Contacts of the helix formed by residues 40 - 66 (chain A) in PDB entry 1VGO
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 ASP 40 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL 3.5 1.0 - - - -
39A THR* 1.3 69.8 - - - +
41A LYS* 1.3 67.3 + - - +
42A GLU* 3.6 6.1 + - - +
43A ALA* 3.0 37.6 + - + +
44A ARG* 3.0 22.7 + - - +
234A ILE 3.6 1.0 - - - +
235A LEU* 4.0 2.9 - - - -
236A GLY* 3.2 27.8 + - - -
39B THR* 3.7 4.9 - - - -
40B ASP* 2.6 37.7 + - - +
237B GLU* 2.7 28.1 + - + +
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Residues in contact with LYS 41 (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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39A THR 2.7 4.9 + - - -
40A ASP* 1.3 69.4 + - - +
42A GLU* 1.3 65.1 + - - +
44A ARG* 2.9 25.2 + - - +
45A GLU* 3.4 6.2 + - - +
237A GLU* 3.5 30.7 + - - +
37B GLY 5.4 5.4 + - - -
39B THR* 2.7 33.0 + - + +
311B BNG 4.7 15.6 + - - -
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 3.4 6.3 + - - +
41A LYS* 1.3 80.4 - - + +
43A ALA* 1.3 62.0 + - - +
45A GLU* 3.2 27.4 + - - +
46A TYR* 3.3 37.4 + - - -
104A LEU* 5.4 2.3 - - - +
107A LYS* 3.1 30.6 + - - -
168A ARG* 4.9 3.8 + - - -
233A ALA 5.2 1.2 - - - +
234A ILE 3.7 4.9 - - - +
235A LEU 4.5 0.5 - - - +
236A GLY 2.5 31.3 - - - +
237A GLU* 3.2 35.7 + - + +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 3.8 11.9 - - + -
40A ASP* 3.0 31.2 + - + +
42A GLU* 1.3 76.7 - - - +
44A ARG* 1.3 61.8 + - - +
45A GLU 3.3 0.2 + - - -
46A TYR* 3.3 6.3 + - - +
47A TYR* 3.1 30.7 + - + -
234A ILE* 3.1 34.7 + - + +
235A LEU* 4.2 5.2 - - + -
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Residues in contact with ARG 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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35A GLY 3.1 22.1 + - - +
36A TRP* 3.3 28.7 + - - +
38A VAL* 2.7 42.5 + - + +
39A THR* 4.4 8.5 - - - +
40A ASP 3.0 16.3 + - - +
41A LYS* 2.9 14.1 + - - +
43A ALA* 1.3 75.9 - - - +
45A GLU* 1.3 61.6 + - - +
47A TYR* 3.8 9.6 - - - +
48A ALA* 3.2 23.0 + - - +
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Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS 3.4 4.5 + - - +
42A GLU* 3.2 25.4 + - - +
43A ALA 3.1 0.6 - - - -
44A ARG* 1.3 78.7 - - - +
46A TYR* 1.3 66.9 + - - +
48A ALA* 3.3 6.8 + - + +
49A ILE* 3.1 39.5 + - + +
104A LEU* 4.0 27.0 - - + +
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Residues in contact with TYR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 3.3 39.6 + - - -
43A ALA 3.3 6.1 + - - +
45A GLU* 1.3 78.5 - - + +
47A TYR* 1.3 60.2 + - - +
49A ILE* 3.4 3.2 + - - +
50A THR* 2.5 33.4 + - - -
101A ASP* 3.5 30.5 - - - +
104A LEU* 3.3 34.4 + - + +
105A LEU* 3.2 41.9 + - + +
107A LYS* 4.1 6.2 + - - -
168A ARG* 4.3 3.3 + - - -
228A LEU* 4.3 6.5 - - + -
229A LEU* 4.2 8.5 - - + -
233A ALA 4.6 1.3 + - - -
234A ILE* 3.4 43.1 - - + -
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Residues in contact with TYR 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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31A PHE* 3.4 20.2 - - - -
34A ARG* 3.1 33.6 + - + +
35A GLY* 3.5 31.0 - - - +
38A VAL* 4.2 19.1 - - + +
43A ALA* 3.1 28.0 + - + +
44A ARG* 3.8 9.2 - - - +
46A TYR* 1.3 79.8 - - - +
48A ALA* 1.3 57.3 + - - +
50A THR* 3.3 1.1 + - - -
51A ILE* 2.9 42.6 + - + +
229A LEU* 3.2 44.4 + - + -
234A ILE* 3.7 22.0 - - + -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG 3.2 15.7 + - - +
45A GLU* 3.3 8.0 + - + +
47A TYR* 1.3 80.0 - - - +
49A ILE* 1.3 63.1 + - + +
51A ILE* 3.7 9.2 + - - +
52A LEU* 3.4 28.0 + - + +
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Residues in contact with ILE 49 (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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45A GLU* 3.1 26.9 + - + +
