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root/owl/trunk/src/tests/proteinstructure/data/1tdrA.grades
Revision: 987
Committed: Thu Mar 18 11:08:58 2010 UTC (11 years, 6 months ago) by jmduarteg
File size: 11017 byte(s)
Log Message:
New package runners for Runner classes. At the moment only contains the new class NaccessRunner (moved out of Pdb class)
Introduced a config file for tests so that one can set externally the executable paths and any other necessary data to run tests (at the moment only implemented in PdbTest.java). PdbTest now should run anywhere (if you have a local pdbase installation!)
Moved the consurf parser out of Pdb to its own class ConsurfConnection in the connection package.

Line User Rev File contents
1 jmduarteg 987 Amino Acid Conservation Scores
2     ===============================
3    
4     - POS: The position of the AA in the SEQRES derived sequence.
5     - SEQ: The SEQRES derived sequence in one letter code.
6     - SCORE: The normalized conservation scores.
7     - 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier.
8     - COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).
9     - MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position.
10     - RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.
11    
12     POS SEQ 3LATOM SCORE COLOR MSA DATA RESIDUE VARIETY
13     1 M MET1:A -0.724 7 30/173 I,L,M,V
14     2 I ILE2:A -0.424 6 105/173 F,I,L,M,V
15     3 S SER3:A -0.621 7 131/173 A,C,D,G,H,I,K,M,N,Q,S,T,V,Y
16     4 L LEU4:A -0.188 6 137/173 A,C,F,G,I,L,M,S,V
17     5 I ILE5:A -0.961 8 140/173 I,K,L,M,V,Y
18     6 A ALA6:A -0.832 8 140/173 A,F,I,L,S,V,W,Y
19     7 A ALA7:A -1.351 9 146/173 A,C,F,S
20     8 L LEU8:A 0.473 4 146/173 A,C,E,G,H,I,K,L,M,N,Q,R,S,T,V
21     9 A ALA9:A -0.312 6 146/173 A,C,D,G,K,N,Q,R,S,T,V
22     10 V VAL10:A 0.808 2 146/173 A,D,E,H,I,K,L,M,P,Q,R,S,T,V
23     11 D ASP11:A -0.555 7 146/173 A,D,E,F,H,K,N,Q,R,S,T,Y
24     12 R ARG12:A -0.045 5 162/173 C,F,G,H,K,L,M,N,R,S,W,Y
25     13 V VAL13:A -0.778 7 162/173 A,C,E,G,I,L,N,V,Y
26     14 I ILE14:A -1.310 9 164/173 F,I,L,M
27     15 G GLY15:A -1.357 9 164/173 G,N,S
28     16 M MET16:A 0.226 4 164/173 A,C,D,E,F,G,I,K,L,M,N,Q,R,S,V,Y
29     17 E GLU17:A 0.014 5 164/173 A,D,E,G,K,L,N,Q,R,S
30     18 N ASN18:A -0.741 7 164/173 D,E,G,L,M,N,P,R,S
31     19 A ALA19:A 1.098 2 164/173 A,D,E,G,H,K,L,M,N,Q,R,S,T,V,Y
32     20 M MET20:A -0.632 7 164/173 F,I,L,M,V
33     21 P PRO21:A -1.362 9 164/173 I,P,R
34     22 W TRP22:A -1.355 9 164/173 L,W
35     23 N ASN23:A -0.243 6 164/173 D,E,H,K,N,P,R,S,T,Y
36     24 L LEU24:A -0.461 6 164/173 A,C,E,I,L,N,S,V,W,X,Y
37     25 P PRO25:A -0.489 7 164/173 A,I,K,M,N,P,R,S,T
