Contacts of the helix formed by residues 69 - 95 (chain A) in PDB entry 2B8Z
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 THR 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA* 1.3 85.6 - - + +
70A ALA* 1.3 67.1 + - - +
71A GLN* 3.4 8.9 + - - +
72A GLN* 3.1 38.5 + - - +
73A PHE* 2.9 24.1 + - - +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 1.3 73.5 - - - +
71A GLN* 1.3 54.3 + - - +
73A PHE* 3.1 7.1 + - - +
74A HIS* 2.7 36.8 + - - +
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Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 3.2 9.0 + - - +
70A ALA* 1.3 81.0 - - - +
72A GLN* 1.3 58.5 + - + +
74A HIS* 3.4 9.2 + - + +
75A ARG* 2.9 75.6 + - + +
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Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 6.0 0.5 - - - -
23A LEU* 4.0 30.9 - - + +
65A CYS 4.6 1.7 - - - +
66A LEU 4.1 1.9 - - - +
67A GLY* 3.8 11.3 - - - -
68A ALA* 2.9 28.9 + - - +
69A THR* 3.1 28.8 + - - +
71A GLN* 1.3 77.9 - - + +
73A PHE* 1.3 58.0 + - - +
75A ARG* 3.5 7.2 + - - +
76A HIS* 3.1 27.4 + - - +
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.2 44.1 + - + +
67A GLY* 5.0 2.7 - - - +
69A THR 2.9 18.3 + - - +
70A ALA* 3.6 5.2 - - - +
72A GLN* 1.3 73.4 - - - +
74A HIS* 1.3 67.1 + - - +
76A HIS* 3.4 4.7 + + - +
77A LYS* 3.1 67.1 + - + +
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Residues in contact with HIS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA 2.7 21.3 + - - +
71A GLN* 3.5 10.5 - - + +
73A PHE* 1.3 74.6 - - - +
75A ARG* 1.3 67.3 + - + +
77A LYS* 3.2 4.5 + - - +
78A GLN* 2.9 52.1 + - + +
81A ARG* 4.2 8.3 - - - -
1003A SO4 2.8 52.0 + - - +
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN* 3.2 22.1 + - + +
21A LYS* 4.1 31.5 + - - +
22A THR* 4.0 7.1 - - + +
71A GLN* 2.9 61.2 + - + +
72A GLN* 4.0 7.0 - - - +
74A HIS* 1.3 82.2 - - + +
76A HIS* 1.3 58.3 + - - +
78A GLN* 4.1 11.9 - - - +
79A LEU* 2.9 26.2 + - - +
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Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 4.8 9.0 + - - +
59A HIS* 3.0 28.0 - - + -
60A GLU* 2.7 22.7 + - - +
65A CYS* 3.4 38.2 + - + +
66A LEU* 3.8 20.8 - - + +
72A GLN 3.1 16.2 + - - +
73A PHE* 3.8 5.6 - + - +
75A ARG* 1.3 77.2 - - - +
77A LYS* 1.3 72.9 + - + +
79A LEU* 3.3 10.8 + - - +
80A ILE* 3.1 42.9 + - + +
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 3.1 65.3 + - + +
74A HIS* 4.4 0.2 - - - +
76A HIS* 1.3 78.5 - - + +
78A GLN* 1.3 66.6 + - - +
80A ILE* 3.4 5.5 + - - +
81A ARG* 2.9 34.9 + - - +
1003A SO4 3.4 43.5 + - - +
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Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN* 2.8 31.1 + - - +
74A HIS* 2.9 35.1 + - - +
75A ARG* 3.4 15.9 - - - +
77A LYS* 1.3 76.0 - - - +
79A LEU* 1.3 63.5 + - - +
81A ARG* 3.1 27.8 - - - +
82A PHE* 2.9 46.0 + - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.4 32.7 - - + +
20A GLN* 4.3 11.2 - - - +
22A THR* 4.0 32.5 - - + +
24A CYS* 5.6 2.9 - - + -
25A THR* 4.1 17.7 - - + +
55A PHE* 4.6 9.9 - - + -
75A ARG 2.9 17.4 + - - +
76A HIS* 3.5 10.3 - - - +
