trunk/proteinstructure/contactTypes.dat

# Contact types definitions: 
#   contact types names in lines starting with '>', then the contact type name and last the type: either "multi" or "single"
#   then list of space separated atom names after each three letter aminoacid code
#   lines starting with # are comments
> ALL multi
TRP: CE2 CA C O CB CG CD1 CD2 CH2 CZ3 CZ2 CE3 NE1 N
CYS: SG CB O CA C N
GLN: CA CG N NE2 OE1 CD C O CB
ALA: CA C N CB O
VAL: CG1 CB O C CA N CG2
LEU: N CA C O CB CG CD2 CD1
ASP: N CB OD2 CG CA C O OD1
SER: C N CA O CB OG
PRO: O C CB CG CA CD N
THR: CA N C CG2 OG1 CB O
PHE: O CE2 CE1 CG C N CA CB CD2 CD1 CZ
ARG: NH2 CZ NE CD CG C CA N NH1 CB O
LYS: C CA N O CB CG CD CE NZ
MET: CA O C CB CE N CG SD
HIS: CE1 CD2 ND1 CG CB O C CA N NE2
GLY: N CA C O
ILE: CG2 CD1 O N CA C CB CG1
GLU: C N CA OE2 OE1 CD CG CB O
ASN: ND2 OD1 CB O CG C CA N
TYR: CD2 CD1 OH CZ CE2 N CA C O CB CG CE1
> BB multi
TRP: CA N C O
CYS: CA N C O
GLN: CA N C O
ALA: CA N C O
VAL: CA N C O
LEU: CA N C O
ASP: CA N C O
SER: CA N C O
PRO: CA N C O
THR: CA N C O
PHE: CA N C O
ARG: CA N C O
LYS: CA N C O
MET: CA N C O
HIS: CA N C O
GLY: CA N C O
ILE: CA N C O
GLU: CA N C O
ASN: CA N C O
TYR: CA N C O
> SC multi
TRP: CE2 CB CG CD1 CD2 CH2 CZ3 CZ2 CE3 NE1
CYS: SG CB
GLN: CG NE2 OE1 CD CB
ALA: CB
VAL: CG1 CB CG2
LEU: CB CG CD2 CD1
ASP: CB OD2 CG OD1
SER: CB OG
PRO: CB CG CD
THR: CG2 OG1 CB
PHE: CE2 CE1 CG CB CD2 CD1 CZ
ARG: NH2 CZ NE CD CG NH1 CB
LYS: CB CG CD CE NZ
MET: CB CE CG SD
HIS: CE1 CD2 ND1 CG CB NE2
GLY:
ILE: CG2 CD1 CB CG1
GLU: OE2 OE1 CD CG CB
ASN: ND2 OD1 CB CG
TYR: CD2 CD1 OH CZ CE2 CB CG CE1
> Ca single
TRP: CA
CYS: CA
GLN: CA
ALA: CA
VAL: CA
LEU: CA
ASP: CA
SER: CA
PRO: CA
THR: CA
PHE: CA
ARG: CA
LYS: CA
MET: CA
HIS: CA
GLY: CA
ILE: CA
GLU: CA
ASN: CA
TYR: CA
> Cb single
TRP: CB
CYS: CB
GLN: CB
ALA: CB
VAL: CB
LEU: CB
ASP: CB
SER: CB
PRO: CB
THR: CB
PHE: CB
ARG: CB
LYS: CB
MET: CB
HIS: CB
GLY: CA
ILE: CB
GLU: CB
ASN: CB
TYR: CB
> Cg single
TRP: CD2
CYS: SG
GLN: CG
ALA:
VAL: CG1
LEU: CG
ASP: CG
SER: OG
PRO: CG
THR: OG1
PHE: CG
ARG: NE
LYS: CD
MET: CG
HIS: CG
GLY:
ILE: CG1
ASN: CG
GLU: CG
TYR: CG
> C single
TRP: C
CYS: C
GLN: C
ALA: C
VAL: C
LEU: C
ASP: C
SER: C
PRO: C
THR: C
PHE: C
ARG: C
LYS: C
MET: C
HIS: C
GLY: C
ILE: C
GLU: C
ASN: C
TYR: C
Revision:	326
Committed:	Thu Sep 20 14:49:55 2007 UTC (13 years, 5 months ago) by duarte
File size:	2237 byte(s)
Log Message:	Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file Changed all references accordingly
Line	File contents
1	# Contact types definitions:
2	# contact types names in lines starting with '>', then the contact type name and last the type: either "multi" or "single"
