Contacts of the helix formed by residues 40 - 66 (chain A) in PDB entry 1EQ1
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 ASN 40 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 5.4 2.4 - - - +
37A GLN 6.3 0.7 - - - -
38A ASP* 4.6 0.4 - - - +
39A PHE* 1.3 115.5 + - - +
41A LYS* 1.3 58.5 + - - +
42A ALA 3.1 2.0 - - - -
43A LEU* 2.5 46.7 + - - +
44A LYS* 3.0 5.5 + - - +
97A VAL* 3.3 30.5 - - + +
98A GLU* 4.2 2.2 - - - -
101A ALA* 2.7 41.8 + - + +
102A ASN 5.1 0.5 - - - +
104A PHE* 5.3 1.7 + - - +
105A LYS* 5.7 0.9 + - - +
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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
----------------------------------------------------------
38A ASP* 4.6 19.8 + - - +
39A PHE 4.5 0.6 - - - +
40A ASN* 1.3 78.5 - - - +
42A ALA* 1.3 64.2 + - - +
44A LYS* 2.9 18.9 + - + +
45A ASP* 3.2 18.4 + - - +
94A HIS* 4.9 4.5 - - - +
95A PRO* 5.6 0.7 - - + -
98A GLU* 3.2 52.7 + - + +
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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
----------------------------------------------------------
38A ASP 5.2 3.0 + - - +
39A PHE* 4.2 11.3 + - - +
40A ASN 3.1 0.8 - - - -
41A LYS* 1.3 80.3 - - - +
43A LEU* 1.3 61.3 + - - +
45A ASP* 3.2 19.4 + - - +
46A GLY* 3.4 9.5 + - - -
162A ALA* 5.1 14.3 - - + +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.7 40.2 - - + -
39A PHE 4.0 1.9 + - - +
40A ASN* 2.5 29.4 + - - +
42A ALA* 1.3 76.0 - - - +
44A LYS* 1.3 66.4 + - + +
46A GLY* 3.6 0.9 + - - -
47A SER* 3.1 31.2 + - - +
97A VAL* 3.3 32.5 - - + -
105A LYS* 3.2 38.4 - - + -
159A LEU* 4.7 7.2 - - + +
162A ALA* 5.0 8.3 - - - +
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASN 3.0 3.2 + - - +
41A LYS* 2.9 12.4 + - + +
43A LEU* 1.3 82.2 - - + +
45A ASP* 1.3 59.0 + - - +
47A SER* 4.3 3.8 - - - -
48A ASP* 2.7 56.0 + - - +
90A LEU* 3.3 33.7 + - + +
93A ALA* 3.5 3.8 - - - +
94A HIS* 3.0 45.4 - - - +
97A VAL* 3.2 44.9 - - + -
104A PHE* 3.5 19.3 - - - +
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Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 3.2 16.1 + - - +
42A ALA* 3.2 15.0 + - - +
44A LYS* 1.3 80.7 - - - +
46A GLY* 1.3 60.2 + - - +
48A ASP* 4.2 1.2 - - - +
49A SER* 3.2 23.0 + - - -
94A HIS* 4.3 9.7 + - - -
158A LYS* 5.3 1.0 - - - +
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Residues in contact with GLY 46 (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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42A ALA 3.4 8.6 + - - -
43A LEU* 3.6 2.0 + - - -
44A LYS 3.3 0.2 - - - -
45A ASP* 1.3 77.6 - - - +
47A SER* 1.3 65.8 + - - +
49A SER* 3.4 2.9 - - - -
50A VAL* 3.4 14.4 + - - +
154A GLU* 3.8 9.0 - - - +
155A VAL* 4.1 2.6 - - - +
158A LYS* 3.9 33.0 - - - +
159A LEU* 4.6 9.2 - - - -
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 4.1 13.2 - - - -
43A LEU* 3.1 27.2 + - - +
44A LYS* 4.0 7.4 - - - -
46A GLY* 1.3 73.5 - - - +
48A ASP* 1.3 66.0 + - - +
49A SER 2.9 4.5 - - - -
50A VAL* 2.6 26.2 - - - +
51A LEU* 3.0 5.5 - - - +
90A LEU* 4.6 4.3 - - - -
105A LYS* 5.3 3.3 + - - -
108A LEU* 2.9 35.2 - - - +
155A VAL* 4.3 1.6 - - - -
159A LEU* 4.3 3.2 - - - +
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Residues in contact with ASP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 2.7 45.5 + - - +
