Contacts of the helix formed by residues 45 - 72 (chain A) in PDB entry 1BG7
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 HIS 45 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 3.3 47.4 + - - +
43A ALA* 3.7 21.5 + - + +
44A LEU* 1.3 71.2 - - - +
46A ASN* 1.3 67.0 + - - +
48A ALA* 3.6 6.0 - - - +
49A LYS* 3.0 27.5 + - - +
167A ASP* 3.6 3.4 + - - +
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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
----------------------------------------------------------
45A HIS* 1.3 79.0 + - - +
47A VAL* 1.3 64.4 + - - +
49A LYS* 3.4 18.3 + - - +
50A PHE* 3.1 22.3 + - - +
167A ASP* 2.9 40.0 + - - +
168A LYS* 4.4 10.4 + - - +
171A MET* 3.6 25.6 + - + +
172A GLY* 3.9 10.8 - - - -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.7 21.5 - - + -
44A LEU* 3.5 18.8 - - + +
46A ASN* 1.3 74.4 - - - +
48A ALA* 1.4 61.1 + - - +
50A PHE* 3.2 5.2 + - - +
51A PHE* 3.2 46.1 + - + -
92A THR* 4.1 26.5 - - + +
96A MET* 4.7 0.2 - - + -
163A GLU 5.8 0.4 - - - +
166A PHE* 4.7 1.1 - - + -
167A ASP* 2.9 24.1 + - + +
171A MET* 3.8 25.6 - - + -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 3.3 36.2 - - - +
37A PHE* 3.9 10.3 - - + +
38A ASP* 4.0 13.7 - - + +
44A LEU 3.0 13.4 + - - +
45A HIS* 3.6 13.5 - - - +
47A VAL* 1.4 75.9 - - - +
49A LYS* 1.3 62.1 + - - +
51A PHE* 3.3 1.8 + - - -
52A LYS* 3.0 21.4 + - - +
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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
----------------------------------------------------------
45A HIS 3.0 17.4 + - - +
46A ASN* 3.6 20.0 - - - +
47A VAL 3.3 0.2 - - - -
48A ALA* 1.3 75.6 - - - +
50A PHE* 1.3 62.9 + - - +
52A LYS* 3.4 8.8 + - + +
53A GLU* 3.3 22.5 + - + +
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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
----------------------------------------------------------
30A TYR* 5.9 0.2 - + - -
46A ASN 3.1 8.7 + - - +
47A VAL 3.4 7.4 - - - +
49A LYS* 1.3 75.5 - - - +
51A PHE* 1.3 87.6 + + - +
53A GLU* 3.4 12.3 + - + +
54A GLN* 3.0 56.7 + - + +
96A MET* 4.1 11.4 - - + -
143A GLN* 4.2 18.2 - - - -
144A LEU* 4.3 16.4 - - + -
147A TYR* 3.9 23.8 - + - -
171A MET* 3.5 29.6 - - + +
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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
----------------------------------------------------------
30A TYR* 3.5 33.2 - + - +
33A MET* 3.8 24.5 - - + -
34A ALA* 3.6 23.1 - - - +
37A PHE* 3.7 24.5 - + - -
47A VAL* 3.2 37.1 + - + -
48A ALA 3.3 1.1 + - - +
50A PHE* 1.3 95.6 - + - +
52A LYS* 1.3 57.4 + - - +
54A GLN* 3.4 3.5 + - + +
55A SER* 2.9 27.5 + - - -
92A THR 5.8 0.2 - - - -
95A ALA* 4.1 17.0 - - + -
96A MET* 3.9 23.6 - - + -
99A ALA* 4.3 8.5 - - + -
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 5.4 5.8 - - + +
34A ALA* 3.6 12.9 - - + +
35A PHE* 4.2 28.0 - - + -
48A ALA 3.0 17.2 + - - +
49A LYS* 3.7 9.9 - - + +
50A PHE 3.3 0.4 - - - -
51A PHE* 1.3 76.4 - - - +
53A GLU* 1.3 57.6 + - - +
55A SER* 3.3 8.9 - - - -
56A HIS* 3.1 49.6 + - + +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 3.3 11.6 + - + +
50A PHE* 3.5 15.3 - - + +
52A LYS* 1.3 76.6 - - - +
54A GLN* 1.3 69.3 + - - +
56A HIS* 3.2 13.6 + - + +
57A GLU* 2.8 29.2 + - - +
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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
