Contacts of the helix formed by residues 48 - 76 (chain A) in PDB entry 3ES3
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 48 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.1 34.2 + - + +
46A VAL* 3.4 14.7 - - + +
47A ALA* 1.3 82.2 - - - +
49A LYS* 1.3 58.4 + - - +
50A ASN 3.3 2.0 - - - -
51A PHE* 3.6 36.6 - - + -
52A ALA* 3.1 22.2 + - - +
167A GLU* 4.2 23.1 - - + +
168A TYR* 4.4 23.1 - - + +
171A ASP* 3.8 18.8 - - + +
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE 4.4 3.6 + - - +
42A ASP* 3.9 30.5 + - - +
43A ARG 5.2 0.2 + - - -
47A ALA* 3.6 35.5 + - - +
48A LEU* 1.3 72.1 - - - +
50A ASN* 1.3 64.0 + - - +
52A ALA* 3.6 8.8 - - + +
53A LYS* 3.1 24.8 + - - +
171A ASP* 3.8 4.4 + - - +
172A LYS* 5.8 0.8 - - - +
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Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 1.3 78.3 - - - +
51A PHE* 1.3 55.3 + - - +
53A LYS* 3.7 19.3 + - - +
54A TYR* 2.7 35.3 + - - +
171A ASP* 2.8 52.4 + - - +
172A LYS* 4.0 11.5 - - - +
175A LEU* 3.6 19.1 - - + +
176A GLY* 3.7 17.5 - - - -
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Residues in contact with PHE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.7 14.8 - + + -
48A LEU* 3.5 33.0 + - + +
50A ASN* 1.3 72.4 - - - +
52A ALA* 1.3 67.0 + - - +
54A TYR* 3.5 1.5 - - - +
55A PHE* 3.1 49.2 + + - -
96A GLY* 3.5 37.9 - - - -
100A MET* 4.1 11.9 - - + -
155A LEU* 4.2 10.1 - - + -
167A GLU* 3.7 12.3 - - + -
170A PHE* 3.7 18.4 - + - -
171A ASP* 3.2 30.2 + - + -
175A LEU* 3.6 22.0 - - + -
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER* 2.6 47.4 + - - +
41A PHE* 3.8 10.0 - - + +
42A ASP* 4.4 8.5 - - + +
48A LEU 3.1 15.0 + - - +
49A LYS* 3.6 12.6 - - + +
51A PHE* 1.3 82.6 - - - +
53A LYS* 1.3 61.0 + - - +
56A LEU* 3.1 11.1 + - - +
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS 3.1 15.4 + - - +
50A ASN* 3.7 17.7 + - - +
51A PHE 3.3 0.2 - - - -
52A ALA* 1.3 78.5 - - - +
54A TYR* 1.3 66.2 + - - +
56A LEU* 3.3 10.3 + - + +
57A HIS* 2.8 49.5 + - - +
175A LEU 4.0 18.2 + - - -
176A GLY 4.5 9.7 - - - -
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Residues in contact with TYR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN 2.7 21.5 + - - +
51A PHE* 3.5 6.7 - - - +
53A LYS* 1.3 75.7 - - - +
55A PHE* 1.3 85.6 + + - +
57A HIS* 3.0 24.8 + - - +
58A GLN* 3.1 38.8 + - + +
100A MET* 3.7 21.1 - - + -
147A CYS* 4.9 6.1 - - - +
148A LEU* 3.4 22.4 - - + +
151A HIS* 3.5 25.4 + + - -
175A LEU* 3.7 20.9 - - + +
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.4 53.1 - + - +
37A MET* 4.1 18.2 - - + -
38A SER* 3.7 7.4 - - - +
41A PHE* 3.3 36.6 - + - -
51A PHE* 3.1 32.9 + + - +
54A TYR* 1.3 103.4 - + - +
56A LEU* 1.3 57.7 + - - +
58A GLN* 3.3 3.5 + - + -
59A SER* 2.8 24.6 + - - -
99A ALA* 4.1 16.6 - - + -
100A MET* 4.2 18.6 - - + -
103A ALA* 4.4 8.5 - - + -
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.1 25.4 - - + -
38A SER* 3.6 11.8 + - - +
39A TYR* 4.4 15.9 - - + +
52A ALA 3.1 14.9 + - - +
53A LYS* 3.6 14.1 - - + +
54A TYR 3.2 0.2 - - - -
55A PHE* 1.3 77.5 - - - +
57A HIS* 1.3 59.5 + - + +
59A SER* 3.4 9.8 + - - -
60A HIS* 3.1 23.4 + - - +
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Residues in contact with HIS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 2.8 50.1 + - + +
