Contacts of the helix formed by residues 38 - 66 (chain A) in PDB entry 1VLG
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 PHE 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 2.8 19.7 + + + +
34A ASP* 4.7 0.4 - - - +
36A GLU* 3.8 29.4 - - + -
37A GLY* 1.3 73.8 - - - +
39A LYS* 1.3 60.1 + - - +
40A GLY 3.4 0.2 + - - -
41A PHE* 3.4 24.9 + + + -
42A ALA* 3.0 26.2 + - - +
85A ILE* 3.6 29.2 - - + -
150A MET* 4.0 27.1 - - + -
153A ILE* 3.7 27.1 - - + -
154A PHE* 4.2 11.7 - + - -
157A ASP* 3.2 24.2 - - + +
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 3.7 16.7 + - - +
37A GLY* 3.7 9.9 + - - +
38A PHE* 1.3 71.4 - - - +
40A GLY* 1.3 60.9 + - - +
42A ALA* 3.6 8.4 - - - +
43A HIS* 2.8 28.4 + - - +
46A LYS* 5.4 1.5 + - - +
157A ASP* 3.5 3.2 + - - +
61F GLU* 5.0 9.3 + - - -
64F TYR* 6.3 1.0 - - - +
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 1.3 75.9 - - - +
41A PHE* 1.3 64.5 + - - -
43A HIS* 3.2 4.2 + - - +
44A TRP* 2.9 21.0 + - - +
157A ASP* 2.8 35.9 + - - -
158A ARG* 5.4 0.2 - - - -
160A LEU 4.4 0.2 - - - -
161A GLY* 3.6 20.5 + - - -
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Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.6 27.7 - + + -
38A PHE* 3.4 39.7 + + + +
40A GLY* 1.3 75.8 - - - +
42A ALA* 1.3 62.8 + - - +
44A TRP* 3.2 7.9 + - - +
45A MET* 3.0 26.7 + - - +
85A ILE* 3.8 28.0 - - + -
89A PHE* 4.1 12.7 - + + -
139A ILE* 5.9 0.7 - - + -
143A LEU* 4.8 5.6 - - + -
153A ILE* 3.8 18.6 - - + -
156A LEU* 3.8 8.3 - - + -
157A ASP* 2.9 37.6 + - + -
160A LEU* 3.7 28.3 - - + -
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 3.7 15.8 - - - +
33A PHE* 3.7 8.9 - - + +
34A ASP* 3.3 36.3 - - - +
38A PHE 3.0 18.7 + - - +
39A LYS 3.6 4.9 - - - +
41A PHE* 1.3 76.3 - - - +
43A HIS* 1.3 57.2 + - - +
45A MET* 3.2 4.3 + - - +
46A LYS* 2.9 37.4 + - - +
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS 2.8 19.6 + - - +
40A GLY 3.3 5.4 - - - +
42A ALA* 1.3 75.9 - - - +
44A TRP* 1.3 60.9 + - - +
46A LYS* 3.2 15.5 + - - +
47A LYS* 3.0 49.1 + - + +
160A LEU 3.7 6.7 - - - -
161A GLY* 3.1 35.4 + - - -
163A ARG* 2.7 26.9 + - + -
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Residues in contact with TRP 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 5.8 0.7 - + - -
40A GLY 2.9 12.1 + - - +
41A PHE* 3.2 10.1 + - - +
43A HIS* 1.3 77.4 - - - +
45A MET* 1.3 92.7 + - + +
47A LYS* 3.5 0.7 + - - +
48A GLN* 2.9 45.4 + - + -
89A PHE* 4.1 13.0 - + + -
92A ALA* 5.7 1.1 - - + -
135A GLN* 3.8 23.5 - - + -
136A VAL* 4.2 19.1 - - + -
139A ILE* 3.8 18.9 - - + +
160A LEU* 3.7 47.0 - - + +
163A ARG* 3.2 49.4 + - + +
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Residues in contact with MET 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 3.4 40.7 - - - +
