Contacts of the helix formed by residues 33 - 64 (chain A) in PDB entry 3EZB
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 ALA 33 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER* 1.3 73.3 - - - +
34A ASP* 1.3 60.3 + - - +
36A VAL* 2.7 40.1 + - + +
37A ASP* 4.0 3.5 + - - -
97A HIS* 4.9 11.9 + - + -
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Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER* 3.3 8.4 + - - +
33A ALA* 1.3 81.5 - - - +
35A GLN* 1.3 62.2 + - + +
36A VAL 3.4 0.5 + - - -
37A ASP* 4.0 6.8 + - - +
38A GLN* 3.7 23.7 + - - +
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Residues in contact with GLN 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LYS 4.5 0.9 - - - +
31A ILE* 3.3 34.3 - - + +
32A SER* 2.9 30.4 + - - +
34A ASP* 1.3 77.9 - - + +
36A VAL* 1.3 65.7 + - - +
37A ASP 3.4 0.2 - - - -
38A GLN* 3.4 21.3 - - + +
39A GLU* 2.8 29.0 + - + +
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.7 15.7 - - + -
32A SER 3.1 12.8 + - - +
33A ALA* 2.7 27.2 + - + +
35A GLN* 1.3 74.3 - - - +
37A ASP* 1.3 65.8 + - - +
39A GLU* 3.2 1.6 + - - +
40A VAL* 3.1 21.5 + - - +
93A ILE* 3.9 7.7 - - + +
94A LYS* 3.7 45.1 - - + +
97A HIS* 3.6 28.3 - - + +
----------------------------------------------------------
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Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA 4.0 3.6 + - - +
34A ASP* 4.0 6.9 + - - +
35A GLN 3.4 0.2 - - - -
36A VAL* 1.3 83.3 - - - +
38A GLN* 1.3 64.8 + - + +
40A VAL* 3.4 7.0 + - - +
41A GLU* 3.2 20.4 + - - +
94A LYS* 3.6 19.8 + - - -
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Residues in contact with GLN 38 (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 + - - +
35A GLN* 3.3 30.3 + - + +
36A VAL 3.2 0.4 - - - -
37A ASP* 1.3 79.4 - - + +
39A GLU* 1.3 62.8 + - + +
41A GLU* 3.3 7.1 + - - +
42A ARG* 3.1 29.4 + - + +
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.8 30.6 - - + +
35A GLN* 2.8 23.9 + - + +
36A VAL 3.8 2.7 - - - +
38A GLN* 1.3 74.7 - - + +
40A VAL* 1.3 68.4 + - - +
42A ARG* 3.1 33.2 + - - +
43A PHE* 3.0 21.7 + - - +
93A ILE* 4.0 17.0 - - + -
99A THR* 4.7 5.3 - - - +
100A ALA* 3.6 32.0 + - + +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL 3.1 15.2 + - - +
37A ASP* 3.8 8.1 - - - +
39A GLU* 1.3 74.9 - - - +
41A GLU* 1.3 61.1 + - - +
43A PHE* 3.0 10.4 + - + +
44A LEU* 2.7 31.9 + - + +
90A ILE* 4.2 38.1 - - + -
93A ILE* 4.3 20.2 - - + -
94A LYS* 4.4 16.8 - - + +
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP 3.2 10.8 + - - +
38A GLN* 3.6 10.3 - - - +
39A GLU 3.2 0.2 - - - -
40A VAL* 1.3 80.6 - - - +
42A ARG* 1.3 59.0 + - + +
44A LEU* 3.5 26.2 - - - +
45A SER* 2.7 38.1 + - - -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 3.1 18.8 + - + +
39A GLU* 3.1 36.5 + - - +
41A GLU* 1.3 76.4 - - + +
43A PHE* 1.3 53.4 + - - +
45A SER* 3.7 5.5 - - - -
46A GLY* 2.7 33.4 + - - -
100A ALA* 5.5 1.3 - - + -
141A ILE* 4.5 21.6 + - + +
142A LEU* 5.6 7.3 - - - +
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Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU 3.0 11.8 + - - +
40A VAL* 3.4 11.4 - - + +
42A ARG* 1.3 78.4 - - - +
44A LEU* 1.3 57.2 + - + +
46A GLY* 3.5 1.3 - - - -
47A ARG* 2.6 67.8 + - + +
80A LEU* 6.5 1.1 - - + -
86A GLU* 6.2 4.5 - - + -
89A ILE* 3.8 39.5 - - + -
90A ILE* 5.6 8.1 - - + -
93A ILE* 5.1 3.6 - - + -
100A ALA* 4.0 18.3 - - + +
104A ALA* 3.8 23.1 - - + -
137A LEU* 4.3 16.6 - - + -
141A ILE* 3.9 25.1 - - + -
