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naccess.config
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naccess.config
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# Contributed by João Rodrigues & Mikael Trellet
name: NACCESS
types:
C_ALI 1.87 apolar
C_CAR 1.76 apolar
C_NUC 1.80 apolar
N_AMN 1.50 polar
N_AMD 1.65 polar
N_NUC 1.60 polar
O 1.40 polar
S 1.85 apolar
SE 1.80 apolar
P 1.90 apolar
atoms:
ANY C C_CAR
ANY O O
ANY CA C_ALI
ANY N N_AMD
ANY CB C_ALI
ANY OXT O
# nucleic acid
ANY P P
ANY OP1 O
ANY OP2 O
ANY OP3 O
ANY O1P O
ANY O2P O
ANY O3P O
ANY O5' O
ANY O4' O
ANY O3' O
ANY O2' O
ANY C5' C_NUC
ANY C4' C_NUC
ANY C3' C_NUC
ANY C2' C_NUC
ANY C1' C_NUC
ALA CB C_ALI # included so that RSA values will be generated
ARG CG C_ALI
ARG CD C_ALI
ARG NE N_AMD
ARG CZ C_CAR
ARG NH1 N_AMD
ARG NH2 N_AMD
ASN CG C_CAR
ASN OD1 O
ASN ND2 N_AMD
ASP CG C_CAR
ASP OD1 O
ASP OD2 O
CYS SG S
GLN CG C_ALI
GLN CD C_CAR
GLN OE1 O
GLN NE2 N_AMD
GLU CG C_ALI
GLU CD C_CAR
GLU OE1 O
GLU OE2 O
GLY CA C_ALI # included so that RSA values will be generated
HIS CG C_CAR
HIS ND1 N_AMD
HIS CD2 C_CAR
HIS NE2 N_AMD
HIS CE1 C_CAR
ILE CG1 C_ALI
ILE CG2 C_ALI
ILE CD1 C_ALI
LEU CG C_ALI
LEU CD1 C_ALI
LEU CD2 C_ALI
LYS CG C_ALI
LYS CD C_ALI
LYS CE C_ALI
LYS NZ N_AMN
MET CG C_ALI
MET SD S
MET CE C_ALI
PHE CG C_CAR
PHE CD1 C_CAR
PHE CD2 C_CAR
PHE CE1 C_CAR
PHE CE2 C_CAR
PHE CZ C_CAR
PRO CG C_ALI
PRO CD C_ALI
SEC SE SE
SER OG O
THR OG1 O
THR CG2 C_ALI
TRP CG C_CAR
TRP CD1 C_CAR
TRP CD2 C_CAR
TRP NE1 N_AMD
TRP CE2 C_CAR
TRP CE3 C_CAR
TRP CZ2 C_CAR
TRP CZ3 C_CAR
TRP CH2 C_CAR
TYR CG C_CAR
TYR CD1 C_CAR
TYR CD2 C_CAR
TYR CE1 C_CAR
TYR CE2 C_CAR
TYR CZ C_CAR
TYR OH O
VAL CG1 C_ALI
VAL CG2 C_ALI
# Modified aa
ALY CG C_ALI
ALY CD C_ALI
ALY CE C_ALI
ALY NZ N_AMN
ASH CG C_CAR
ASH OD1 O
ASH OD2 O
CYM SG S
CSP SG S
CYF SG S
CYC SG S
CFE SG S
DDZ CB C_ALI
GLH CG C_ALI
GLH CD C_CAR
GLH OE1 O
GLH OE2 O
HYP CG C_ALI
HYP CD C_ALI
MLZ CG C_ALI
MLZ CD C_ALI
MLZ CE C_ALI
MLZ NZ N_AMN
MLY CG C_ALI
MLY CD C_ALI
MLY CE C_ALI
MLY NZ N_AMN
M3L CG C_ALI
M3L CD C_ALI
M3L CE C_ALI
M3L NZ N_AMN
NEP CG C_CAR
NEP ND1 N_AMD
NEP CD2 C_CAR
NEP NE2 N_AMD
NEP CE1 C_CAR
PTR CG C_CAR
PTR CD1 C_CAR
PTR CD2 C_CAR
PTR CE1 C_CAR
PTR CE2 C_CAR
PTR CZ C_CAR
PTR OH O
SEP OG O
TOP OG1 O
TOP CG2 C_ALI