77A LYS 3.3 0.2 - - - -
78A GLN* 1.3 76.0 - - - +
80A ILE* 1.3 64.3 + - + +
82A PHE* 3.3 1.9 + - - +
83A LEU* 2.9 44.3 + - + +
109A LEU* 4.5 13.7 - - + -
113A LEU* 5.4 0.4 - - + -
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Residues in contact with ILE 80 (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 PHE* 5.3 1.1 - - + -
56A TYR* 4.0 22.0 - - + -
59A HIS* 4.3 5.2 - - + -
60A GLU* 3.6 52.9 - - + +
76A HIS* 3.1 38.7 + - + +
77A LYS* 3.9 5.4 - - - +
79A LEU* 1.3 81.4 - - + +
81A ARG* 1.3 63.1 + - - +
83A LEU* 3.4 11.5 + - + +
84A LYS* 3.1 38.8 + - + +
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Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A HIS* 4.2 2.2 - - - -
77A LYS* 2.9 28.0 + - - +
78A GLN* 3.1 35.8 - - - +
80A ILE* 1.3 79.5 - - - +
82A PHE* 1.3 62.4 + - + +
84A LYS* 3.5 8.7 + - - +
85A ALA* 3.1 26.5 + - - +
1003A SO4 3.1 41.0 + - - -
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 6.0 4.3 - - - -
13A THR* 3.3 23.1 - - + +
16A SER* 3.7 30.1 - - - -
17A LEU* 3.6 25.6 - - + -
20A GLN* 3.3 24.7 - - - -
78A GLN* 2.9 46.7 + - + +
79A LEU 3.8 0.4 - - - +
81A ARG* 1.3 79.6 - - + +
83A LEU* 1.3 59.9 + - - +
85A ALA* 4.4 4.7 - - + -
86A LEU* 2.9 30.7 + - - +
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Residues in contact with LEU 83 (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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17A LEU* 3.8 25.1 - - + -
52A LEU* 4.2 28.1 - - + +
55A PHE* 3.7 36.3 - - + -
56A TYR* 4.0 25.9 - - + +
79A LEU* 2.9 32.1 + - + +
80A ILE* 3.8 6.7 - - + +
82A PHE* 1.3 75.7 - - - +
84A LYS* 1.3 52.2 + - - +
86A LEU* 3.6 6.3 - - + +
87A ASP* 2.7 36.5 + - - +
109A LEU* 4.5 6.7 - - + -
113A LEU* 4.3 7.9 - - + -
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Residues in contact with LYS 84 (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 TYR* 3.7 40.2 - - + +
60A GLU* 3.3 25.6 + - - -
80A ILE* 3.1 35.4 + - + +
81A ARG* 3.7 7.4 - - - +
83A LEU* 1.3 73.8 - - - +
85A ALA* 1.3 56.2 + - - +
87A ASP* 3.6 5.9 - - - +
88A ARG* 2.8 35.7 + - - +
1001A SO4 4.3 13.7 + - - +
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Residues in contact with ALA 85 (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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13A THR* 4.4 11.2 - - + +
81A ARG 3.1 16.5 + - - +
82A PHE* 3.8 10.3 - - + +
83A LEU 3.4 0.2 - - - -
84A LYS* 1.3 73.8 - - - +
86A LEU* 1.3 65.9 + - - +
88A ARG* 3.3 10.7 + - - +
89A ASN* 3.0 34.2 + - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.9 33.7 - - + +
13A THR* 3.9 12.6 - - + +
14A LEU* 3.9 26.0 - - + -
17A LEU* 3.8 20.2 - - + -
52A LEU* 3.3 27.1 - - + -
82A PHE 2.9 17.9 + - - +
83A LEU* 3.6 5.6 - - + +
85A ALA* 1.3 74.4 - - - +
87A ASP* 1.3 60.2 + - - +
89A ASN* 3.0 8.3 + - - +
90A LEU* 2.8 45.6 + - + +
113A LEU* 4.0 5.8 - - + -
116A LEU* 4.4 3.1 - - + -
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 2.6 34.7 - - - +
52A LEU* 3.5 11.7 - - + +
53A ARG* 3.5 14.8 - - - +
56A TYR* 3.7 20.6 + - + +
83A LEU 2.7 22.5 + - - +