54A TYR* 3.0 11.2 + - + +
56A LEU* 1.3 73.2 - - + +
58A GLN* 1.3 75.5 + - - +
59A SER 3.0 1.3 - - - -
60A HIS* 3.0 2.9 + - - +
61A GLU* 2.8 29.6 + - + +
731A AU 2.5 31.0 - - - -
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.6 36.1 + - + +
54A TYR* 3.1 52.4 + - + +
55A PHE* 3.3 9.8 + - - +
57A HIS* 1.3 81.0 - - - +
59A SER* 1.3 62.3 + - - +
61A GLU* 3.3 16.1 + - - +
62A GLU* 3.0 28.8 + - - +
107A GLU* 5.3 2.3 - - - +
144A ALA* 5.5 6.6 - - - +
148A LEU* 6.1 1.1 - - + -
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 2.8 50.4 + - - +
34A TYR* 3.7 10.5 - - - +
35A LEU* 3.7 17.9 - - - +
55A PHE 2.8 13.5 + - - -
56A LEU* 3.4 16.1 - - - +
57A HIS 3.0 0.2 - - - -
58A GLN* 1.3 77.8 - - - +
60A HIS* 1.3 62.7 + - - +
62A GLU 3.4 0.3 + - - -
63A ARG* 3.1 12.6 + - - +
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Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU 3.1 7.8 + - - +
57A HIS 3.0 4.2 + - - +
59A SER* 1.3 77.9 - - - +
61A GLU* 1.3 67.6 + - - +
63A ARG* 3.4 34.2 + - - +
64A CYS* 2.8 53.0 + - + +
731A AU 2.7 29.1 - - - -
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A HIS* 2.8 19.7 + - + +
58A GLN* 3.5 22.9 - - - +
60A HIS* 1.3 89.1 + - + +
62A GLU* 1.3 58.8 + - + +
64A CYS* 3.2 8.0 + - - +
65A HIS* 2.8 53.0 + - + +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 2.8 46.7 - - - +
30A ALA* 4.0 14.4 - - + +
31A SER* 3.8 10.5 - - - +
34A TYR* 3.7 18.1 - - + -
58A GLN* 3.0 21.8 + - - +
61A GLU* 1.3 75.3 - - + +
63A ARG* 1.3 62.9 + - - +
65A HIS* 3.2 14.6 + - - +
66A ALA* 3.0 22.2 + - - +
107A GLU* 2.6 31.3 - - - +
110A VAL* 4.9 3.2 - - - +
141A GLN* 3.9 8.9 - - - +
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 4.3 16.4 - - + -
31A SER* 3.6 15.4 + - - +
59A SER 3.1 15.7 + - - +
60A HIS* 3.6 44.1 + - - +
62A GLU* 1.3 77.7 - - - +
64A CYS* 1.3 68.0 + - - +
66A ALA* 3.0 16.9 + - - +
67A GLU* 3.1 39.8 + - + +
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Residues in contact with CYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS* 2.8 48.1 + - + +
61A GLU* 3.6 8.7 - - - +
63A ARG* 1.3 79.1 - - - +
65A HIS* 1.3 62.0 + - - +
66A ALA 3.2 0.2 + - - -
67A GLU* 3.3 14.8 + - - +
68A LYS* 3.1 30.4 + - - +
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Residues in contact with HIS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 4.2 11.2 - - - +
61A GLU* 2.8 46.1 + - + +
62A GLU* 3.2 20.7 + - - +
64A CYS* 1.3 72.2 - - - +
66A ALA* 1.3 59.7 + - - +
68A LYS* 3.7 15.1 + - - +
69A LEU* 3.5 5.7 + - - +
136A HIS 3.9 9.0 + - - -
137A TYR* 2.5 54.6 + + + -
140A CYS* 4.7 7.5 - - + +
141A GLN* 5.3 7.9 + - - -
732A AU 2.9 25.8 - - - -
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 3.8 16.7 - - + +
27A GLU* 3.7 24.7 - - + +
28A LEU* 3.8 20.4 - - + -
62A GLU 3.0 7.6 + - - +
63A ARG 3.0 7.8 + - - +
65A HIS* 1.3 74.7 - - - +
67A GLU* 1.3 59.9 + - - +
68A LYS 3.1 2.0 - - - -
69A LEU* 2.8 24.2 + - - +
70A MET* 3.0 18.1 + - + +
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 6.0 0.2 - - + -
63A ARG* 3.1 42.5 + - + +
64A CYS* 3.3 15.5 + - - +
66A ALA* 1.3 75.8 - - - +
68A LYS* 1.3 56.0 + - - +
70A MET* 3.1 29.8 + - + +
71A LYS* 3.0 32.4 + - - +
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A CYS* 3.1 21.2 + - - +
65A HIS* 4.1 22.8 + - - +
66A ALA 3.1 0.4 - - - -
