Contacts of the helix formed by residues 37 - 63 (chain A) in PDB entry 3BFR
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 LYS 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU* 6.3 0.2 - - - -
33A LEU* 3.0 36.9 + - + +
36A THR* 1.3 98.1 - - - +
38A HIS* 1.3 62.7 + - + +
39A HIS 3.6 0.2 - - - -
40A GLN* 3.7 1.8 + - - +
41A THR* 2.7 39.2 + - - -
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Residues in contact with HIS 38 (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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33A LEU* 3.1 31.6 + - + +
34A HIS* 3.4 26.2 - - + +
37A LYS* 1.3 75.8 - - + +
39A HIS* 1.3 66.4 + - - +
41A THR* 3.3 14.9 + - - -
42A TYR* 3.1 29.6 + - + -
89A HIS* 5.1 0.2 - - - +
180A HIS* 3.6 49.2 + + + +
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Residues in contact with HIS 39 (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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12A LEU* 3.5 14.1 - - + +
13A PRO* 3.5 18.9 - - + +
34A HIS 2.9 16.8 + - - +
35A TYR* 3.3 17.0 + + - +
38A HIS* 1.3 73.2 - - - +
40A GLN* 1.3 63.0 + - - +
42A TYR* 3.1 8.0 + - - +
43A VAL* 3.0 21.2 + - + +
85A GLY 4.0 4.0 + - - -
86A PHE* 3.1 46.0 + + - -
89A HIS* 3.4 23.7 - - + +
90A CYS* 3.6 9.1 + - - -
93A TRP* 3.0 27.6 + - - +
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Residues in contact with GLN 40 (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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12A LEU* 3.5 27.7 - - + +
35A TYR 3.4 4.5 + - - +
36A THR 3.2 26.6 - - - +
37A LYS 3.7 2.0 + - - +
38A HIS 3.3 0.4 - - - -
39A HIS* 1.3 78.7 - - - +
41A THR* 1.3 58.8 + - - +
43A VAL* 3.2 18.7 + - - +
44A ASN* 2.8 62.4 + - - +
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Residues in contact with THR 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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37A LYS 2.7 24.3 + - - -
38A HIS* 3.6 7.0 - - - -
39A HIS 3.2 0.2 - - - -
40A GLN* 1.3 76.3 - - - +
42A TYR* 1.3 61.4 + - + +
44A ASN* 3.5 9.5 + - + +
45A GLY* 2.8 26.0 + - - -
82A HIS* 3.8 11.7 + - + -
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Residues in contact with TYR 42 (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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38A HIS* 3.1 32.1 + - + -
39A HIS* 3.1 6.7 + - - +
41A THR* 1.3 77.0 - - + +
43A VAL* 1.3 60.9 + - - +
46A PHE* 2.8 33.8 + - - +
81A PHE* 3.6 25.9 - + - -
82A HIS* 3.6 26.4 - + - +
85A GLY* 3.6 18.4 - - - +
86A PHE* 3.6 19.3 - - - +
89A HIS* 3.4 28.3 - + - -
162A GLN* 3.0 22.5 + - + -
178A TRP* 3.6 21.8 - - - -
180A HIS* 4.3 4.1 - + - -
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Residues in contact with VAL 43 (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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10A VAL* 3.4 34.0 - - + +
11A THR* 4.0 6.3 - - - -
12A LEU* 3.9 27.4 - - + +
39A HIS* 3.0 17.9 + - - +
40A GLN* 3.3 26.5 - - - +
42A TYR* 1.3 75.8 - - - +
44A ASN* 1.3 63.6 + - - +
46A PHE* 3.3 2.3 + - - +
47A ASN* 3.1 32.5 + - - +
86A PHE* 3.8 26.2 - - + +
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Residues in contact with ASN 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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40A GLN* 2.8 54.3 + - - +
41A THR* 3.8 7.5 - - + +
43A VAL* 1.3 73.2 - - - +
45A GLY* 1.3 58.1 + - - +
47A ASN* 3.4 7.9 + - - +
48A THR* 3.0 35.4 + - - +
