core/structure/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
> ALL_H multi
ALA: C CA CB H HA HB1 HB2 HB3 N O
ARG: C CA CB CD CG CZ H HA HB2 HB3 HD2 HD3 HE HG2 HG3 HH11 HH12 HH21 HH22 N NE NH1 NH2 O
ASN: C CA CB CG H HA HB2 HB3 HD21 HD22 N ND2 O OD1
ASP: C CA CB CG H HA HB2 HB3 N O OD1 OD2
CYS: C CA CB H HA HB2 HB3 N O SG
GLN: C CA CB CD CG H HA HB2 HB3 HE21 HE22 HG2 HG3 N NE2 O OE1
GLU: C CA CB CD CG H HA HB2 HB3 HG2 HG3 N O OE1 OE2
GLY: C CA H HA2 HA3 N O
HIS: C CA CB CD2 CE1 CG H HA HB2 HB3 HD1 HD2 HE1 N ND1 NE2 O
ILE: C CA CB CD1 CG1 CG2 H HA HB HD11 HD12 HD13 HG12 HG13 HG21 HG22 HG23 N O
LEU: C CA CB CD1 CD2 CG H HA HB2 HB3 HD11 HD12 HD13 HD21 HD22 HD23 HG N O
LYS: C CA CB CD CE CG H HA HB2 HB3 HD2 HD3 HE2 HE3 HG2 HG3 HZ1 HZ2 HZ3 N NZ O
MET: C CA CB CE CG H HA HB2 HB3 HE1 HE2 HE3 HG2 HG3 N O SD
PHE: C CA CB CD1 CD2 CE1 CE2 CG CZ H HA HB2 HB3 HD1 HD2 HE1 HE2 HZ N O
PRO: C CA CB CD CG HA HB2 HB3 HD2 HD3 HG2 HG3 N O
SER: C CA CB H H1 H2 H3 HA HB2 HB3 HG N O OG
THR: C CA CB CG2 H HA HB HG1 HG21 HG22 HG23 N O OG1
TRP: C CA CB CD1 CD2 CE2 CE3 CG CH2 CZ2 CZ3 H HA HB2 HB3 HD1 HE1 HE3 HH2 HZ2 HZ3 N NE1 O
TYR: C CA CB CD1 CD2 CE1 CE2 CG CZ H HA HB2 HB3 HD1 HD2 HE1 HE2 HH N O OH
VAL: C CA CB CG1 CG2 H HA HB HG11 HG12 HG13 HG21 HG22 HG23 N O
> 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
> SC_CAGLY 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: CA
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:	1005
Committed:	Wed Mar 31 12:29:26 2010 UTC (12 years, 1 month ago) by hstehr
File size:	3850 byte(s)
Log Message:	refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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	> ALL_H multi
27	ALA: C CA CB H HA HB1 HB2 HB3 N O
28	ARG: C CA CB CD CG CZ H HA HB2 HB3 HD2 HD3 HE HG2 HG3 HH11 HH12 HH21 HH22 N NE NH1 NH2 O
29	ASN: C CA CB CG H HA HB2 HB3 HD21 HD22 N ND2 O OD1
30	ASP: C CA CB CG H HA HB2 HB3 N O OD1 OD2
31	CYS: C CA CB H HA HB2 HB3 N O SG
32	GLN: C CA CB CD CG H HA HB2 HB3 HE21 HE22 HG2 HG3 N NE2 O OE1
33	GLU: C CA CB CD CG H HA HB2 HB3 HG2 HG3 N O OE1 OE2
34	GLY: C CA H HA2 HA3 N O
35	HIS: C CA CB CD2 CE1 CG H HA HB2 HB3 HD1 HD2 HE1 N ND1 NE2 O
36	ILE: C CA CB CD1 CG1 CG2 H HA HB HD11 HD12 HD13 HG12 HG13 HG21 HG22 HG23 N O
37	LEU: C CA CB CD1 CD2 CG H HA HB2 HB3 HD11 HD12 HD13 HD21 HD22 HD23 HG N O
38	LYS: C CA CB CD CE CG H HA HB2 HB3 HD2 HD3 HE2 HE3 HG2 HG3 HZ1 HZ2 HZ3 N NZ O
39	MET: C CA CB CE CG H HA HB2 HB3 HE1 HE2 HE3 HG2 HG3 N O SD
40	PHE: C CA CB CD1 CD2 CE1 CE2 CG CZ H HA HB2 HB3 HD1 HD2 HE1 HE2 HZ N O
41	PRO: C CA CB CD CG HA HB2 HB3 HD2 HD3 HG2 HG3 N O
42	SER: C CA CB H H1 H2 H3 HA HB2 HB3 HG N O OG
