000 0.00 H
ATOM CG1 CT 0.358 N 0.000 1.94 C.3
ATOM HG11 HC 0.000 N 0.000 0.00 H
ATOM HG12 HC 0.000 N 0.000 0.00 H
ATOM CD1 CT 0.528 N 0.000 1.94 C.3
ATOM HD11 HC 0.000 N 0.000 0.00 H
ATOM HD12 HC 0.000 N 0.000 0.00 H
ATOM HD13 HC 0.000 N 0.000 0.00 H
ATOM OXT O2 -0.880 A -0.500 1.66 O.co2
#
RESI LEU 20 0.00 ! Leucine
ATOM N N -0.096 D 0.000 1.83 N.am
ATOM H H 0.000 N 0.000 0.00 H
ATOM C C -0.030 N 0.000 1.90 C.2
ATOM O O -0.399 A 0.000 1.66 O.2
ATOM CA CT -0.305 N 0.000 1.94 C.3
ATOM HA H1 0.000 N 0.000 0.00 H
ATOM CB CT 0.358 N 0.000 1.94 C.3
ATOM HB1 HC 0.000 N 0.000 0.00 H
ATOM HB2 HC 0.000 N 0.000 0.00 H
ATOM CG CT 0.127 N 0.000 1.94 C.3
ATOM HG HC 0.000 N 0.000 0.00 H
ATOM CD1 CT 0.528 N 0.000 1.94 C.3
ATOM HD11 HC 0.000 N 0.000 0.00 H
ATOM HD12 HC 0.000 N 0.000 0.00 H
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