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Residues in contact with GLY 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 THR 2.8 15.2 + - - -
44A ASN* 1.3 72.4 - - - +
46A PHE* 1.3 57.2 + - - +
48A THR* 3.6 6.2 + - - -
49A ALA* 3.1 28.9 + - - +
78A ASN* 5.3 0.2 - - - +
82A HIS* 3.5 35.4 - - - -
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Residues in contact with PHE 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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10A VAL* 3.7 31.9 - - + -
42A TYR 2.8 21.9 + - - +
43A VAL* 3.8 4.9 - - - +
45A GLY* 1.3 71.2 - - - +
47A ASN* 1.3 64.3 + - - +
49A ALA* 3.9 1.1 - - - +
50A VAL* 3.0 53.8 + - + +
79A ILE* 3.8 23.6 - - + -
82A HIS* 3.3 11.1 - - - +
83A GLY* 3.4 28.3 - - - -
86A PHE* 4.3 17.7 - + + -
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Residues in contact with ASN 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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9A LYS* 3.1 36.6 + - + +
10A VAL* 3.0 52.6 + - - +
43A VAL* 3.1 27.6 + - - +
44A ASN* 3.8 7.9 + - - +
46A PHE* 1.3 75.6 - - - +
48A THR* 1.3 61.0 + - - +
51A ASP* 3.1 26.1 + - - +
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Residues in contact with THR 48 (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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44A ASN* 3.0 20.2 + - - +
45A GLY* 3.9 6.7 - - - -
47A ASN* 1.3 77.5 - - - +
49A ALA* 1.3 56.6 + - - +
51A ASP* 3.4 7.8 + - - +
52A GLN* 2.9 53.1 + - + +
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Residues in contact with ALA 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 GLY 3.1 18.6 + - - +
46A PHE* 3.9 3.8 - - - +
47A ASN 3.4 0.2 - - - -
48A THR* 1.3 78.0 - - - +
50A VAL* 1.3 56.8 + - - +
52A GLN* 3.3 10.0 + - - +
53A PHE* 2.9 29.1 + - - +
75A ILE* 3.6 9.6 - - + +
78A ASN* 4.0 14.1 - - + +
79A ILE* 3.6 36.7 - - + +
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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
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9A LYS* 3.5 21.8 - - + +
46A PHE* 3.0 46.8 + - + +
49A ALA* 1.3 72.3 - - - +
51A ASP* 1.3 64.9 + - - +
53A PHE* 3.4 12.2 + - + +
54A GLN* 3.1 23.2 + - + +
79A ILE* 4.7 10.3 - - + -
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Residues in contact with ASP 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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9A LYS* 2.6 28.7 + - - +
47A ASN* 3.1 24.9 + - - +
48A THR* 3.5 7.4 - - - +
50A VAL* 1.3 75.1 - - - +
52A GLN* 1.3 62.4 + - + +
54A GLN* 3.2 8.6 + - - +
55A GLU* 3.1 32.5 + - + +
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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
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48A THR* 2.9 40.3 + - + +
49A ALA* 3.3 12.9 + - - +
51A ASP* 1.3 75.4 - - + +
53A PHE* 1.3 56.9 + - - +
55A GLU* 3.4 16.5 + - - +
56A LEU* 3.0 34.4 + - + +
75A ILE* 3.4 31.7 - - + +
78A ASN* 5.0 5.4 + - - -
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Residues in contact with PHE 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 ALA 2.9 16.3 + - - +
50A VAL* 3.6 11.4 - - + +
51A ASP 3.2 0.2 - - - -
52A GLN* 1.3 75.6 - - - +
54A GLN* 1.3 62.9 + - + +
56A LEU* 3.3 6.9 + - + -
57A SER* 2.7 43.9 + - - -
72A MET* 2.9 33.7 - - + -
75A ILE* 4.4 4.0 - - + +
76A GLN* 3.6 25.8 - - - -
79A ILE* 4.0 16.2 - - + -