43	THR: C CA CB CG2 H HA HB HG1 HG21 HG22 HG23 N O OG1
44	TRP: C CA CB CD1 CD2 CE2 CE3 CG CH2 CZ2 CZ3 H HA HB2 HB3 HD1 HE1 HE3 HH2 HZ2 HZ3 N NE1 O
45	TYR: C CA CB CD1 CD2 CE1 CE2 CG CZ H HA HB2 HB3 HD1 HD2 HE1 HE2 HH N O OH
46	VAL: C CA CB CG1 CG2 H HA HB HG11 HG12 HG13 HG21 HG22 HG23 N O
47	> BB multi
48	TRP: CA N C O
49	CYS: CA N C O
50	GLN: CA N C O
51	ALA: CA N C O
52	VAL: CA N C O
53	LEU: CA N C O
54	ASP: CA N C O
55	SER: CA N C O
56	PRO: CA N C O
57	THR: CA N C O
58	PHE: CA N C O
59	ARG: CA N C O
60	LYS: CA N C O
61	MET: CA N C O
62	HIS: CA N C O
63	GLY: CA N C O
64	ILE: CA N C O
65	GLU: CA N C O
66	ASN: CA N C O
67	TYR: CA N C O
68	> SC multi
69	TRP: CE2 CB CG CD1 CD2 CH2 CZ3 CZ2 CE3 NE1
70	CYS: SG CB
71	GLN: CG NE2 OE1 CD CB
72	ALA: CB
73	VAL: CG1 CB CG2
74	LEU: CB CG CD2 CD1
75	ASP: CB OD2 CG OD1
76	SER: CB OG
77	PRO: CB CG CD
78	THR: CG2 OG1 CB
79	PHE: CE2 CE1 CG CB CD2 CD1 CZ
80	ARG: NH2 CZ NE CD CG NH1 CB
81	LYS: CB CG CD CE NZ
82	MET: CB CE CG SD
83	HIS: CE1 CD2 ND1 CG CB NE2
84	GLY:
85	ILE: CG2 CD1 CB CG1
86	GLU: OE2 OE1 CD CG CB
87	ASN: ND2 OD1 CB CG
88	TYR: CD2 CD1 OH CZ CE2 CB CG CE1
89	> SC_CAGLY multi
90	TRP: CE2 CB CG CD1 CD2 CH2 CZ3 CZ2 CE3 NE1
91	CYS: SG CB
92	GLN: CG NE2 OE1 CD CB
93	ALA: CB
94	VAL: CG1 CB CG2
95	LEU: CB CG CD2 CD1
96	ASP: CB OD2 CG OD1
97	SER: CB OG
98	PRO: CB CG CD
99	THR: CG2 OG1 CB
100	PHE: CE2 CE1 CG CB CD2 CD1 CZ
101	ARG: NH2 CZ NE CD CG NH1 CB
102	LYS: CB CG CD CE NZ
103	MET: CB CE CG SD
104	HIS: CE1 CD2 ND1 CG CB NE2
105	GLY: CA
106	ILE: CG2 CD1 CB CG1
107	GLU: OE2 OE1 CD CG CB
108	ASN: ND2 OD1 CB CG
109	TYR: CD2 CD1 OH CZ CE2 CB CG CE1
110	> Ca single
111	TRP: CA
112	CYS: CA
113	GLN: CA
114	ALA: CA
115	VAL: CA
116	LEU: CA
117	ASP: CA
118	SER: CA
119	PRO: CA
120	THR: CA
121	PHE: CA
122	ARG: CA
123	LYS: CA
124	MET: CA
125	HIS: CA
126	GLY: CA
127	ILE: CA
128	GLU: CA
129	ASN: CA
130	TYR: CA
131	> Cb single
132	TRP: CB
133	CYS: CB
134	GLN: CB
135	ALA: CB
136	VAL: CB
137	LEU: CB
138	ASP: CB
139	SER: CB
140	PRO: CB
141	THR: CB
142	PHE: CB
143	ARG: CB
144	LYS: CB
145	MET: CB
146	HIS: CB
147	GLY: CA
148	ILE: CB
149	GLU: CB
150	ASN: CB
151	TYR: CB
152	> Cg single
153	TRP: CD2
154	CYS: SG
155	GLN: CG
156	ALA:
157	VAL: CG1
158	LEU: CG
159	ASP: CG
160	SER: OG
161	PRO: CG
162	THR: OG1
163	PHE: CG
164	ARG: NE
165	LYS: CD
166	MET: CG
167	HIS: CG
168	GLY:
169	ILE: CG1
170	ASN: CG
171	GLU: CG
172	TYR: CG
173	> C single
174	TRP: C
175	CYS: C
176	GLN: C
177	ALA: C
178	VAL: C
179	LEU: C
180	ASP: C
181	SER: C
182	PRO: C
183	THR: C
184	PHE: C
185	ARG: C
186	LYS: C
187	MET: C
188	HIS: C
189	GLY: C
190	ILE: C
191	GLU: C
192	ASN: C
193	TYR: C