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root/owl/trunk/proteinstructure/contactTypes.dat
Revision: 885
Committed: Fri Aug 14 10:37:31 2009 UTC (10 years, 10 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 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 duarte 885 > 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 duarte 326 > 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 filippis 407 > 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 duarte 326 > 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