46A TYR 3.7 3.4 - - - +
48A ALA* 1.3 78.8 - - + +
50A THR* 1.3 62.8 + - - +
52A LEU* 3.6 17.5 + - - +
53A VAL* 3.6 11.3 - - + +
97A LEU* 3.4 42.7 - - + +
100A LEU* 3.7 24.0 - - + -
101A ASP* 3.5 15.9 - - - +
104A LEU* 3.6 31.6 - - + -
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Residues in contact with THR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.1 5.6 - - + -
46A TYR 2.5 24.2 + - - -
47A TYR 3.8 2.5 - - - -
49A ILE* 1.3 73.4 - - - +
51A ILE* 1.3 60.6 + - - +
52A LEU 3.1 2.5 - - - -
53A VAL* 2.9 13.1 + - + +
54A PRO* 2.9 27.5 - - - +
98A LEU* 5.9 1.6 - - + -
101A ASP* 3.1 21.1 + - - +
221A LYS 4.9 2.5 - - - +
224A PHE* 5.8 1.3 - - + -
225A GLY* 3.7 22.9 - - - -
228A LEU* 3.7 8.3 - - + +
229A LEU* 3.6 27.9 - - + +
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Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 3.5 18.5 - - + +
31A PHE* 3.9 28.3 - - + +
32A ILE* 3.6 44.9 - - + -
35A GLY* 5.9 1.3 - - - -
47A TYR* 2.9 38.3 + - + +
48A ALA* 3.9 8.5 - - - +
50A THR* 1.3 75.8 - - - +
52A LEU* 1.3 63.0 + - + +
53A VAL 3.3 0.2 + - - -
54A PRO* 3.6 3.1 - - - +
55A GLY* 3.1 21.1 + - - -
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Residues in contact with LEU 52 (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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48A ALA* 3.4 18.4 + - + +
49A ILE* 3.6 12.9 + - - +
50A THR 3.1 0.8 - - - -
51A ILE* 1.3 80.6 - - + +
53A VAL* 1.3 66.3 + - - +
55A GLY* 3.7 4.5 - - - +
56A ILE* 3.0 36.4 + - + +
97A LEU* 3.9 20.0 - - + -
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Residues in contact with VAL 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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49A ILE 3.6 16.4 - - - +
50A THR* 2.9 14.2 + - + +
52A LEU* 1.3 81.4 - - - +
54A PRO* 1.3 69.0 - - + +
57A ALA* 3.1 19.7 + - - +
94A THR* 3.5 27.3 + - + +
97A LEU* 3.8 22.2 - - + -
98A LEU* 3.9 26.5 - - + +
101A ASP* 5.3 0.9 - - - +
221A LYS* 3.4 33.7 - - + +
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Residues in contact with PRO 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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24A MET* 3.3 23.4 - - + +
28A THR* 3.1 19.3 - - - +
31A PHE* 4.0 26.2 - - + -
50A THR 2.9 24.2 - - - +
51A ILE 3.6 5.4 - - - +
53A VAL* 1.3 86.0 - - + +
55A GLY* 1.3 57.7 + - - +
57A ALA* 3.7 2.0 - - + -
58A SER* 2.8 33.3 + - - -
221A LYS* 4.6 7.4 - - + +
222A VAL* 4.1 19.1 - - + -
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Residues in contact with GLY 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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28A THR* 3.2 18.9 + - - -
51A ILE 3.1 17.5 + - - -
52A LEU* 4.0 3.4 - - - -
53A VAL 3.1 1.6 - - - -
54A PRO* 1.3 76.7 - - - +
56A ILE* 1.3 60.7 - - - +
58A SER* 3.2 19.3 + - - -
59A ALA* 3.4 7.6 + - - +
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Residues in contact with ILE 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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52A LEU* 3.0 36.2 + - + +
53A VAL 4.0 1.3 - - - +
55A GLY* 1.3 75.1 - - - +
57A ALA* 1.3 63.3 + - - +
59A ALA* 3.4 8.4 + - + +
60A ALA* 3.0 20.3 + - + +
89A ALA 5.2 0.7 - - - +
90A ASP* 4.4 17.5 - - - +
93A PHE* 4.1 22.4 - - + -
94A THR* 4.1 12.6 - - - +
97A LEU* 4.0 20.4 - - + -
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Residues in contact with ALA 57 (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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24A MET* 3.3 36.6 - - + -
53A VAL 3.1 16.8 + - - +
