Contacts of the helix formed by residues 132 - 155 (chain F) in PDB entry 1VEQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 132 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ARG* 4.9 2.3 - - - +
124E ILE* 4.6 19.3 - - + -
125E GLU* 4.7 19.1 - - - +
128E GLU* 4.7 18.8 - - - +
135E GLN* 4.8 8.5 - - - +
139E ILE* 4.3 21.9 - - + +
127F LEU 5.0 0.7 - - - -
128F GLU* 4.5 28.9 + - + +
130F LEU 4.3 0.6 + - - -
131F ASP* 1.3 71.0 + - - +
133F VAL* 1.3 66.8 + - + +
135F GLN* 3.0 40.4 + - - +
136F ASP* 3.1 10.0 + - - +
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Residues in contact with VAL 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ARG* 4.1 6.5 - - - +
124E ILE* 5.1 6.7 - - + -
139E ILE* 4.1 17.9 - - + -
142E ALA* 3.8 24.2 - - + -
143E GLY* 3.9 20.4 - - - +
146E GLU* 3.9 10.1 - - - +
71F ARG* 3.4 31.4 - - - +
131F ASP* 3.2 8.7 + - - +
132F LEU* 1.3 73.3 - - + +
134F SER* 1.3 57.0 + - - +
135F GLN 2.6 15.4 + - - -
136F ASP* 3.2 12.5 + - - +
137F LEU* 3.2 14.2 + - + +
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Residues in contact with SER 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F VAL* 3.9 25.5 - - - +
21F LEU* 4.9 7.4 - - - +
71F ARG* 3.0 24.8 + - - +
75F LEU* 4.8 1.7 - - - +
127F LEU* 3.3 19.0 - - - +
131F ASP* 2.5 34.9 + - - -
132F LEU 3.5 0.4 - - - -
133F VAL* 1.3 73.1 - - - +
135F GLN* 1.3 58.0 + - - +
137F LEU* 4.0 11.2 - - - +
138F LEU* 3.7 17.2 + - - +
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Residues in contact with GLN 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LEU* 5.0 8.3 - - - +
124F ILE* 3.5 35.4 + - + +
127F LEU* 4.3 9.2 - - + -
128F GLU* 3.2 46.5 + - - +
131F ASP 3.4 10.4 + - - +
132F LEU* 3.0 28.2 - - - +
133F VAL 2.6 6.5 + - - -
134F SER* 1.3 74.5 - - - +
136F ASP* 1.3 65.2 + - - +
137F LEU 2.7 6.3 + - - -
138F LEU* 2.7 13.3 + - - +
139F ILE* 2.8 23.9 + - + +
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Residues in contact with ASP 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ASP* 2.4 36.2 - - - +
136E ASP* 2.5 21.0 - - - +
139E ILE* 4.0 28.3 - - + +
140E ALA* 5.3 6.6 - - - +
132F LEU 3.1 5.3 + - - +
133F VAL 3.2 1.3 + - - +
135F GLN* 1.3 78.6 + - - +
137F LEU* 1.3 65.2 + - - +
139F ILE* 3.6 10.5 - - - +
140F ALA* 3.1 23.7 + - - +
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Residues in contact with LEU 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU* 6.1 0.7 - - + -
67F GLU* 4.6 27.6 - - + +
68F VAL* 4.4 8.7 - - + -
71F ARG* 4.7 22.0 - - + -
133F VAL* 3.2 18.2 + - + +
134F SER* 4.0 8.5 - - - +
135F GLN 2.7 0.8 + - - -
136F ASP* 1.3 81.8 - - - +
138F LEU* 1.3 78.0 + - + +
140F ALA* 3.2 7.5 + - - +
141F HIS* 3.1 50.4 - - + +
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Residues in contact with LEU 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU* 4.0 22.7 - - + -
24F GLN* 3.1 42.4 - - + +
28F TYR* 4.0 6.3 - - - +
68F VAL* 4.9 4.7 - - + -
120F THR* 3.6 19.2 - - + +
123F SER* 5.1 4.9 - - - -
124F ILE* 4.1 15.7 - - + -
127F LEU* 4.5 11.4 - - + -
134F SER 3.7 14.1 + - - +
135F GLN 2.7 11.4 + - - +
137F LEU* 1.3 93.2 - - + +
139F ILE* 1.3 64.2 + - - +
141F HIS* 3.2 13.0 + - - +
142F ALA* 3.2 10.7 + - - +
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Residues in contact with ILE 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LEU* 4.5 24.2 - - + +
133D VAL* 4.1 22.4 - - + +
136D ASP* 3.9 28.3 - - + -
124F ILE* 3.9 31.2 - - + -
135F GLN* 2.8 37.0 + - + +
136F ASP* 3.6 15.0 - - - +
138F LEU* 1.3 70.8 - - - +
140F ALA* 1.3 70.6 + - - +
142F ALA* 2.6 22.9 + - - +
143F GLY* 3.2 3.1 + - - -