38     26 A ALA26:A 0.003 5 164/173 A,D,E,G,K,L,N,Q,R,S,T,V
39     27 D ASP27:A -1.190 9 164/173 D,E,T
40     28 L LEU28:A -0.580 7 164/173 F,I,K,L,M,Q,W,Y
41     29 A ALA29:A 0.032 5 164/173 A,D,E,K,L,M,N,Q,R,S,T,V,Y
42     30 W TRP30:A -0.122 5 164/173 F,H,I,L,M,Q,R,W,Y
43     31 F PHE31:A -1.232 9 164/173 E,F,I,V,Y
44     32 K LYS32:A -0.465 6 172/173 A,K,N,Q,R,S,T,X,Y
45     33 R ARG33:A 0.410 4 172/173 A,D,E,H,K,N,Q,R,S,T,V
46     34 N ASN34:A 0.346 4 173/173 C,D,H,I,K,L,M,N,P,Q,R,T,V,Y
47     35 T THR35:A -1.256 9 173/173 I,K,N,S,T
48     36 L LEU36:A -0.121 5 173/173 A,E,I,K,L,M,N,Q,R,S,T,V,Y
49     37 D ASP37:A -0.433 6 173/173 D,F,G,K,M,N,Q,R,S,T
50     38 K LYS38:A -0.849 8 173/173 A,C,D,H,K,L,N,Q,R,S,V
51     39 P PRO39:A -0.541 7 173/173 A,C,I,K,L,N,P,S,T,V,W
52     40 V VAL40:A -0.778 7 173/173 I,L,M,N,T,V
53     41 I ILE41:A -0.781 7 173/173 I,L,V
54     42 M MET42:A -1.370 9 173/173 L,M,V
55     43 G GLY43:A -1.396 9 173/173 A,G
56     44 R ARG44:A -1.308 9 173/173 K,R
57     45 H HIS45:A -0.857 8 173/173 A,H,K,L,N,R,S,T,V
58     46 T THR46:A -1.216 9 173/173 C,N,S,T,V,X
59     47 W TRP47:A -0.280 6 173/173 A,F,L,M,R,W,Y
60     48 E GLU48:A -0.711 7 173/173 A,D,E,F,H,L,N,Q
61     49 S SER49:A -1.280 9 173/173 C,E,G,S,T,V
62     50 I ILE50:A -0.811 8 173/173 I,L,M,P,T,V
63     51 G GLY51:A -0.818 8 173/173 A,D,E,G,K,L,N,P,R,V
64     52 R ARG52:A -0.882 8 161/173 D,F,G,H,K,N,R,V
65     53 P PRO53:A -0.792 7 173/173 A,D,G,K,L,P,R,S,V
66     54 L LEU54:A -1.395 9 173/173 L,Y
67     55 P PRO55:A -0.490 7 173/173 A,E,K,L,N,P,Q,S,V
68     56 G GLY56:A -0.319 6 173/173 C,D,E,G,H,K,M,N,P,Y
69     57 R ARG57:A -1.335 9 173/173 G,K,Q,R,S
70     58 K LYS58:A 0.179 4 173/173 A,E,H,I,K,L,M,N,P,R,T,V
71     59 N ASN59:A -1.068 8 173/173 C,D,E,H,I,N,Q,S,T,V,Y
72     60 I ILE60:A -0.717 7 173/173 A,F,I,L,T,V
73     61 I ILE61:A -1.093 8 173/173 I,L,V
74     62 L LEU62:A -0.290 6 173/173 F,I,L,M,V
75     63 S SER63:A -1.114 8 173/173 F,L,S,T
76     64 S SER64:A -0.702 7 173/173 C,G,H,K,N,R,S,T
77     65 Q GLN65:A 0.159 5 172/173 A,D,E,G,K,N,Q,R,S,T
78     66 P PRO66:A 1.808 1 170/173 A,D,E,F,G,H,I,K,L,N,P,Q,R,S,T,V,Y
79     67 G GLY67:A 1.577 1 169/173 A,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y
80     68 T THR68:A 1.593 1 169/173 A,C,D,E,F,H,I,K,L,M,N,P,Q,R,S,T,V,Y
81     69 D ASP69:A 1.476 1 170/173 A,C,D,E,F,G,H,I,K,L,N,P,Q,R,S,T,V,Y
82     70 D ASP70:A 0.605 3 170/173 A,C,D,E,F,G,H,K,N,P,Q,R,S,T
83     71 R ARG71:A 0.323 4 170/173 D,E,G,H,I,K,L,N,P,Q,R,S,T
84     72 V VAL72:A -0.039 5 170/173 A,C,D,G,I,K,L,M,N,P,R,S,T,V,W,Y
85     73 T THR73:A 1.420 1 170/173 A,C,D,E,F,G,H,I,K,L,M,Q,R,S,T,V,Y
86     74 W TRP74:A 0.159 5 170/173 A,C,E,F,G,H,I,L,P,Q,R,S,T,V,W,Y
