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root/owl/trunk/proteinstructure/contactTypes.dat
Revision: 885
Committed: Fri Aug 14 10:37:31 2009 UTC (10 years, 2 months ago) by duarte
File size: 3850 byte(s)
Log Message:
Major change: now hydrogens are read in Pdb and subclasses
New getChirality method in Residue.
Added some more unit tests.
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