TYP CG C_CAR
TYP CD1 C_CAR
TYP CD2 C_CAR
TYP CE1 C_CAR
TYP CE2 C_CAR
TYP CZ C_CAR
TYP OH O
TYS CG C_CAR
TYS CD1 C_CAR
TYS CD2 C_CAR
TYS CE1 C_CAR
TYS CE2 C_CAR
TYS CZ C_CAR
TYS OH O
PNS OG O
PNS O1P O
PNS O2P O
PNS O3P O
PNS O33 O
PNS O35 O
PNS O40 O
PNS S44 S
PNS N36 N_AMD
PNS N41 N_AMD
PNS C32 C_CAR
PNS C34 C_CAR
PNS C39 C_CAR
PNS C28 C_ALI
PNS C29 C_ALI
PNS C30 C_ALI
PNS C31 C_ALI
PNS C37 C_ALI
PNS C38 C_ALI
PNS C42 C_ALI
PNS C43 C_ALI
# Nucleic acids
A N9 N_NUC
A C8 C_NUC
A N7 N_NUC
A C5 C_NUC
A C6 C_NUC
A N6 N_NUC
A N1 N_NUC
A C2 C_NUC
A N3 N_NUC
A C4 C_NUC
C N1 N_NUC
C C2 C_NUC
C O2 O
C N3 N_NUC
C C4 C_NUC
C N4 N_NUC
C C5 C_NUC
C C6 C_NUC
G N9 N_NUC
G C8 C_NUC
G N7 N_NUC
G C5 C_NUC
G C6 C_NUC
G O6 O
G N1 N_NUC
G C2 C_NUC
G N2 N_NUC
G N3 N_NUC
G C4 C_NUC
I N9 N_NUC
I C8 C_NUC
I N7 N_NUC
I C5 C_NUC
I C6 C_NUC
I O6 O
I N1 N_NUC
I C2 C_NUC
I N3 N_NUC
I C4 C_NUC
T N1 N_NUC
T C2 C_NUC
T O2 O
T N3 N_NUC
T C4 C_NUC
T O4 O
T C5 C_NUC
T C7 C_NUC
T C6 C_NUC
U N1 N_NUC
U C2 C_NUC
U O2 O
U N3 N_NUC
U C4 C_NUC
U O4 O
U C5 C_NUC
U C6 C_NUC
DA N9 N_NUC
DA C8 C_NUC
DA N7 N_NUC
DA C5 C_NUC
DA C6 C_NUC
DA N6 N_NUC
DA N1 N_NUC
DA C2 C_NUC
DA N3 N_NUC
DA C4 C_NUC
DC N1 N_NUC
DC C2 C_NUC
DC O2 O
DC N3 N_NUC
DC C4 C_NUC
DC N4 N_NUC
DC C5 C_NUC
DC C6 C_NUC
DG N9 N_NUC
DG C8 C_NUC
DG N7 N_NUC
DG C5 C_NUC
DG C6 C_NUC
DG O6 O
DG N1 N_NUC
DG C2 C_NUC
DG N2 N_NUC
DG N3 N_NUC
DG C4 C_NUC
DI N9 N_NUC
DI C8 C_NUC
DI N7 N_NUC
DI C5 C_NUC
DI C6 C_NUC
DI O6 O
DI N1 N_NUC
DI C2 C_NUC
DI N3 N_NUC
DI C4 C_NUC
DT N1 N_NUC
DT C2 C_NUC
DT O2 O
DT N3 N_NUC
DT C4 C_NUC
DT O4 O
DT C5 C_NUC
DT C7 C_NUC
DT C6 C_NUC
DU N1 N_NUC
DU C2 C_NUC
DU O2 O
DU N3 N_NUC
DU C4 C_NUC
DU O4 O
DU C5 C_NUC
DU C6 C_NUC
ADE N9 N_NUC
ADE C8 C_NUC
ADE N7 N_NUC
ADE C5 C_NUC
ADE C6 C_NUC
ADE N6 N_NUC
ADE N1 N_NUC
ADE C2 C_NUC
ADE N3 N_NUC
ADE C4 C_NUC
CYT N1 N_NUC
CYT C2 C_NUC
CYT O2 O
CYT N3 N_NUC
CYT C4 C_NUC
CYT N4 N_NUC
CYT C5 C_NUC
CYT C6 C_NUC
GUA N9 N_NUC
GUA C8 C_NUC
GUA N7 N_NUC
GUA C5 C_NUC
GUA C6 C_NUC
GUA O6 O
GUA N1 N_NUC
GUA C2 C_NUC
GUA N2 N_NUC
GUA N3 N_NUC
GUA C4 C_NUC
THY N1 N_NUC
THY C2 C_NUC
THY O2 O
THY N3 N_NUC
THY C4 C_NUC
THY O4 O
THY C5 C_NUC
THY C7 C_NUC
THY C6 C_NUC
URA N1 N_NUC
URA C2 C_NUC
URA O2 O
URA N3 N_NUC
URA C4 C_NUC
URA O4 O
URA C5 C_NUC
URA C6 C_NUC