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Residues in contact with ALA 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ASP* 5.2 7.6 - - - +
64F TYR* 4.5 5.4 + - + -
136F ASP* 3.1 12.4 + - - +
137F LEU* 3.4 10.8 - - - +
139F ILE* 1.3 82.7 - - - +
141F HIS* 1.3 69.5 + - + +
143F GLY* 3.0 14.1 + - - -
144F GLU* 3.6 5.4 + - - +
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Residues in contact with HIS 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F TYR* 2.7 28.8 + + - +
64F TYR* 3.1 50.0 - + + -
67F GLU* 3.0 21.5 + - - -
68F VAL* 3.9 7.2 - - + -
120F THR* 5.7 0.4 - - + -
137F LEU* 3.1 39.5 - - + +
138F LEU* 3.4 10.0 - - + +
139F ILE 2.8 3.6 + - - -
140F ALA* 1.3 77.0 - - + +
142F ALA* 1.3 64.8 + - - +
144F GLU* 2.9 5.7 + - - +
145F LEU* 2.8 39.6 + - + +
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Residues in contact with ALA 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D VAL* 3.8 13.0 - - + -
117F ILE* 5.6 3.1 - - + +
120F THR* 4.4 17.2 - - + +
121F ARG* 5.3 1.6 - - + +
124F ILE* 4.5 3.8 - - + -
138F LEU 3.2 6.7 + - - +
139F ILE* 2.6 18.4 + - - +
141F HIS* 1.3 73.4 - - - +
143F GLY* 1.3 56.8 + - - +
145F LEU* 4.1 8.9 - - - +
146F GLU* 2.7 57.2 + - - +
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Residues in contact with GLY 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ARG* 4.3 7.3 + - - -
133D VAL* 3.9 20.6 - - - +
139F ILE 3.2 3.2 + - - -
140F ALA 3.0 10.5 + - - -
141F HIS 3.0 0.2 + - - -
142F ALA* 1.3 77.5 - - - +
144F GLU* 1.3 60.3 + - - +
146F GLU* 4.1 1.6 - - - +
147F LYS* 3.2 26.0 + - - +
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Residues in contact with GLU 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F GLN* 4.2 4.6 - - - +
60F LEU* 3.5 27.9 - - + +
64F TYR* 3.3 23.6 + - + +
140F ALA 3.6 4.6 + - - +
141F HIS 2.9 2.8 + - - +
143F GLY* 1.3 74.3 - - - +
145F LEU* 1.3 61.9 + - - +
147F LYS* 3.5 21.8 + - + +
148F PHE* 2.8 33.2 + - + +
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Residues in contact with LEU 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F TYR* 4.5 10.5 - - + +
31F LEU* 4.0 18.8 - - + -
57F GLN* 3.6 13.7 - - - +
61F VAL* 4.5 3.6 - - + -
64F TYR* 4.0 15.3 - - + -
113F TYR* 3.6 29.4 - - + -
116F VAL* 4.7 14.4 - - + -
117F ILE* 4.6 12.8 - - + -
120F THR* 5.7 4.0 - - + +
141F HIS* 2.8 51.5 + - + +
142F ALA* 3.6 7.2 - - - +
144F GLU* 1.3 74.8 - - - +
146F GLU* 1.3 64.4 + - - +
148F PHE* 3.2 2.6 + - - +
149F GLN* 3.0 20.8 + - - +
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Residues in contact with GLU 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 3.6 16.6 - - + +
71D ARG* 2.8 45.3 + - - +
74D THR* 3.4 15.3 - - + +
133D VAL* 3.7 1.5 - - - +
117F ILE* 3.5 33.4 - - + +
121F ARG* 3.0 34.7 + - - -
142F ALA* 2.7 36.3 + - - +
145F LEU* 1.3 74.2 - - - +
147F LYS* 1.3 62.0 + - - +
149F GLN* 3.2 7.3 + - - +
150F TRP 3.1 15.6 + - - -
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Residues in contact with LYS 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ASP 5.1 0.4 + - - -
67D GLU* 5.1 11.5 + - - +
70D GLU* 2.7 44.5 + - - +
71D ARG* 5.1 1.1 - - - +
74D THR* 4.2 17.5 - - - +
143F GLY 3.2 19.7 + - - +
144F GLU* 3.5 25.5 + - + +
145F LEU 3.2 0.2 - - - -
146F GLU* 1.3 78.6 - - - +
148F PHE* 1.3 64.9 + - - +
150F TRP* 2.8 30.3 + - + +
151F PHE* 3.3 25.8 + - + -
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Residues in contact with PHE 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LEU* 4.2 11.0 - - + -
53F MET* 4.0 33.7 - - + -
54F ILE* 4.7 5.2 - - + -
57F GLN* 3.0 50.3 - - + +
109F LEU* 4.2 7.6 - - + -
