Contacts of the helix formed by residues 36 - 61 (chain A) in PDB entry 3CUQ
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 MET 36 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLN* 1.3 103.0 - - + +
37A SER* 1.3 64.4 + - - +
38A LYS 3.2 4.8 + - - -
39A GLN* 3.3 41.0 + - - +
40A LEU 3.3 8.0 + - - -
190B GLU 5.9 0.2 - - - +
191B MET* 5.9 0.2 - - - -
194B LEU* 3.1 33.0 - - + +
198B ILE* 4.3 21.1 - - + -
217B PHE* 5.5 2.9 - - + -
220B TYR* 2.9 53.5 + - + +
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 3.5 24.9 + - - +
36A MET* 1.3 75.2 - - - +
38A LYS* 1.3 63.6 + - - +
40A LEU* 3.2 26.4 - - - +
41A ASP* 3.1 26.0 + - - +
220B TYR* 4.9 1.8 - - - -
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 3.6 12.2 + - - +
35A GLN 4.5 7.2 - - - +
36A MET 3.2 0.2 - - - -
37A SER* 1.3 79.9 - - - +
39A GLN* 1.3 70.4 + - + +
40A LEU 3.1 1.3 + - - -
41A ASP* 3.5 4.8 + - - +
42A MET* 3.4 26.9 + - + +
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLN* 5.1 6.5 + - - +
36A MET* 3.3 33.8 + - + +
38A LYS* 1.3 84.1 - - + +
40A LEU* 1.3 63.7 + - - +
42A MET* 3.3 42.4 - - + +
43A PHE 3.4 1.7 + - - -
190B GLU* 5.2 12.4 - - - +
191B MET* 3.4 34.8 + - + +
194B LEU* 5.6 5.3 - - - +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A MET 3.3 6.3 + - - +
37A SER* 3.2 31.0 - - - +
38A LYS 3.1 0.2 - - - -
39A GLN* 1.3 74.8 - - - +
41A ASP* 1.3 70.3 + - - +
43A PHE* 3.2 15.1 + - - +
44A LYS* 3.3 15.7 + - + +
86A PHE* 4.4 24.5 - - + -
191B MET* 4.6 6.7 - - - -
219B SER 5.7 1.1 - - - +
220B TYR* 3.7 46.0 - - + +
223B SER* 4.8 4.9 - - - +
224B MET* 5.3 9.6 - - + -
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Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 3.1 21.5 + - - +
38A LYS 3.5 6.0 + - - +
40A LEU* 1.3 77.5 - - - +
42A MET* 1.3 67.9 + - - +
44A LYS* 3.5 32.3 + - + +
45A THR* 3.3 13.7 + - - +
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Residues in contact with MET 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 3.4 23.2 + - + +
39A GLN* 3.3 39.5 - - + +
41A ASP* 1.3 80.3 - - - +
43A PHE* 1.3 63.4 + - - +
45A THR* 3.1 11.1 + - - -
46A ASN* 3.1 25.2 + - - +
187B LYS* 6.4 1.8 - - + -
191B MET* 4.9 7.4 - - + -
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Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN 3.4 0.2 + - - -
40A LEU* 3.2 10.1 + - + +
42A MET* 1.3 76.8 - - - +
44A LYS* 1.3 67.6 + - - +
46A ASN* 3.1 21.1 + - - +
47A LEU* 3.1 37.1 + - + +
86A PHE* 4.9 4.0 - + + -
87A TRP* 4.0 12.3 - + - -
184B LEU* 3.6 25.4 - - + -
187B LYS* 3.6 19.7 - - + -
188B ALA* 3.2 39.9 - - + -
191B MET* 3.7 27.8 - - + -
224B MET* 3.4 29.2 - - + -
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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 LEU* 3.3 9.2 + - + +
41A ASP* 3.5 31.7 + - + +
42A MET 3.3 0.4 - - - -
43A PHE* 1.3 79.5 - - - +
45A THR* 1.3 58.6 + - + +
47A LEU* 3.5 4.4 + - - +
48A GLU* 3.1 45.4 + - - +
86A PHE* 3.4 44.8 - - + -
90A MET* 4.4 7.9 - - + +
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Residues in contact with THR 45 (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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41A ASP 3.3 8.8 + - - +
