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root/owl/trunk/proteinstructure/contactTypes.dat
Revision: 326
Committed: Thu Sep 20 14:49:55 2007 UTC (13 years, 2 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 User Rev File contents
1 duarte 326 # 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