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 2.7 24.1 + - + +
41A GLU* 3.5 28.3 - - - +
43A PHE* 1.3 78.8 - - + +
45A SER* 1.3 58.6 + - - +
47A ARG* 3.2 13.7 + - + +
48A ALA* 2.8 28.3 + - + +
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Residues in contact with SER 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU* 2.7 30.0 + - - -
42A ARG* 3.9 4.7 - - - -
44A LEU* 1.3 74.7 - - - +
46A GLY* 1.3 64.1 + - - +
48A ALA* 2.9 23.9 + - - +
49A LYS* 3.3 6.2 + - - +
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG 2.7 22.3 + - - -
43A PHE 3.6 0.9 - - - -
45A SER* 1.3 73.2 - - - +
47A ARG* 1.3 61.2 + - - +
49A LYS* 3.1 22.6 + - - +
50A ALA* 3.3 14.0 + - - +
137A LEU* 5.8 0.7 - - - -
140A ASN* 4.4 3.1 - - - +
141A ILE* 4.3 28.0 - - - -
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 2.6 49.0 + - + +
44A LEU* 3.5 14.1 - - + +
46A GLY* 1.3 69.5 - - - +
48A ALA* 1.3 67.1 + - - +
50A ALA* 4.6 7.0 - - + -
51A SER* 2.9 49.4 + - - +
80A LEU* 3.4 43.9 + - + +
81A GLU* 3.4 30.5 + - - +
86A GLU* 6.3 2.0 - - - +
89A ILE* 6.4 0.2 - - - +
137A LEU* 5.4 6.9 - - + +
141A ILE* 5.3 0.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 2.8 13.8 + - + +
45A SER* 3.0 20.2 - - - +
47A ARG* 1.3 77.0 - - - +
49A LYS* 1.3 59.2 + - - +
51A SER* 2.8 20.3 + - - -
52A ALA* 3.6 7.8 + - - +
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER 3.3 4.0 + - - +
46A GLY* 3.1 11.2 + - - +
47A ARG 3.1 0.4 - - - -
48A ALA* 1.3 75.5 - - - +
50A ALA* 1.3 70.4 + - - +
51A SER 3.0 1.1 - - - -
52A ALA* 2.7 20.4 + - - +
53A GLN* 2.9 41.1 + - + +
140A ASN* 2.5 42.7 + - - +
141A ILE 5.2 0.8 + - - -
143A GLY* 4.6 12.2 - - - -
144A LEU 6.1 0.4 - - - -
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY 3.3 9.0 + - - +
47A ARG* 4.1 4.9 - - + +
49A LYS* 1.3 79.3 - - - +
51A SER* 1.3 62.9 + - - +
53A GLN* 3.9 7.6 - - - +
54A LEU* 2.9 38.9 + - + +
80A LEU* 5.3 5.2 - - + -
137A LEU* 4.6 13.0 - - + -
140A ASN* 2.8 37.4 + - + +
----------------------------------------------------------
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 2.9 37.5 + - - +
48A ALA* 2.8 19.1 + - - -
49A LYS 2.7 4.4 + - - -
50A ALA* 1.3 75.7 - - - +
52A ALA* 1.3 71.9 + - - +
54A LEU* 3.4 7.0 + - - +
55A GLU* 3.2 27.1 + - - +
77A ILE* 6.1 0.2 - - - +
80A LEU* 5.8 2.0 - - - +
81A GLU* 5.7 4.5 - - - -
----------------------------------------------------------
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA 3.9 8.1 - - - +
49A LYS* 2.7 12.3 + - - +
51A SER* 1.3 80.7 + - - +
53A GLN* 1.3 63.4 + - + +
55A GLU* 3.3 9.0 + - - +
56A THR* 3.0 26.8 + - - +
----------------------------------------------------------
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Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 2.9 48.4 + - + +
50A ALA* 3.8 5.1 - - - +
52A ALA* 1.3 77.8 - - + +
54A LEU* 1.3 65.6 + - + +
56A THR* 3.1 8.1 + - - -
57A ILE* 3.1 31.6 + - + +
140A ASN* 3.6 30.7 + - - +
146A ILE* 4.1 22.1 - - + +
----------------------------------------------------------
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA* 2.9 32.2 + - + +
51A SER* 3.8 5.8 - - - +
53A GLN* 1.3 73.1 - - + +
55A GLU* 1.3 63.6 + - - +
57A ILE* 3.3 19.5 + - + +
58A LYS* 3.1 21.3 + - - +
73A PHE* 4.7 10.9 - - + -
76A HIS* 6.0 4.3 - - + -
77A ILE* 3.9 29.3 - - + +
80A LEU* 3.4 33.4 - - + -
133A ILE* 5.4 9.2 - - + -
136A ARG* 5.6 10.8 - - + +
140A ASN* 5.6 2.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A SER 3.2 16.3 + - - +
52A ALA* 3.6 11.0 - - - +
53A GLN 3.2 0.6 - - - -
