ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/owl/trunk/src/tests/proteinstructure/data/1tdrA.grades
Revision: 987
Committed: Thu Mar 18 11:08:58 2010 UTC (11 years, 10 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 File contents
1 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