45A ASP* 4.5 1.8 - - - +
47A SER* 1.3 71.2 - - - +
49A SER* 1.3 60.0 + - - +
51A LEU* 3.4 25.0 - - + +
52A GLN* 3.7 13.1 + - - +
90A LEU* 3.2 11.6 - - - +
91A ARG* 3.6 18.1 - - + +
93A ALA 3.4 6.2 - - - +
94A HIS* 2.4 47.6 + - + +
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP 3.2 21.0 + - - -
46A GLY* 3.4 9.6 - - - -
47A SER 2.8 1.8 + - - -
48A ASP* 1.3 75.5 - - - +
50A VAL* 1.3 62.7 + - - -
51A LEU 2.9 4.8 + - - -
52A GLN* 3.1 19.0 + - - +
53A GLN* 2.9 28.2 + - - +
154A GLU* 3.4 13.5 + - - -
158A LYS* 4.5 12.1 - - - -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY 3.4 0.6 + - - -
47A SER 2.6 25.1 + - - +
49A SER* 1.3 80.4 - - - +
51A LEU* 1.3 58.6 + - + +
53A GLN* 3.6 2.5 - - - -
54A LEU* 2.7 53.4 + - + +
108A LEU* 3.0 14.8 - - + -
112A VAL* 5.2 3.1 - - + -
151A HIS 3.6 23.3 - - - +
152A ALA* 5.1 0.7 - - - +
154A GLU* 3.0 25.1 + - + +
155A VAL* 2.8 33.9 - - + -
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER 3.0 17.5 - - - +
48A ASP* 3.4 13.7 - - - +
49A SER 2.9 0.4 - - - -
50A VAL* 1.3 89.1 - - + +
52A GLN* 1.3 51.4 + - - +
54A LEU* 3.6 4.2 - - + +
55A SER* 2.4 43.5 + - - -
87A ALA* 3.1 24.2 - - + +
88A GLU* 3.8 9.2 - - - -
90A LEU* 3.3 18.8 - - + -
91A ARG* 3.2 44.9 - - + +
108A LEU* 3.5 19.1 - - + -
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Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP 3.7 11.6 + - - -
49A SER* 3.1 22.1 + - - +
51A LEU* 1.3 80.1 - - - +
53A GLN* 1.3 72.0 + - + +
55A SER* 3.9 5.7 - - - -
56A ALA* 3.5 16.5 + - - +
91A ARG* 3.4 36.5 - - - +
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Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER* 2.9 24.2 + - - +
50A VAL* 3.7 4.0 - - - +
52A GLN* 1.3 84.1 + - + +
54A LEU* 1.3 63.4 + - - +
56A ALA* 3.1 12.7 - - - +
150A LYS* 5.9 1.1 - - - +
151A HIS* 2.9 38.1 + - - +
154A GLU* 3.2 37.2 - - + +
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Residues in contact with LEU 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 VAL* 2.7 46.3 + - + +
51A LEU* 4.0 3.6 - - + +
53A GLN* 1.3 71.5 - - - +
55A SER* 1.3 61.3 + - - +
56A ALA 2.9 8.3 + - - -
57A PHE* 2.6 48.3 + - + -
83A VAL 4.1 7.2 - - - +
87A ALA* 2.9 38.8 - - + -
112A VAL* 4.7 16.4 - - + -
115A THR* 4.4 11.9 - - + +
148A PHE* 6.3 0.7 - - + -
151A HIS* 3.3 28.9 - - + -
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Residues in contact with SER 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU 2.4 28.1 + - - -
52A GLN* 4.1 7.2 - - - -
54A LEU* 1.3 81.2 - - - +
56A ALA* 1.3 57.8 + - - +
58A SER* 2.3 33.1 + - - -
59A SER* 4.1 0.7 + - - -
84A GLU* 3.3 40.9 + - - +
87A ALA* 3.5 10.6 - - - +
88A GLU* 3.8 5.1 + - - +
91A ARG* 5.7 2.5 - - - -
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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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52A GLN 3.5 11.4 + - - +
53A GLN* 3.1 16.5 + - - +
54A LEU 2.9 0.6 - - - -
55A SER* 1.3 76.4 - - - +
57A PHE* 1.3 67.6 + - - +
58A SER 3.1 1.8 - - - -
59A SER* 2.9 22.8 + - - -
60A SER* 3.7 3.3 + - - -
147A ASP* 5.8 0.2 - - - +
151A HIS* 4.2 7.2 - - + +