54A PRO 3.6 0.2 - - - +
56A ILE* 1.3 76.9 - - - +
58A SER* 1.3 54.6 + - - +
60A ALA* 3.2 0.9 + - - +
61A TYR* 2.7 40.2 + - + +
90A ASP* 3.7 16.6 + - - +
221A LYS* 3.7 15.7 - - + -
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.9 6.7 - - - +
24A MET* 3.0 33.7 + - - +
25A LEU* 3.0 29.5 + - - +
28A THR* 3.7 1.6 + - - -
54A PRO 2.8 19.0 + - - -
55A GLY* 3.2 12.8 + - - -
57A ALA* 1.3 75.6 - - - +
59A ALA* 1.3 57.2 + - - +
61A TYR* 3.2 5.8 + - - +
62A LEU* 2.9 29.0 + - - +
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Residues in contact with ALA 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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55A GLY 3.4 7.4 + - - +
56A ILE* 3.7 10.1 - - + +
57A ALA 3.3 0.4 - - - -
58A SER* 1.3 76.2 - - - +
60A ALA* 1.3 61.3 + - - +
62A LEU* 3.1 9.8 + - - +
63A ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 60 (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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56A ILE* 3.0 18.3 + - + +
57A ALA 3.6 4.3 - - - +
59A ALA* 1.3 75.2 - - - +
61A TYR* 1.3 58.6 + - - +
63A ALA* 3.5 7.0 + - - +
64A MET* 3.1 37.0 + - + +
86A ALA* 3.7 15.8 - - + +
89A ALA* 6.1 0.2 - - + -
90A ASP* 3.6 32.5 - - + +
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Residues in contact with TYR 61 (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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17A LEU* 3.5 44.4 - - + +
20A GLY* 3.8 22.2 - - - +
21A THR* 3.2 24.2 + - - +
24A MET* 4.2 19.1 - - + -
57A ALA 2.7 30.0 + - - +
58A SER 3.6 3.6 - - - +
60A ALA* 1.3 73.5 - - - +
62A LEU* 1.3 63.3 + - - +
64A MET* 3.7 21.0 + - + +
65A PHE* 3.1 18.0 + - - +
87A ARG* 5.6 2.3 + - - -
90A ASP* 4.4 8.7 - - - -
210A THR 5.2 0.4 + - - -
213A PHE* 3.7 2.9 + - - +
214A MET* 3.3 30.8 + - + -
217A ASP* 2.8 29.1 + - + +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.8 21.3 + - + +
25A LEU* 6.2 0.7 - - + -
58A SER 2.9 13.4 + - - +
59A ALA* 3.1 11.4 + - - +
61A TYR* 1.3 73.7 - - - +
63A ALA* 1.3 67.0 + - - +
65A PHE* 3.1 18.6 + - + +
66A PHE* 3.2 47.2 + - + -
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Residues in contact with ALA 63 (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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59A ALA 2.9 14.9 + - - +
60A ALA* 3.7 7.0 - - - +
62A LEU* 1.3 77.2 - - - +
64A MET* 1.3 61.9 + - - +
65A PHE 3.2 0.3 + - - -
66A PHE* 3.2 3.1 + - - -
67A GLY 3.2 3.5 + - - -
68A ILE* 2.8 56.8 + - + +
86A ALA* 4.4 13.0 - - + -
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Residues in contact with MET 64 (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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11A ARG* 2.8 26.9 + - - -
17A LEU* 3.6 23.5 - - + +
60A ALA* 3.1 23.1 + - + +
61A TYR* 3.9 39.5 - - + +
63A ALA* 1.3 76.8 - - - +
65A PHE* 1.3 58.6 + - - +
67A GLY 3.1 2.6 + - - +
68A ILE 4.6 2.2 - - - -
84A TYR* 3.6 43.4 - - + -
86A ALA* 3.7 14.4 - - + -
87A ARG* 4.0 34.5 - - + +
90A ASP* 5.3 0.9 - - - +
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.5 24.7 - - + -
7A LEU* 3.1 48.1 - - + +
11A ARG* 3.6 7.3 + - - -
14A THR* 3.4 28.6 - - - +
17A LEU* 4.3 8.9 - - + +
18A GLY* 3.8 18.2 - - - -
21A THR* 4.6 3.8 - - - +
61A TYR 3.1 15.2 + - - +
62A LEU* 3.1 17.3 + - + +
64A MET* 1.3 79.0 - - - +
66A PHE* 1.3 91.5 + + - +
67A GLY 3.0 3.3 + - - -
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.9 16.3 - - + +
11A ARG* 4.7 0.4 - - - -
62A LEU* 3.2 49.4 + - + +
63A ALA 3.2 2.7 + - - +
65A PHE* 1.3 103.1 - + - +
67A GLY* 1.3 63.1 + - - +
68A ILE* 3.2 22.7 + - + +
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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