84A LYS 3.6 4.0 - - - +
85A ALA 3.2 0.2 - - - -
86A LEU* 1.3 74.4 - - - +
88A ARG* 1.3 63.2 + - - +
90A LEU* 3.2 5.9 + - - +
91A TRP* 2.8 54.5 + - - -
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS 2.8 21.0 + - - +
85A ALA* 3.3 11.2 - - - +
87A ASP* 1.3 73.8 - - - +
89A ASN* 1.3 61.8 + - - +
91A TRP* 3.5 7.6 + - - +
92A GLY* 3.1 24.8 + - - -
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Residues in contact with ASN 89 (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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6A THR* 3.4 24.8 + - + +
9A GLU* 3.8 35.1 + - - +
10A ILE* 3.4 23.3 - - + -
13A THR* 4.9 2.4 + - - -
85A ALA* 3.0 25.5 + - - +
86A LEU* 3.0 6.8 + - - +
88A ARG* 1.3 79.3 - - - +
90A LEU* 1.3 60.2 + - - +
92A GLY* 3.5 1.8 + - - -
93A LEU* 3.0 27.4 + - - +
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Residues in contact with LEU 90 (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 ILE* 4.0 17.0 - - + -
45A PHE* 3.9 33.7 - - + +
48A ALA* 4.2 2.5 - - + -
49A ALA* 3.7 26.7 - - + +
52A LEU* 3.6 31.0 - - + -
86A LEU* 2.8 34.3 + - + +
87A ASP* 3.2 4.2 + - - +
89A ASN* 1.3 72.6 - - - +
91A TRP* 1.3 50.8 + - - +
93A LEU* 3.0 6.2 + - - +
94A ALA* 2.7 36.9 + - - +
116A LEU* 4.1 17.9 - - + -
120A MET* 4.8 6.7 - - - -
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Residues in contact with TRP 91 (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 CYS* 3.7 19.3 - - - -
49A ALA* 3.3 24.9 - - + -
50A THR* 3.3 24.9 - - + -
53A ARG* 4.1 17.9 - - - +
87A ASP* 2.8 53.0 + - - +
88A ARG* 3.8 6.5 - - - +
90A LEU* 1.3 72.3 - - - +
92A GLY* 1.3 63.8 + - - +
94A ALA* 3.9 1.4 - - + +
95A GLY* 3.2 21.5 + - - -
96A LEU 3.1 31.2 + - - -
97A ASN* 3.5 33.0 - - - +
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Residues in contact with GLY 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A HIS* 5.5 6.9 - - - -
6A THR* 5.6 2.2 - - - -
88A ARG 3.1 15.4 + - - -
89A ASN* 3.5 4.5 + - - -
90A LEU 3.3 0.2 - - - -
91A TRP* 1.3 76.9 - - - +
93A LEU* 1.3 60.2 + - - +
95A GLY* 4.0 5.9 + - - -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A HIS* 4.8 15.3 - - - +
2A LYS* 5.3 5.2 - - - +
4A ASP* 5.7 2.2 - - + -
6A THR* 3.9 21.5 - - + +
7A LEU* 4.1 21.3 - - + -
10A ILE* 3.4 26.5 - - + -
42A LYS* 4.4 8.3 - - - +
45A PHE* 3.6 41.8 - - + -
89A ASN 3.0 9.3 + - - +
90A LEU* 3.4 8.1 - - - +
92A GLY* 1.3 77.6 - - - +
94A ALA* 1.3 65.0 + - - +
95A GLY* 3.3 0.9 + - - -
120A MET* 4.1 1.6 - - + -
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 2.8 40.2 + - - +
45A PHE* 3.8 7.2 - - + -
46A CYS* 3.5 37.7 - - + +
90A LEU 2.7 19.1 + - - +
91A TRP* 3.4 7.8 + - - +
93A LEU* 1.3 72.4 - - - +
95A GLY* 1.3 61.6 + - - +
96A LEU* 3.2 9.9 + - - +
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Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 3.2 18.9 + - - -
91A TRP 3.2 11.4 + - - -
92A GLY 4.0 4.6 + - - -
93A LEU 3.2 3.8 - - - -
94A ALA* 1.3 76.9 - - - +
96A LEU* 1.3 59.9 + - - +
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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