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Residues in contact with PHE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN 4.3 0.8 + - - -
54A LEU* 2.6 39.7 + - + -
56A ALA* 1.3 79.2 - - - +
58A SER* 1.3 56.7 + - - +
60A SER* 2.4 42.5 + - - -
61A LEU* 3.7 11.0 + - + +
79A ALA 4.7 1.3 - - - -
83A VAL* 3.2 43.7 - - + -
115A THR* 3.9 8.5 - - + -
144A ALA* 3.4 22.7 - - + -
147A ASP* 3.1 33.3 + - + +
148A PHE* 3.3 41.7 - + - -
151A HIS* 4.3 5.5 + + - -
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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
----------------------------------------------------------
55A SER* 2.3 29.4 + - - -
57A PHE* 1.3 92.8 - - - +
59A SER* 1.3 60.1 + - - +
60A SER 3.2 1.0 + - - -
61A LEU* 3.5 8.1 + - - +
80A ARG* 2.8 56.6 - - - +
83A VAL* 3.6 12.3 - - - -
84A GLU* 3.2 20.0 + - - +
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER 5.0 0.9 - - - -
56A ALA* 2.9 13.0 + - - -
58A SER* 1.3 82.1 + - - +
60A SER* 1.3 58.5 + - - +
61A LEU 3.3 0.2 - - - -
62A GLN* 2.3 75.7 + - - +
80A ARG* 3.9 5.2 - - - +
84A GLU* 5.4 3.8 - - - -
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Residues in contact with SER 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA 3.8 1.7 + - - -
57A PHE* 2.4 43.1 + - - -
59A SER* 1.3 73.5 - - - +
61A LEU* 1.3 61.8 + - - +
62A GLN 3.5 0.2 + - - -
63A GLY* 3.6 7.4 + - - -
140A LYS* 3.6 9.1 - - - +
143A GLN* 3.2 52.8 + - - +
144A ALA* 4.5 2.7 - - - -
147A ASP* 3.3 9.8 + - - -
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 4.8 17.0 - - + +
58A SER 3.5 10.8 + - - +
59A SER 3.3 0.2 - - - -
60A SER* 1.3 76.7 - - - +
62A GLN* 1.3 55.3 + - - +
63A GLY 2.9 2.7 - - - -
64A ALA* 2.6 27.9 + - - +
65A ILE* 2.7 14.5 - - + +
76A LEU* 3.9 24.7 - - + +
79A ALA* 4.2 14.4 - - + +
80A ARG* 4.4 8.1 - - + +
122A LEU* 3.5 26.9 - - + -
140A LYS* 3.9 17.7 - - + +
141A ILE* 3.5 32.5 - - + -
144A ALA* 5.6 4.7 - - + -
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 2.3 50.7 + - - +
61A LEU* 1.3 79.1 - - - +
63A GLY* 1.3 57.8 + - - +
65A ILE* 2.9 12.0 + - - +
66A SER* 2.4 43.2 + - - +
80A ARG* 3.8 29.0 + - - +
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER 3.6 7.0 + - - -
61A LEU 2.8 1.8 + - - -
62A GLN* 1.3 88.1 - - - +
64A ALA* 1.3 59.8 + - - +
66A SER* 3.7 14.8 + - - -
67A ASP* 4.8 0.5 - - - +
136A LYS* 3.2 16.3 + - - +
140A LYS* 3.5 16.6 - - - -
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU 2.6 14.7 + - - +
63A GLY* 1.3 72.8 - - - -
65A ILE* 1.3 51.3 + - - +
67A ASP 3.4 1.4 - - - -
68A ALA* 2.7 41.8 + - - +
76A LEU* 3.3 30.1 - - + -
136A LYS* 3.4 10.8 - - - -
137A LEU* 3.3 17.3 - - + -
140A LYS* 3.3 19.3 - - + +
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Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU 2.7 39.3 - - - +
62A GLN* 2.9 7.5 + - - +
64A ALA* 1.3 73.3 - - - +
66A SER* 1.3 59.7 + - - +
67A ASP* 2.8 11.8 + - - -
68A ALA 3.7 4.0 + - - -
73A LYS* 2.8 49.7 - - + +
76A LEU* 3.0 37.2 - - + +
77A GLU* 3.7 20.0 - - + +
80A ARG* 5.3 2.2 - - - +
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 2.4 33.7 + - - +
63A GLY* 3.8 11.0 - - - -
64A ALA 3.3 0.4 - - - -
65A ILE* 1.3 71.9 - - - +
67A ASP* 1.3 74.1 + - - +
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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