3	# then list of space separated atom names after each three letter aminoacid code
4	# lines starting with # are comments
5	> ALL multi
6	TRP: CE2 CA C O CB CG CD1 CD2 CH2 CZ3 CZ2 CE3 NE1 N
7	CYS: SG CB O CA C N
8	GLN: CA CG N NE2 OE1 CD C O CB
9	ALA: CA C N CB O
10	VAL: CG1 CB O C CA N CG2
11	LEU: N CA C O CB CG CD2 CD1
12	ASP: N CB OD2 CG CA C O OD1
13	SER: C N CA O CB OG
14	PRO: O C CB CG CA CD N
15	THR: CA N C CG2 OG1 CB O
16	PHE: O CE2 CE1 CG C N CA CB CD2 CD1 CZ
17	ARG: NH2 CZ NE CD CG C CA N NH1 CB O
18	LYS: C CA N O CB CG CD CE NZ
19	MET: CA O C CB CE N CG SD
20	HIS: CE1 CD2 ND1 CG CB O C CA N NE2
21	GLY: N CA C O
22	ILE: CG2 CD1 O N CA C CB CG1
23	GLU: C N CA OE2 OE1 CD CG CB O
24	ASN: ND2 OD1 CB O CG C CA N
25	TYR: CD2 CD1 OH CZ CE2 N CA C O CB CG CE1
26	> BB multi
27	TRP: CA N C O
28	CYS: CA N C O
29	GLN: CA N C O
30	ALA: CA N C O
31	VAL: CA N C O
32	LEU: CA N C O
33	ASP: CA N C O
34	SER: CA N C O
35	PRO: CA N C O
36	THR: CA N C O
37	PHE: CA N C O
38	ARG: CA N C O
39	LYS: CA N C O
40	MET: CA N C O
41	HIS: CA N C O
42	GLY: CA N C O
43	ILE: CA N C O
44	GLU: CA N C O
45	ASN: CA N C O
46	TYR: CA N C O
47	> SC multi
48	TRP: CE2 CB CG CD1 CD2 CH2 CZ3 CZ2 CE3 NE1
49	CYS: SG CB
50	GLN: CG NE2 OE1 CD CB
51	ALA: CB
52	VAL: CG1 CB CG2
53	LEU: CB CG CD2 CD1
54	ASP: CB OD2 CG OD1
55	SER: CB OG
56	PRO: CB CG CD
57	THR: CG2 OG1 CB
58	PHE: CE2 CE1 CG CB CD2 CD1 CZ
59	ARG: NH2 CZ NE CD CG NH1 CB
60	LYS: CB CG CD CE NZ
61	MET: CB CE CG SD
62	HIS: CE1 CD2 ND1 CG CB NE2
63	GLY:
64	ILE: CG2 CD1 CB CG1
65	GLU: OE2 OE1 CD CG CB
66	ASN: ND2 OD1 CB CG
67	TYR: CD2 CD1 OH CZ CE2 CB CG CE1
68	> Ca single
69	TRP: CA
70	CYS: CA
71	GLN: CA
72	ALA: CA
73	VAL: CA
74	LEU: CA
75	ASP: CA
76	SER: CA
77	PRO: CA
78	THR: CA
79	PHE: CA
80	ARG: CA
81	LYS: CA
82	MET: CA
83	HIS: CA
84	GLY: CA
85	ILE: CA
86	GLU: CA
87	ASN: CA
88	TYR: CA
89	> Cb single
90	TRP: CB
91	CYS: CB
92	GLN: CB
93	ALA: CB
94	VAL: CB
95	LEU: CB
96	ASP: CB
97	SER: CB
98	PRO: CB
99	THR: CB
100	PHE: CB
101	ARG: CB
102	LYS: CB
103	MET: CB
104	HIS: CB
105	GLY: CA
106	ILE: CB
107	GLU: CB
108	ASN: CB
109	TYR: CB
110	> Cg single
111	TRP: CD2
112	CYS: SG
113	GLN: CG
114	ALA:
115	VAL: CG1
116	LEU: CG
117	ASP: CG
118	SER: OG
119	PRO: CG
120	THR: OG1
121	PHE: CG
122	ARG: NE
123	LYS: CD
124	MET: CG
125	HIS: CG
126	GLY:
127	ILE: CG1
128	ASN: CG
129	GLU: CG
130	TYR: CG
131	> C single
132	TRP: C
133	CYS: C
134	GLN: C
135	ALA: C
136	VAL: C
137	LEU: C
138	ASP: C
139	SER: C
140	PRO: C
141	THR: C
142	PHE: C
143	ARG: C
144	LYS: C
145	MET: C
146	HIS: C
147	GLY: C
148	ILE: C
149	GLU: C
150	ASN: C
151	TYR: C