29A MET* 3.4 31.2 - - + -
30A ALA* 3.9 7.9 - - + +
33A PHE* 3.6 22.4 - - + -
41A PHE 3.0 15.5 + - - +
42A ALA 3.2 8.0 + - - +
44A TRP* 1.3 100.3 - - + +
46A LYS* 1.3 58.9 + - - +
48A GLN* 3.7 2.3 - - - +
49A ALA* 2.9 29.5 + - - +
88A ALA 4.9 0.7 - - - +
89A PHE* 3.8 22.9 - - + -
92A ALA* 4.3 8.7 - - + -
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.6 6.1 - - + -
30A ALA* 3.9 10.5 - - + -
34A ASP* 2.8 31.4 + - - -
39A LYS* 5.4 1.4 + - - +
42A ALA* 2.9 25.3 + - - +
43A HIS* 3.2 12.6 + - - +
45A MET* 1.3 74.3 - - - +
47A LYS* 1.3 64.4 + - + +
49A ALA* 3.4 8.0 + - - +
50A GLN* 3.1 30.1 + - - +
57F MET* 4.1 19.5 - - + -
60F TYR* 3.5 16.3 - - - -
61F GLU* 2.9 27.7 + - - +
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A HIS* 3.0 48.0 + - + +
44A TRP 3.7 5.2 - - - +
46A LYS* 1.3 75.7 - - + +
48A GLN* 1.3 64.5 + - - +
50A GLN* 3.2 21.6 + - + +
51A GLU* 3.0 22.3 + - - +
163A ARG* 3.6 32.1 + - - +
164A GLU* 2.7 33.6 + - - +
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Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 3.5 27.1 - - + -
44A TRP* 2.9 35.8 + - + +
45A MET* 3.7 6.3 - - - +
46A LYS 3.3 0.2 - - - -
47A LYS* 1.3 76.9 - - - +
49A ALA* 1.3 56.1 + - - +
51A GLU* 3.1 13.6 + - - +
52A GLU* 2.7 57.8 + - - +
96A GLU* 6.5 0.2 - - - -
132A GLU* 3.3 20.5 + - - +
135A GLN* 2.9 25.3 + - - -
163A ARG* 3.0 20.9 + - - +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER* 2.7 53.2 + - - +
26A TYR* 4.0 2.8 - - - +
27A LEU* 4.1 14.8 - - + +
45A MET 2.9 14.8 + - - +
46A LYS* 3.5 12.3 - - - +
48A GLN* 1.3 75.8 - - - +
50A GLN* 1.3 61.9 + - + +
52A GLU* 3.3 1.4 + - - -
53A LEU* 3.2 13.9 + - - +
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Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LYS* 3.1 18.7 + - - +
47A LYS* 3.5 30.2 + - + +
49A ALA* 1.3 76.0 - - + +
51A GLU* 1.3 62.6 + - - +
53A LEU* 3.1 25.5 + - + +
54A THR* 3.2 17.0 + - - +
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS 3.0 12.5 + - - +
48A GLN* 3.1 18.6 + - - +
50A GLN* 1.3 75.7 - - - +
52A GLU* 1.3 63.0 + - - +
54A THR* 2.7 32.9 + - - +
55A HIS* 3.2 14.3 + - - +
128A GLU* 3.0 15.4 - - - +
132A GLU* 2.8 32.7 - - - +
135A GLN* 4.3 0.3 + - - -
163A ARG* 2.7 32.1 + - - +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 3.0 14.5 - - - +
22A SER* 3.9 8.5 - - - -
23A SER* 3.7 16.8 - - - +
26A TYR* 3.5 31.3 - - + -
48A GLN* 2.7 42.0 + - - +
49A ALA 3.3 7.2 + - - +
51A GLU* 1.3 74.3 - - - +
53A LEU* 1.3 58.1 + - - +
55A HIS* 3.1 13.7 + - - +
56A ALA* 3.0 25.5 + - - +
96A GLU* 3.7 10.6 - - - +
132A GLU* 4.4 0.9 - - - +