54A LEU* 1.3 79.5 - - - +
56A THR* 1.3 62.0 + - - +
58A LYS* 3.2 38.4 + - - +
59A THR* 3.1 17.2 + - - -
77A ILE* 3.5 32.6 - - + +
81A GLU* 4.7 3.8 - - - +
----------------------------------------------------------
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Residues in contact with THR 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 3.0 15.5 + - - +
53A GLN* 3.1 10.8 + - - -
55A GLU* 1.3 77.4 - - - +
57A ILE* 1.3 64.9 + - + +
59A THR* 3.3 16.5 + - - -
60A LYS* 3.3 30.8 + - - +
----------------------------------------------------------
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN* 3.1 20.5 + - + +
54A LEU* 3.3 22.9 + - + +
56A THR* 1.3 77.8 - - + +
58A LYS* 1.3 63.6 + - - +
60A LYS* 3.1 21.2 + - + +
61A ALA* 3.2 11.1 + - - +
73A PHE* 3.2 32.3 - - + -
136A ARG* 4.9 14.1 - - - +
166A SER* 4.4 6.5 - - - +
169A ALA* 5.1 0.6 - - + +
170A GLN* 3.7 33.4 - - + +
----------------------------------------------------------
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU 3.1 13.2 + - - +
55A GLU* 3.2 36.3 + - - +
56A THR 3.2 0.2 - - - -
57A ILE* 1.3 78.4 - - - +
59A THR* 1.3 71.6 + - - +
61A ALA* 3.0 14.0 + - - +
62A GLY 3.1 10.0 + - - -
70A GLU* 3.7 37.0 + - + +
73A PHE* 3.9 27.3 - - + -
74A GLU* 4.9 11.0 - - + +
77A ILE* 4.5 10.3 - - + -
----------------------------------------------------------
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Residues in contact with THR 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU 3.1 14.4 + - - -
56A THR* 3.3 9.4 + - - -
58A LYS* 1.3 87.0 - - - +
60A LYS* 1.3 63.3 + - - +
62A GLY* 3.3 3.0 + - - +
63A GLU* 3.2 37.4 + - + +
70A GLU* 5.6 2.7 - - - -
----------------------------------------------------------
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 3.6 29.8 - - + +
57A ILE* 3.1 14.2 + - - +
59A THR* 1.3 77.4 - - - +
61A ALA* 1.3 57.9 + - - +
63A GLU* 4.1 4.1 - - - +
64A THR* 2.4 42.9 + - - +
148A ASP* 5.1 6.7 + - - -
150A SER* 3.8 26.4 + - - -
169A ALA 4.8 0.4 - - - -
170A GLN* 4.3 30.3 - - + +
----------------------------------------------------------
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE 3.2 2.0 + - - +
58A LYS 3.0 9.8 + - - +
60A LYS* 1.3 78.7 - - - +
62A GLY* 1.3 67.4 + - - +
64A THR* 4.3 3.8 - - - -
65A PHE* 2.8 23.0 + - - +
66A GLY 2.9 8.1 + - - -
69A LYS* 4.1 15.0 - - + +
70A GLU 4.3 0.4 - - - +
73A PHE* 3.5 34.3 - - + -
169A ALA* 3.7 15.7 - - + +
----------------------------------------------------------
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Residues in contact with GLY 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LYS 3.1 9.0 + - - -
59A THR* 3.3 3.7 + - - -
61A ALA* 1.3 81.3 - - - +
63A GLU* 1.3 61.5 + - - +
66A GLY* 3.1 32.7 + - - -
70A GLU* 4.0 20.6 - - - +
----------------------------------------------------------
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 3.2 27.0 + - + +
60A LYS* 4.2 3.4 - - - +
62A GLY* 1.3 77.6 - - - +
64A THR* 1.3 68.3 + - - +
65A PHE 4.8 0.3 - - - -
66A GLY 4.8 0.3 + - - -
----------------------------------------------------------
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LYS* 2.4 36.9 + - - +
63A GLU* 1.3 77.1 - - - +
65A PHE* 1.3 89.4 + - + +
169A ALA 3.6 10.3 + - - +
170A GLN* 5.6 0.3 - - - -
171A LEU 4.0 11.4 - - - +
172A ASN* 6.0 1.8 - - - +
173A LEU* 5.1 10.9 - - + +
----------------------------------------------------------
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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