87     75 V VAL75:A 0.112 5 170/173 A,C,F,G,I,K,L,M,N,P,Q,S,T,V,Y
88     76 K LYS76:A 1.374 1 170/173 A,C,D,E,F,G,H,I,K,L,N,P,Q,R,S,T,V,Y
89     77 S SER77:A -0.849 8 170/173 A,D,E,G,K,N,Q,R,S,T
90     78 V VAL78:A 0.424 4 170/173 A,E,F,G,I,K,L,M,P,R,T,V,Y
91     79 D ASP79:A 0.508 3 170/173 A,D,E,F,I,K,L,M,N,P,Q,S,V
92     80 E GLU80:A 0.425 4 170/173 A,D,E,G,H,I,K,N,Q,R,S,V
93     81 A ALA81:A -0.897 8 170/173 A,E,H,I,L,P,S,T,V,Y
94     82 I ILE82:A 0.302 4 170/173 A,E,F,G,I,K,L,M,Q,R,V,W,Y
95     83 A ALA83:A 1.270 1 170/173 A,D,E,I,K,L,M,N,P,Q,R,S,T,V,Y
96     84 A ALA84:A 1.484 1 169/173 A,E,F,G,H,I,K,L,N,P,Q,R,S,T,V,W,Y
97     85 C CYS85:A 0.800 2 166/173 A,C,D,E,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y
98     86 G GLY86:A 3.577 1 167/173 A,D,E,G,I,K,L,N,P,Q,R,S,T,V
99     87 D ASP87:A 0.241 4 167/173 A,D,E,G,H,K,L,N,Q,S,T,Y
100     88 V VAL88:A 1.406 1 168/173 A,C,D,E,F,G,H,I,K,L,N,P,Q,S,T,V,Y
101     89 P PRO89:A 0.407 4 165/173 D,E,G,K,N,P,Q,R,S,T,Y
102     90 E GLU90:A -0.550 7 163/173 A,D,E,H,K,M,N,P,Q,R,S,T,V
103     91 I ILE91:A -0.318 6 163/173 A,C,I,L,M,N,P,T,V
104     92 M MET92:A -0.277 6 169/173 A,C,F,I,L,M,S,V,W,Y
105     93 V VAL93:A -0.752 7 169/173 C,I,L,N,V
106     94 I ILE94:A -0.896 8 169/173 A,C,F,I,L,M,S,T,V
107     95 G GLY95:A -1.396 9 169/173 G,R
108     96 G GLY96:A -1.435 9 169/173 G
109     97 G GLY97:A -0.365 6 169/173 A,E,G,K,N,Q,R,S,T,Y
110     98 R ARG98:A 0.183 4 169/173 A,D,E,G,K,N,Q,R,S,T,V,Y
111     99 V VAL99:A -0.731 7 169/173 A,I,L,V
112     100 Y TYR100:A -0.746 7 169/173 F,L,Y
113     101 E GLU101:A 0.767 3 169/173 A,D,E,G,K,L,N,Q,R,S,T,V
114     102 Q GLN102:A 0.594 3 169/173 A,D,E,L,M,N,Q,R,S,V,W
115     103 F PHE103:A -0.355 6 169/173 A,C,F,H,I,L,M,S,T,V,Y
116     104 L LEU104:A -0.250 6 169/173 A,E,F,I,K,L,M,Q,W
117     105 P PRO105:A 1.195 1 169/173 A,C,D,E,F,G,H,K,L,N,P,Q,R,S,T
118     106 K LYS106:A 1.466 1 169/173 A,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,V,Y
119     107 A ALA107:A -0.342 6 169/173 A,C,D,H,I,K,L,N,P,S,T,V
120     108 Q GLN108:A 0.162 4 169/173 A,D,E,G,H,K,L,N,Q,R,S,T,V
121     109 K LYS109:A 0.129 5 169/173 A,D,E,G,H,I,K,L,Q,R,S,T,V
122     110 L LEU110:A -0.646 7 169/173 C,I,L,M,V,W
123     111 Y TYR111:A -0.063 5 169/173 E,F,G,H,I,L,M,R,S,V,W,Y
124     112 L LEU112:A -0.035 5 169/173 A,E,F,I,L,M,R,V
125     113 T THR113:A -1.372 9 169/173 S,T
126     114 H HIS114:A 0.430 4 169/173 D,E,F,H,I,K,L,Q,R,T,V,Y
127     115 I ILE115:A -1.060 8 169/173 I,L,V
128     116 D ASP116:A 0.327 4 168/173 A,D,E,F,G,H,K,L,M,N,P,Q,R,Y
129     117 A ALA117:A 0.477 4 168/173 A,E,G,H,I,K,L,M,N,P,Q,R,S,T,V
130     118 E GLU118:A 0.396 4 168/173 A,D,E,H,K,L,N,P,Q,R,S,T,V,Y
131     119 V VAL119:A 0.388 4 167/173 A,D,E,F,H,I,L,P,Q,R,S,T,V,Y