200A FE 2.0 32.5 - - - -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 4.0 25.8 - - + -
23A SER* 3.4 29.4 - - - +
49A ALA 3.2 6.5 + - - +
50A GLN* 3.1 17.9 + - + +
52A GLU* 1.3 72.7 - - - +
54A THR* 1.3 60.8 + - + +
56A ALA* 3.2 4.9 + - + +
57A MET* 2.9 37.0 + - + +
53F LEU* 3.8 29.8 - - + -
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN 3.5 15.0 - - - +
51A GLU* 2.7 22.8 + - - +
53A LEU* 1.3 77.9 - - + +
55A HIS* 1.3 69.7 + - - +
57A MET* 3.3 7.2 + - - +
58A LYS* 3.0 39.4 + - - +
124A TRP* 5.5 0.2 - - - -
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Residues in contact with HIS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU* 3.5 15.2 + - - +
51A GLU* 3.6 19.5 + - + +
52A GLU* 3.1 19.3 + - - +
54A THR* 1.3 81.4 + - - +
56A ALA* 1.3 65.2 + - - +
58A LYS* 3.1 5.4 + - - +
59A PHE* 3.1 29.0 + - - -
124A TRP* 3.8 19.5 - + - -
125A PHE* 4.1 16.0 - + + -
128A GLU* 3.3 27.5 + - + +
129A GLN* 4.6 5.3 + - - -
132A GLU* 3.5 21.5 - - - -
200A FE 2.4 28.4 - - - -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.7 15.5 - - + +
19A GLU* 3.8 19.4 - - + +
20A ILE* 3.8 29.8 - - + +
52A GLU 3.0 12.5 + - - +
53A LEU* 3.2 10.3 + - + +
55A HIS* 1.3 74.8 - - - +
57A MET* 1.3 63.4 + - + +
59A PHE* 3.2 6.5 + - - +
60A TYR* 2.9 26.6 + - - +
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Residues in contact with MET 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 6.4 0.9 - - - -
20A ILE* 6.2 0.2 - - - -
53A LEU* 2.9 23.7 + - + +
54A THR* 3.8 7.9 - - - +
55A HIS 3.2 0.2 - - - -
56A ALA* 1.3 78.2 - - - +
58A LYS* 1.3 60.2 + - - +
60A TYR* 3.6 41.7 - - + -
61A GLU* 3.0 47.0 + - + +
27F LEU* 4.1 27.4 - - + -
46F LYS* 4.3 15.5 - - + -
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR* 3.0 33.0 + - - +
55A HIS* 3.1 7.1 + - - +
57A MET* 1.3 75.4 - - - +
59A PHE* 1.3 65.6 + - - +
61A GLU* 3.4 4.0 + - - +
62A TYR* 3.1 23.4 + - - +
121A PHE* 3.7 9.7 - - + -
124A TRP* 3.6 48.7 - - + -
125A PHE* 3.7 14.4 - - + -
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Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.0 31.6 - - + +
15A GLN* 3.4 31.0 - - + -
16A LEU* 4.1 20.2 - - + -
19A GLU* 3.8 18.8 - - + -
55A HIS 3.1 26.8 + - - -
56A ALA* 3.5 6.3 - - - +
58A LYS* 1.3 72.8 - - - +
60A TYR* 1.3 66.4 + - - +
62A TYR* 3.2 3.2 + - - +
63A ILE* 3.0 28.4 + - + +
103A ILE* 3.7 14.6 - - + -
106A ILE* 4.4 0.7 - - + -
121A PHE* 4.0 11.6 - + - -
122A LEU* 4.0 20.6 - - + -
125A PHE* 3.4 29.6 - + - -
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.4 17.6 - - + +
56A ALA 2.9 17.5 + - - +
57A MET* 3.4 32.3 - - + +
59A PHE* 1.3 74.5 - - - +
61A GLU* 1.3 85.7 + - - +
63A ILE* 3.3 8.8 + - - +
64A TYR* 3.4 31.8 - + - -
70A VAL* 4.0 14.8 - - + -
