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root/owl/trunk/proteinstructure/contactTypes.dat
Revision: 326
Committed: Thu Sep 20 14:49:55 2007 UTC (12 years 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