113F TYR* 3.4 38.4 - + - -
144F GLU 2.8 15.8 + - - +
145F LEU 3.6 2.7 - - - +
147F LYS* 1.3 74.6 - - - +
149F GLN* 1.3 65.9 + - - +
151F PHE* 2.8 39.9 + + + +
152F VAL* 3.1 28.0 + - + -
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Residues in contact with GLN 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 5.0 3.6 - - - +
7D PRO* 4.0 5.7 - - - +
74D THR* 5.7 1.4 - - - +
110F ASP* 3.4 16.1 + - - +
113F TYR* 3.5 23.3 - - + +
114F ASN* 2.9 32.5 + - - +
117F ILE* 3.4 19.3 - - + +
145F LEU 3.0 12.6 + - - +
146F GLU* 3.2 11.4 - - - +
148F PHE* 1.3 77.8 - - - +
150F TRP* 1.3 65.6 + - - +
152F VAL* 2.7 23.1 + - + +
153F ARG* 2.8 47.1 + - + +
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Residues in contact with TRP 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PHE* 4.5 12.5 - + - -
70D GLU* 4.2 35.9 - - + -
73D ALA* 3.4 47.0 + - + +
74D THR* 3.7 27.6 - - + +
146F GLU 3.1 2.6 + - - -
147F LYS* 2.8 23.4 + - + +
149F GLN* 1.3 79.1 + - - +
151F PHE* 1.3 83.9 + + - -
153F ARG* 3.0 10.7 + - - +
154F ALA* 2.6 46.0 + - + +
157F GLU* 5.4 1.6 + - - -
39G HIS 5.0 0.2 - - - -
40G TRP* 3.7 17.9 - - - -
42G VAL 5.2 1.3 - - - -
43G VAL* 6.1 0.9 - - + -
47G PHE* 4.1 17.9 - + - -
51G HIS* 4.4 10.8 - + - -
99G ARG* 4.9 4.8 - - - +
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Residues in contact with PHE 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D GLU* 4.9 1.1 - - - -
53F MET* 4.0 21.5 - - + -
147F LYS* 3.3 30.7 + - + -
148F PHE* 2.8 40.2 + + + +
150F TRP* 1.3 89.5 - + - +
152F VAL* 1.3 64.3 + - - +
154F ALA* 3.3 5.5 + - - +
155F HIS* 2.8 23.6 + - - -
47G PHE* 3.3 21.1 - + - -
48G ILE* 4.1 11.4 - - + -
51G HIS* 3.7 33.2 - + - -
52G GLU* 6.0 0.7 - - - -
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Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F MET* 4.7 1.8 - - + -
106F LEU* 3.1 56.4 - - + +
109F LEU* 4.3 7.9 - - + -
110F ASP* 4.1 14.4 - - + +
113F TYR* 5.5 2.5 - - + -
148F PHE* 3.3 43.5 - - + +
149F GLN* 2.7 15.8 + - + +
151F PHE* 1.3 76.2 - - - +
153F ARG* 1.3 64.2 + - + +
155F HIS* 3.0 19.4 + - - +
156F LEU* 3.9 6.0 - - + +
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Residues in contact with ARG 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D PHE* 3.5 56.5 - - + +
5D THR 3.6 23.6 + - - -
6D ILE* 4.4 1.6 - - - +
7D PRO* 4.1 2.2 - - - +
74D THR* 4.9 2.8 + - - +
110F ASP* 2.8 32.2 + - - +
114F ASN* 3.1 32.7 + - - +
149F GLN* 2.8 43.4 + - + +
150F TRP* 3.4 10.1 - - - +
152F VAL* 1.3 70.0 - - + +
154F ALA* 1.3 53.9 + - - +
155F HIS 2.8 5.6 - - - -
156F LEU* 2.6 39.3 + - + +
157F GLU* 3.5 10.2 + - + +
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Residues in contact with ALA 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F TRP* 2.6 32.2 + - + +
151F PHE 3.3 0.6 + - - +
153F ARG* 1.3 71.1 - - - +
155F HIS* 1.3 58.4 + - - +
156F LEU 3.2 0.7 + - - -
157F GLU* 4.1 9.5 + - - -
43G VAL* 3.7 20.6 - - + +
44G GLY* 3.0 26.7 + - - +
47G PHE* 3.6 38.1 - - + +
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Residues in contact with HIS 155 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F ASN* 4.4 1.5 + - - -
49F GLY* 6.0 0.4 - - - -
50F VAL* 4.0 16.2 + - + +
53F MET* 3.8 9.6 - - + -
103F GLN* 4.0 9.9 + - - +
106F LEU* 3.4 27.6 - - + +
151F PHE 2.8 20.9 + - - -
152F VAL* 3.0 12.2 + - - +
153F ARG 2.7 0.8 + - - -
154F ALA* 1.3 76.1 - - - +
156F LEU* 1.3 63.0 + - + +
157F GLU 3.8 0.4 - - - +
44G GLY 2.9 17.0 - - - +
45G PRO* 3.1 36.6 + - - +
46G ASN 4.8 0.6 - - - -
47G PHE* 3.3 26.4 + + + -
48G ILE* 3.5 33.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il