42A MET* 3.1 14.4 + - - -
44A LYS* 1.3 77.4 - - + +
46A ASN* 1.3 66.1 + - - +
47A LEU 3.4 0.2 - - - -
48A GLU* 4.0 17.6 - - + +
49A GLU* 3.6 22.2 + - - +
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Residues in contact with ASN 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 MET* 3.1 25.9 + - - +
43A PHE* 3.1 27.6 + - + +
45A THR* 1.3 80.0 + - - +
47A LEU* 1.3 58.7 + - - +
49A GLU* 3.6 4.7 + - - +
50A PHE* 3.1 24.7 + - - +
184B LEU* 4.2 14.4 - - + +
187B LYS* 4.5 22.5 - - + +
191B MET* 6.0 0.2 - - - +
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Residues in contact with LEU 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 PHE* 3.1 40.9 + - + +
44A LYS* 3.8 4.5 - - - +
46A ASN* 1.3 78.4 - - - +
48A GLU* 1.3 53.6 + - - +
50A PHE* 3.0 14.2 - - + +
51A ALA* 2.7 32.8 + - + +
86A PHE* 4.3 23.6 - - + +
87A TRP* 4.2 22.7 - - + +
90A MET* 3.7 29.8 - - + -
91A LEU* 4.3 21.1 - - + -
184B LEU* 4.7 10.3 - - + +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 3.1 39.0 + - - +
45A THR* 4.1 16.7 + - + +
46A ASN 3.4 0.2 - - - -
47A LEU* 1.3 73.7 - - - +
49A GLU* 1.3 59.3 + - - +
51A ALA* 3.3 9.4 + - - +
52A SER* 2.9 28.2 + - - -
90A MET* 3.8 31.8 - - + +
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Residues in contact with GLU 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 THR 3.6 11.6 + - - +
46A ASN* 3.7 8.7 - - - +
48A GLU* 1.3 75.0 - - - +
50A PHE* 1.3 69.0 + - - +
52A SER* 2.7 29.1 + - - +
53A LYS* 3.5 6.8 + - - +
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Residues in contact with PHE 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 ASN 3.1 12.7 + - - +
47A LEU* 3.0 21.1 - - + +
49A GLU* 1.3 79.0 - - - +
51A ALA* 1.3 59.6 + - - +
54A HIS* 3.1 57.4 + + + +
58A ILE* 5.4 4.5 - - + -
64A PHE* 5.4 2.7 - + - -
68A PHE* 5.2 9.2 - + - -
87A TRP* 5.9 2.2 - + - -
91A LEU* 4.4 25.8 - - + -
177B ALA* 4.7 1.6 - - - -
180B ASP* 4.2 7.4 - - + -
181B LEU* 3.7 54.3 - - + -
184B LEU* 3.7 29.8 - - + -
185B MET* 6.0 0.9 - - + -
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Residues in contact with ALA 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 LEU 2.7 14.9 + - - +
48A GLU* 3.3 13.2 - - - +
50A PHE* 1.3 73.0 - - - +
52A SER* 1.3 61.2 + - - +
54A HIS 3.0 1.3 + - - -
55A LYS* 2.8 38.6 + - + +
90A MET* 4.0 30.1 - - + +
91A LEU* 4.6 16.4 - - + -
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Residues in contact with SER 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 GLU 2.9 11.7 + - - -
49A GLU* 2.7 36.0 + - - +
51A ALA* 1.3 71.2 - - - +
53A LYS* 1.3 58.4 + - - +
55A LYS* 4.7 6.8 + - - +
56A GLN* 5.7 1.4 + - - +
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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
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49A GLU 3.5 5.7 + - - +
51A ALA 3.2 0.8 - - - -
52A SER* 1.3 80.9 + - - +
54A HIS* 1.3 77.0 + - + +
55A LYS 3.7 1.6 - - - -
56A GLN* 4.6 10.3 + - - -
57A GLU* 5.0 3.3 - - - +
173B ASN* 3.6 38.5 - - - +
176B GLU* 4.0 20.8 + - + +
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Residues in contact with HIS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 3.1 46.3 + + + +