132     120 E GLU120:A 0.500 3 167/173 A,D,E,G,H,K,N,P,Q,R,S,T,V,W
133     121 G GLY121:A -0.724 7 164/173 A,C,D,E,F,G,N,Q,R,S
134     122 D ASP122:A -1.243 9 165/173 A,C,D,N,S
135     123 T THR123:A -0.711 7 165/173 A,D,I,R,S,T,V
136     124 H HIS124:A 0.799 2 164/173 A,D,E,F,G,H,K,L,N,P,Q,R,T,V,Y
137     125 F PHE125:A -0.696 7 164/173 A,D,F,H,I,L,M,V,Y
138     126 P PRO126:A -0.815 8 164/173 A,D,E,F,G,K,M,P,V
139     127 D ASP127:A 1.872 1 162/173 A,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V
140     128 Y TYR128:A 0.420 4 161/173 A,D,E,F,I,K,L,M,P,S,T,V,W,Y
141     129 E GLU129:A -0.007 5 150/173 A,D,E,F,G,K,L,N,P,R,T,V
142     130 P PRO130:A 2.079 1 144/173 A,D,E,F,G,I,K,L,M,P,R,S,T,W,Y
143     131 D ASP131:A 0.942 2 140/173 A,D,E,F,G,H,K,L,M,N,P,Q,R,S,T,V
144     132 D ASP132:A 1.796 1 142/173 A,D,E,F,G,H,I,K,L,N,P,Q,R,S,T,V,Y
145     133 W TRP133:A 0.499 3 142/173 A,D,F,I,K,L,M,R,S,W,Y
146     134 E GLU134:A 0.806 2 160/173 A,E,H,I,K,L,M,N,P,Q,R,S,T,V
147     135 S SER135:A 1.641 1 154/173 C,D,E,G,I,K,L,M,N,P,Q,R,S,T,V,W
148     136 V VAL136:A -0.029 5 155/173 A,D,E,F,G,I,K,L,M,N,Q,R,S,T,V,W,Y
149     137 F PHE137:A 1.006 2 146/173 A,C,D,E,F,G,I,K,L,M,P,Q,R,S,T,V,W,Y
150     138 S SER138:A 1.260 1 147/173 D,E,G,K,N,Q,R,S,T,V,W
151     139 E GLU139:A 0.426 4 156/173 A,C,D,E,G,H,K,L,P,Q,S,T,V,Y
152     140 F PHE140:A 4.597 1 151/173 A,D,E,F,G,H,I,K,L,M,P,Q,S,T,V,W,Y
153     141 H HIS141:A 0.489 3 146/173 A,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y
154     142 D ASP142:A 1.710 1 136/173 A,D,E,G,H,I,K,L,N,P,Q,R,S,T,V,W,Y
155     143 A ALA143:A 0.330 4 140/173 A,C,D,E,G,H,I,K,L,P,Q,R,S,T,V
156     144 D ASP144:A 0.136 5 146/173 A,D,E,F,G,I,K,L,N,Q,S,T,V,Y
157     145 A ALA145:A 0.778 3 148/173 A,C,D,E,F,G,H,I,K,L,N,Q,R,S,T,V,Y
158     146 Q GLN146:A 0.845 2 155/173 A,D,E,G,H,I,K,L,M,N,P,Q,R,S,T,V,Y
159     147 N ASN147:A -0.367 6 155/173 A,C,D,E,G,H,I,K,L,N,Q,S,T,Y
160     148 S SER148:A 1.307 1 154/173 A,D,E,F,G,H,K,L,N,P,Q,R,S,T,V,W,Y
161     149 H HIS149:A 0.376 4 151/173 A,D,E,F,G,H,I,K,L,N,P,R,S,T,V,Y
162     150 S SER150:A 1.041 2 154/173 A,D,E,F,G,I,K,N,P,Q,R,S,T,W,Y
163     151 Y TYR151:A 0.557 3 154/173 A,C,E,F,H,I,L,M,S,T,V,W,Y
164     152 C CYS152:A 1.525 1 149/173 A,C,D,E,F,G,H,I,K,L,N,Q,R,S,T,V,Y
165     153 F PHE153:A -0.371 6 150/173 E,F,H,I,K,L,M,S,T,V,Y
166     154 K LYS154:A 1.346 1 150/173 D,E,F,G,H,I,K,L,M,N,Q,R,S,T,V,W,Y
167     155 I ILE155:A 0.448 4 148/173 D,E,F,G,H,I,K,L,M,S,T,V,Y
168     156 L LEU156:A 0.926 2 147/173 F,I,L,N,P,R,V,W,Y
169     157 E GLU157:A 0.957 2 130/173 A,C,E,G,I,K,L,P,Q,R,S,T,V,Y
170     158 R ARG158:A -0.933 8 127/173 G,H,K,P,R
171     159 R ARG159:A -0.360 6 69/173 H,K,Q,R,S