67A GLU* 1.3 76.9 - - - +
69A LEU* 1.3 58.1 + - - +
71A LYS* 3.5 14.6 + - + +
72A LEU* 3.1 24.6 + - - +
132A PHE* 4.2 21.5 - - + -
136A HIS* 4.2 31.9 + - + +
137A TYR* 3.6 13.0 - - + +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.7 21.3 - - + +
23A GLN* 3.7 30.5 - - + -
24A ILE* 3.6 25.8 - - + +
27A GLU* 4.0 9.2 - - + +
65A HIS 3.5 3.3 + - - +
66A ALA* 2.8 13.4 + - - +
68A LYS* 1.3 75.5 - - - +
70A MET* 1.3 59.6 + - - +
72A LEU* 3.6 29.8 - - + +
73A GLN 3.2 18.7 + - - -
114A LEU* 5.3 1.1 - - + -
117A LEU* 6.0 0.2 - - + -
132A PHE* 3.9 6.1 - - + -
133A ILE* 5.2 4.5 - - + -
137A TYR* 3.5 39.0 - - + +
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Residues in contact with MET 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 3.9 26.5 - - + -
28A LEU* 5.1 11.9 - - + -
66A ALA* 3.0 15.2 + - + +
67A GLU* 3.1 44.1 + - + +
69A LEU* 1.3 77.0 - - - +
71A LYS* 1.3 64.3 + - - +
73A GLN* 3.3 1.3 + - - -
74A ASN* 3.2 20.8 + - - +
80A ILE* 3.4 31.6 - - + +
82A LEU* 4.5 16.2 - - - -
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 3.0 16.7 + - - +
68A LYS* 3.7 16.4 - - + +
69A LEU 3.4 0.2 - - - -
70A MET* 1.3 76.6 - - - +
72A LEU* 1.3 56.6 + - - +
74A ASN* 3.3 7.9 + - + +
75A GLN* 2.8 46.9 + - + +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 5.1 3.1 - - - +
20A ILE* 4.0 7.2 - - + -
68A LYS 3.1 16.3 + - - +
69A LEU* 3.6 19.5 - - + +
70A MET 3.2 0.4 - - - -
71A LYS* 1.3 73.9 - - - +
73A GLN* 1.3 68.3 + - - +
75A GLN* 3.3 12.8 + - + +
76A ARG* 3.2 44.7 + - + +
128A HIS* 3.9 16.6 - - + +
129A LEU* 3.7 23.6 - - + -
132A PHE* 3.4 42.8 - - + -
133A ILE* 5.6 0.2 - - + -
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 2.9 39.5 + - - -
17A GLU* 3.2 36.7 + - - +
20A ILE* 3.2 19.0 - - + +
21A ASN* 3.4 17.8 + - - -
24A ILE* 4.4 1.4 - - + +
69A LEU 3.2 10.4 + - - +
70A MET* 3.3 8.7 + - - +
72A LEU* 1.3 80.9 - - - +
74A ASN* 1.3 64.3 + - - +
76A ARG* 3.2 1.7 + - - +
77A GLY 3.2 3.1 + - - -
78A GLY* 3.0 24.3 + - - -
79A ARG 3.5 27.8 - - - +
80A ILE* 3.9 11.4 - - + -
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Residues in contact with ASN 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.4 4.2 - - - +
70A MET 3.2 12.4 + - - +
71A LYS* 3.7 10.8 - - + +
73A GLN* 1.3 79.9 - - - +
75A GLN* 1.3 63.2 + - - +
76A ARG 3.2 1.0 + - - -
77A GLY* 3.2 11.3 + - - -
78A GLY 4.3 3.7 - - - +
79A ARG* 4.0 17.6 + - - +
80A ILE* 4.0 21.5 + - - +
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.8 14.2 - - - +
71A LYS* 2.8 40.2 + - + +
72A LEU* 3.3 21.3 + - + +
74A ASN* 1.3 73.0 - - - +
76A ARG* 1.3 64.0 + - + +
77A GLY 3.7 0.3 + - - -
128A HIS* 5.3 12.7 - - + +
132A PHE* 5.0 8.0 - - - -
----------------------------------------------------------
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.0 7.9 + - - -
9A ARG* 3.4 24.6 - - - +
10A GLN* 3.4 26.7 + - - +
11A ASN* 4.0 4.9 + - - +
12A TYR* 3.7 39.7 - - + +
72A LEU* 3.2 27.9 + - + +
73A GLN 4.3 0.7 - - - +
74A ASN 3.2 0.6 - - - -
75A GLN* 1.3 80.0 - - + +
77A GLY* 1.3 61.1 + - - +
78A GLY 3.3 2.3 + - - -
126A ASP* 2.8 36.4 + - - -
128A HIS* 3.3 41.2 - - + +
129A LEU* 4.6 3.8 - - - +
----------------------------------------------------------
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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