51A ALA* 3.0 5.8 + - - -
53A LYS* 1.3 91.7 - - + +
55A LYS* 1.3 66.7 + - - +
56A GLN* 3.7 0.9 - - - +
57A GLU* 3.8 25.6 + - + +
58A ILE* 4.2 13.0 + - + +
64A PHE* 5.4 4.3 - - + -
91A LEU* 5.3 2.5 - - + +
173B ASN* 3.7 12.4 + - - -
176B GLU* 3.4 37.6 - - + +
177B ALA* 3.2 37.4 + - + -
180B ASP* 5.1 2.2 - - + -
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Residues in contact with LYS 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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51A ALA* 2.8 17.6 + - + +
52A SER* 4.8 6.3 - - - +
53A LYS 3.7 1.4 - - - -
54A HIS* 1.3 81.7 - - - +
56A GLN* 1.3 92.9 + - - +
57A GLU 3.1 3.5 + - - -
58A ILE* 3.6 12.5 + - - +
59A ARG* 3.3 41.0 + - - +
90A MET 5.9 2.2 - - - +
91A LEU* 5.3 10.9 - - - +
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Residues in contact with GLN 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 SER 5.7 1.7 + - - +
53A LYS 4.6 13.9 + - - -
55A LYS* 1.3 113.8 + - - +
57A GLU* 1.3 60.2 + - + +
58A ILE 3.4 0.4 - - - -
59A ARG* 3.2 14.3 + - + +
60A LYS* 2.6 51.2 + - + +
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Residues in contact with GLU 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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53A LYS 5.0 2.1 - - - +
54A HIS* 3.9 28.2 - - + +
55A LYS 3.1 0.6 + - - -
56A GLN* 1.3 81.2 - - + +
58A ILE* 1.3 62.1 + - - +
60A LYS* 2.9 24.3 + - - +
61A ASN* 3.0 31.2 + - - +
64A PHE* 4.1 17.0 - - + -
173B ASN* 3.9 11.4 - - - +
174B ILE* 3.4 40.7 + - - +
177B ALA* 5.9 1.3 - - + -
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Residues in contact with ILE 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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50A PHE* 5.4 5.4 - - + -
54A HIS* 4.5 8.7 - - + +
55A LYS 3.6 7.5 + - - +
57A GLU* 1.3 78.9 - - - +
59A ARG* 1.3 62.9 + - + +
60A LYS 3.6 0.2 + - - -
61A ASN 4.1 4.1 + - - +
64A PHE* 3.5 30.1 - - + -
65A ARG* 3.2 48.6 + - + +
68A PHE* 4.7 22.2 - - + -
91A LEU* 3.7 35.7 - - + +
93A VAL* 4.1 22.0 - - + -
181B LEU* 6.1 0.2 - - + -
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 3.3 49.6 + - - +
56A GLN* 3.2 16.5 + - + +
57A GLU 3.1 0.6 - - - -
58A ILE* 1.3 83.0 - - + +
60A LYS* 1.3 56.6 + - - +
65A ARG* 4.1 16.9 + - - +
91A LEU 4.3 20.0 + - - +
92A GLY* 4.4 14.3 + - - -
96A PHE* 6.3 5.4 - - + -
138A ASP* 5.0 11.6 - - - +
279B MET* 5.0 13.5 - - - +
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN* 2.6 30.9 + - + +
57A GLU* 2.9 13.7 + - - +
59A ARG* 1.3 76.0 - - - +
61A ASN* 1.3 58.9 + - + +
62A PRO* 4.1 4.8 - - - +
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Residues in contact with ASN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 3.0 32.1 + - - +
58A ILE 4.1 7.0 - - - +
60A LYS* 1.3 80.2 - - + +
62A PRO* 1.3 70.2 - - + +
63A GLU* 3.7 10.6 + - - +
64A PHE* 3.0 44.8 + - - +
65A ARG* 3.8 4.4 + - - -
178B PHE* 6.1 0.2 - - - -
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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) + - + + + + + -
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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