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Residues in contact with GLN 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* 3.1 14.0 + - + +
51A ASP* 3.2 12.3 + - - +
53A PHE* 1.3 82.4 - - + +
55A GLU* 1.3 63.6 - - + +
57A SER* 3.4 14.6 + - - -
58A ASP* 3.2 47.8 + - - +
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Residues in contact with GLU 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 ASP* 3.1 20.2 + - - +
52A GLN* 3.6 19.5 + - - +
53A PHE 3.3 0.2 - - - -
54A GLN* 1.3 78.1 - - + +
56A LEU* 1.3 57.7 + - + +
58A ASP* 3.5 9.3 + - - +
59A LEU* 3.1 25.0 + - - +
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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
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52A GLN* 3.0 20.2 + - + +
53A PHE* 3.8 5.4 - - - +
55A GLU* 1.3 75.2 - - + +
57A SER* 1.3 60.9 + - - +
59A LEU* 3.2 15.2 + - + +
60A LEU* 2.9 38.3 + - + +
68A ASN 5.1 0.4 - - - +
71A LYS* 3.4 62.4 - - + +
72A MET* 3.8 19.1 - - + +
75A ILE* 3.7 20.6 - - + -
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Residues in contact with SER 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 PHE* 2.7 32.9 + - - -
54A GLN* 3.4 21.2 + - - -
56A LEU* 1.3 73.1 - - - +
58A ASP* 1.3 57.2 + - - +
60A LEU* 3.4 5.9 + - - +
61A ALA* 3.1 26.0 + - - +
72A MET* 3.9 15.4 - - - +
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Residues in contact with ASP 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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54A GLN* 3.2 35.2 + - - +
55A GLU* 3.7 9.3 - - - +
56A LEU 3.3 0.2 - - - -
57A SER* 1.3 75.7 + - - +
59A LEU* 1.3 64.2 + - - +
61A ALA* 3.4 9.3 + - - +
62A LYS* 3.3 20.4 + - - +
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Residues in contact with LEU 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 GLU 3.1 14.4 + - - +
56A LEU* 3.2 29.1 + - + +
58A ASP* 1.3 77.9 - - - +
60A LEU* 1.3 56.6 + - - +
62A LYS* 3.3 6.3 + - + +
63A GLU* 2.9 48.9 + - + +
68A ASN* 3.3 28.9 - - + +
71A LYS* 4.4 7.6 - - + +
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Residues in contact with LEU 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 LEU* 2.9 28.2 + - + +
57A SER* 3.7 5.8 - - - +
59A LEU* 1.3 73.5 - - + +
61A ALA* 1.3 64.5 + - - +
62A LYS 3.2 0.7 - - - -
63A GLU 3.6 2.5 - - - -
64A PRO* 3.0 53.9 - - + +
65A SER 3.9 8.1 - - - +
68A ASN* 3.3 43.5 - - + +
69A ALA* 4.0 8.7 - - + +
72A MET* 3.6 24.9 - - + -
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Residues in contact with ALA 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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57A SER 3.1 13.0 + - - +
58A ASP* 3.6 12.3 - - - +
60A LEU* 1.3 76.8 - - - +
62A LYS* 1.3 58.9 + - - +
64A PRO* 4.9 2.6 - - - +
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Residues in contact with LYS 62 (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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58A ASP 3.3 10.8 + - - +
59A LEU* 3.6 11.9 - - + +
60A LEU 3.2 0.2 - - - -
61A ALA* 1.3 79.8 - - - +
63A GLU* 1.3 64.5 + - + +
64A PRO* 4.0 4.5 - - - +
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Residues in contact with GLU 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 LEU* 2.9 24.8 + - + +
60A LEU* 3.2 6.0 - - - +
62A LYS* 1.3 82.9 - - + +
64A PRO* 1.3 56.6 - - - +
65A SER* 2.8 25.8 + - - +
68A ASN* 2.8 51.5 + - - +
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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