27F LEU* 4.2 14.8 - - + -
30F ALA* 3.1 26.7 + - - +
31F THR* 3.3 23.1 + - + -
34F ASP* 2.7 30.3 + - - -
46F LYS* 3.8 6.7 - - - -
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET* 3.0 32.2 + - + +
58A LYS* 3.4 3.8 + - - +
59A PHE 3.3 0.2 - - - -
60A TYR* 1.3 88.4 - - + +
62A TYR* 1.3 57.8 + - - +
64A TYR* 3.4 8.0 + - - +
65A GLU* 2.9 30.2 + - - +
34F ASP* 4.7 3.6 - - - +
46F LYS* 2.8 34.7 + - - +
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Residues in contact with TYR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.7 0.9 - - + -
12A LEU* 3.8 24.0 - - + -
58A LYS 3.1 7.4 + - - +
59A PHE* 3.7 2.9 - - - +
61A GLU* 1.3 76.3 - - - +
63A ILE* 1.3 65.0 + - - +
65A GLU* 3.1 21.6 + - - +
66A ARG* 3.0 52.3 + - + +
117A ALA* 3.3 9.1 - - - +
118A THR* 2.7 46.9 + - - -
121A PHE* 3.5 62.6 - + + -
130G VAL* 4.7 8.7 - - + -
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.5 7.6 - - + +
9A ARG* 4.5 7.4 - - + +
12A LEU* 3.9 28.0 - - + +
13A ASN* 3.8 33.4 - - + +
16A LEU* 4.2 5.8 - - + -
59A PHE 3.0 18.8 + - - +
60A TYR 3.3 7.6 + - - +
62A TYR* 1.3 79.1 - - + +
64A TYR* 1.3 60.6 + - + +
66A ARG* 3.2 9.7 + - - +
67A GLY 3.2 0.2 + - - -
68A GLY* 2.9 26.1 + - - -
69A ARG* 3.6 37.5 - - - +
70A VAL* 3.8 19.3 - - + -
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Residues in contact with TYR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 3.4 50.3 + + - -
61A GLU* 4.0 9.6 - - - +
62A TYR 3.3 0.4 - - - -
63A ILE* 1.3 73.0 - - - +
65A GLU* 1.3 65.8 + - - +
67A GLY* 3.0 14.6 + - - -
68A GLY 3.2 22.4 - - - -
69A ARG* 3.7 6.5 - - - +
70A VAL* 3.1 37.8 + - + -
31F THR* 2.6 31.8 + - - -
34F ASP* 3.7 23.8 - - + +
35F ALA* 3.5 26.5 - - - -
134G ASP* 4.9 2.3 - - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU 2.9 17.4 + - - +
62A TYR* 3.4 22.9 - - + +
64A TYR* 1.3 77.4 - - - +
66A ARG* 1.3 65.0 + - + +
67A GLY 3.4 0.4 + - - -
130G VAL* 3.6 28.9 - - + +
131G GLU* 4.2 17.8 - - - +
134G ASP* 3.7 39.4 - - + +
137G ARG* 4.0 15.8 + - - -
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.6 0.4 - - - -
2A MET* 3.6 1.2 - - - +
3A VAL* 2.8 64.9 + - + +
4A ILE* 3.6 26.6 + - + +
62A TYR* 3.0 55.4 + - + +
63A ILE 3.2 3.1 + - - +
64A TYR 3.1 0.2 - - - -
65A GLU* 1.3 79.7 + - - +
67A GLY* 1.3 55.1 + - - +
68A GLY 3.4 3.0 + - - -
115A ASP* 5.0 3.4 + - - -
117A ALA* 3.8 20.8 - - - +
100G THR* 5.5 3.0 - - - +
104G TYR* 4.2 8.3 + - - -
130G VAL* 3.8 29.3 + - - +
133G GLU* 3.2 25.9 + - - -
137G ARG* 4.4 6.3 - - - +
----------------------------------------------------------
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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).
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