----------------------------------------------------------
30A TYR* 3.9 33.9 - - + +
50A PHE* 3.0 52.3 + - + +
51A PHE* 3.5 10.3 - - - +
53A GLU* 1.3 79.2 - - - +
55A SER* 1.3 59.5 + - - +
57A GLU* 3.2 36.2 + - - +
58A GLU* 3.0 39.7 + - - +
103A GLU* 4.6 0.9 - - - +
140A SER* 4.0 12.4 + - - -
143A GLN* 5.0 5.2 + - - +
144A LEU* 6.4 0.7 - - + -
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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
----------------------------------------------------------
27A SER* 2.7 50.2 + - - +
30A TYR* 3.7 11.6 - - - +
31A LEU* 3.7 21.5 + - - +
51A PHE 2.9 13.7 + - - -
52A LYS* 3.3 12.6 - - - -
54A GLN* 1.3 76.2 - - - +
56A HIS* 1.3 68.9 + - - +
58A GLU 3.5 0.3 + - - -
59A ARG* 3.2 10.9 + - - +
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Residues in contact with HIS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 5.8 5.2 - - + -
52A LYS* 3.1 40.6 + - + +
53A GLU* 3.2 15.2 + - + +
55A SER* 1.3 81.2 + - - +
57A GLU* 1.3 58.3 + - - +
59A ARG* 3.3 25.9 + - - +
60A GLU* 2.9 35.5 + - + +
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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
----------------------------------------------------------
53A GLU 2.8 16.8 + - - +
54A GLN* 3.2 35.1 + - - +
56A HIS* 1.3 74.4 - - - +
58A GLU* 1.3 71.1 + - - +
60A GLU* 3.2 10.3 + - - +
61A HIS* 3.1 39.8 + - + +
103A GLU* 5.3 0.5 - - - +
136A GLU* 3.3 21.4 - - - +
137A GLN* 5.7 0.3 - - - +
140A SER* 4.4 11.1 + - - -
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 2.6 49.0 - - - +
26A ALA* 3.9 10.5 - - + +
27A SER* 3.8 9.2 - - - +
30A TYR* 3.8 20.0 - - + -
54A GLN* 3.0 22.8 + - - +
56A HIS 3.4 0.2 - - - -
57A GLU* 1.3 88.1 - - - +
59A ARG* 1.3 65.9 + - - +
61A HIS* 3.3 18.1 + - - +
62A ALA* 3.1 17.8 + - - +
103A GLU* 3.1 25.9 - - - +
106A VAL* 4.6 3.5 - - - +
137A GLN* 4.4 6.2 - - - +
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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
----------------------------------------------------------
24A LEU* 4.5 15.3 - - + -
27A SER* 3.7 19.4 + - - +
55A SER 3.2 8.8 + - - +
56A HIS* 3.3 37.9 + - - +
58A GLU* 1.3 75.1 - - - +
60A GLU* 1.3 89.3 + - - +
62A ALA* 3.4 6.5 + - - +
63A GLU* 3.1 47.3 + - + +
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Residues in contact with GLU 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 HIS* 2.9 18.5 + - + +
57A GLU* 3.2 12.5 + - - +
59A ARG* 1.3 104.1 + - - +
61A HIS* 1.3 64.4 + - + +
63A GLU* 3.2 19.8 + - - +
64A LYS* 3.0 22.8 + - - +
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Residues in contact with HIS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 3.5 20.9 + - + +
57A GLU* 3.1 33.4 + - + +
58A GLU* 3.3 26.9 + - - +
60A GLU* 1.3 74.4 - - + +
62A ALA* 1.3 64.2 + - - +
64A LYS* 3.1 9.3 + - + +
65A LEU* 3.0 29.7 + - + +
136A GLU* 3.3 36.5 + - - -
137A GLN* 4.5 10.5 + - - -
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Residues in contact with ALA 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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20A VAL* 4.0 12.7 - - + +
23A GLU* 3.8 22.1 - - + +
24A LEU* 3.7 28.5 - - + -
58A GLU 3.1 6.3 + - - +
59A ARG 3.5 8.5 - - - +
60A GLU 3.3 0.2 - - - -
61A HIS* 1.3 78.2 - - - +
63A GLU* 1.3 60.8 + - + +
65A LEU* 3.4 9.0 + - - +
66A MET* 3.1 30.1 + - - +
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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
----------------------------------------------------------
24A LEU* 6.4 0.4 - - + -
59A ARG* 3.1 46.2 + - + +
60A GLU* 3.2 26.5 + - - +
62A ALA* 1.3 74.3 - - + +
64A LYS* 1.3 57.5 + - - +
66A MET* 3.3 16.7 + - - +
67A LYS* 3.0 28.7 + - - +
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU 3.0 12.7 + - - +
61A HIS* 3.1 12.8 + - + +
63A GLU* 1.3 73.7 - - - +
65A LEU* 1.4 59.6 + - + +
67A LYS* 3.2 10.0 - - - +
68A ASP* 2.9 35.7 + - - +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.8 22.0 - - + +
19A MET* 3.8 45.3 - - + +
20A VAL* 3.8 9.9 - - + +
23A GLU* 4.1 14.4 - - + +
61A HIS* 3.0 20.2 + - + +
62A ALA* 3.7 8.1 - - - +
64A LYS* 1.4 71.8 - - + +
66A MET* 1.3 60.7 + - - +
68A ASP* 3.2 14.8 + - + +
69A GLN* 2.8 28.9 + - - +
110A LEU* 5.6 4.0 - - + -
113A LEU* 5.1 10.8 - - + -
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Residues in contact with MET 66 (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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20A VAL* 3.8 28.0 - - + -
24A LEU* 5.7 3.6 - - - -
62A ALA* 3.1 20.9 + - - +
63A GLU* 3.3 17.5 + - - +
65A LEU* 1.3 76.1 - - - +
67A LYS* 1.3 61.6 + - - +
69A GLN* 3.3 6.0 + - - +
70A ASN* 3.2 21.3 + - - +
76A ILE* 3.5 47.8 - - + +
78A LEU* 4.0 18.4 - - + -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU 3.0 13.8 + - - +
64A LYS* 3.2 14.1 - - - +
66A MET* 1.3 73.8 - - - +
68A ASP* 1.3 60.8 + - - +
70A ASN* 3.4 9.0 + - + +
71A LYS* 3.0 44.9 + - + +
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 5.3 8.5 - - + -
64A LYS* 2.9 23.2 + - - +
65A LEU* 3.2 17.5 + - + +
67A LYS* 1.3 73.7 - - - +
69A GLN* 1.3 64.7 + - - +
71A LYS* 3.3 28.6 + - - +
72A ARG* 3.1 33.0 + - + +
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.3 34.3 - - - -
13A GLU* 3.1 32.6 + - - +
16A ILE* 3.5 19.4 - - + +
17A ASN* 3.1 23.6 + - - +
65A LEU 2.8 14.6 + - - +
66A MET* 3.4 9.9 - - - +
67A LYS 3.3 0.2 - - - -
68A ASP* 1.3 77.0 - - - +
70A ASN* 1.3 60.6 + - - +
72A ARG* 3.4 3.4 + - - +
73A GLY 3.2 3.5 + - - -
74A GLY* 2.9 39.5 + - - -
75A ARG 3.9 1.2 + - - -
76A ILE* 3.7 23.6 - - + +
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Residues in contact with ASN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 4.3 5.0 - - - +
66A MET 3.2 6.4 + - - +
67A LYS* 3.8 9.7 - - + +
69A GLN* 1.3 74.5 - - - +
71A LYS* 1.3 65.7 + - - +
73A GLY* 3.1 12.8 + - - -
74A GLY 3.9 12.9 - - - +
75A ARG* 4.2 11.7 + - - +
76A ILE* 3.6 28.1 + - - +
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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
----------------------------------------------------------
4A VAL* 3.7 14.7 - - - +
67A LYS* 3.0 31.7 + - + +
68A ASP* 3.3 33.8 + - - +
70A ASN* 1.3 76.9 - - - +
72A ARG* 1.3 68.1 + - + +
73A GLY 3.5 0.2 + - - -
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Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 4.3 5.0 - - - +
5A ARG* 3.6 23.0 - - - +
6A GLN 3.4 23.5 + - - +
7A ASN* 3.7 13.9 + - - +
8A PHE* 3.5 60.6 - - + +
16A ILE* 5.9 0.9 - - + -
68A ASP* 3.1 21.4 + - + +
69A GLN 3.9 2.9 - - - +
70A ASN 3.3 0.2 - - - -
71A LYS* 1.3 82.0 - - + +
73A GLY* 1.3 59.7 + - - +
74A GLY 3.4 0.6 + - - -
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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