Contacts of the helix formed by residues 40 - 66 (chain A) in PDB entry 4HYJ
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 TYR 40 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.8 12.8 - - + +
37A ALA* 2.8 23.7 + - + +
39A GLU* 1.3 96.0 - - + +
41A ARG* 1.3 57.5 + - - +
42A SER* 3.2 3.8 - - - -
43A THR* 2.9 31.7 + - - -
100A LEU* 6.3 0.2 - - + -
176A ILE* 4.3 16.7 - - + +
236A VAL* 3.4 41.1 - - + -
239A MET* 3.5 40.0 + - + +
240A SER* 3.3 19.5 - - - -
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Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 3.5 36.0 + - + +
34A ASN* 3.4 38.1 + - - +
36A LEU* 3.1 25.8 + - + +
37A ALA 3.6 8.7 - - - +
38A PRO* 3.6 36.2 + - + +
39A GLU 3.6 2.2 - - - -
40A TYR* 1.3 77.0 - - - +
42A SER* 1.3 61.7 + - - +
44A ALA* 3.1 14.0 + - - +
45A THR* 3.1 18.0 + - - -
304A LFA 4.1 21.1 - - + +
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Residues in contact with SER 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO 5.2 0.6 + - - -
39A GLU 4.6 7.0 + - - -
40A TYR 4.5 2.8 + - - -
41A ARG* 1.3 77.9 - - - +
43A THR* 1.3 58.9 + - - +
45A THR* 4.1 0.4 - - - -
46A VAL* 2.9 35.8 + - - +
99A LEU* 3.6 25.7 - - - +
304A LFA 3.8 40.2 - - - +
302B LFA 5.7 3.1 - - - -
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Residues in contact with THR 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 5.5 0.2 - - + -
40A TYR* 2.9 17.8 + - - -
42A SER* 1.3 82.5 + - - +
44A ALA* 1.3 59.9 + - - +
46A VAL 4.0 0.2 + - - -
47A ALA* 3.4 21.9 + - + +
96A LYS* 3.5 25.4 - - - +
99A LEU* 4.0 16.3 + - - +
100A LEU* 4.1 10.0 - - + +
232A ALA* 4.1 18.2 - - + +
233A PHE* 4.3 4.9 - - + +
236A VAL* 3.9 33.2 - - + +
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.6 24.5 - - + +
33A ARG* 3.7 20.6 - - + -
36A LEU* 4.0 16.4 - - + +
40A TYR 3.9 0.8 + - - -
41A ARG 3.1 10.1 + - - +
43A THR* 1.3 80.0 - - - +
45A THR* 1.3 59.3 + - - +
47A ALA* 3.3 6.1 + - - +
48A ALA* 2.8 31.4 + - - +
233A PHE* 4.5 9.2 - - + -
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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
----------------------------------------------------------
30A LEU* 5.2 0.9 - - + -
33A ARG* 2.9 30.9 + - - +
41A ARG 3.1 14.2 + - - -
42A SER 3.2 6.0 + - - -
44A ALA* 1.3 73.6 - - - +
46A VAL* 1.3 60.3 + - - +
48A ALA* 3.3 6.3 + - - +
49A LEU* 2.9 28.5 + - + +
304A LFA 3.3 29.3 - - + +
60B PHE* 3.5 36.3 - - + -
314B LFA 4.4 5.5 - - + +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER* 2.9 21.9 + - - +
43A THR 4.4 0.2 - - - +
45A THR* 1.3 74.8 - - - +
47A ALA* 1.3 63.2 + - - +
49A LEU* 3.2 8.1 + - - +
50A VAL* 3.2 22.7 + - + +
92A LEU* 3.4 42.6 - - + +
95A VAL* 5.5 4.9 - - + -
96A LYS* 4.0 16.4 - - + -
99A LEU* 4.4 9.2 - - + -
304A LFA 4.3 18.2 - - + -
302B LFA 4.2 25.1 - - + -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.9 28.9 - - + -
43A THR 3.4 17.0 + - - +
44A ALA 3.3 5.7 + - - +
45A THR 3.2 0.4 - - - -
46A VAL* 1.3 78.6 - - - +
48A ALA* 1.3 61.7 + - - +
50A VAL* 3.4 8.7 + - - +
51A THR* 3.3 25.5 + - - +
93A LEU* 6.4 1.1 - - - -
96A LYS* 4.0 15.8 - - - +
225A LYS 5.1 1.7 - - - +
229A GLY* 4.2 9.4 - - - +
233A PHE* 6.3 0.2 - - + -
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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
----------------------------------------------------------
26A THR* 3.7 7.6 - - + +
29A PHE* 3.6 19.7 - - + -
30A LEU* 3.9 30.1 - - + -
44A ALA 2.8 17.0 + - - +
45A THR 3.7 4.3 - - - +
47A ALA* 1.3 75.0 - - - +
49A LEU* 1.3 59.2 + - - +
51A THR* 3.1 9.6 + - - -
52A PHE* 2.9 31.6 + - - +
314B LFA 4.4 3.6 - - + -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR 2.9 17.2 + - - +
46A VAL* 3.2 8.3 + - - +
48A ALA* 1.3 75.6 - - - +
50A VAL* 1.3 56.9 + - - +
52A PHE* 3.3 19.7 + - + +
53A VAL* 2.9 36.3 + - + +
92A LEU* 3.7 25.1 - - + -
304A LFA 3.6 45.1 - - + -
305A LFA 4.3 11.7 - - + -
56B ILE* 4.2 18.2 - - + -
60B PHE* 4.6 4.5 - - + -
314B LFA 4.0 17.5 - - + +
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL 3.2 11.1 + - - +
47A ALA* 3.6 10.8 - - - +
48A ALA 3.2 0.2 - - - -
49A LEU* 1.3 74.7 - - - +
51A THR* 1.3 67.4 + - + +
53A VAL* 3.1 5.1 + - - +
54A ALA* 2.9 20.6 + - - +
89A THR* 3.7 19.8 - - - +
92A LEU* 3.5 40.2 - - + +
93A LEU* 4.1 14.8 - - + -
225A LYS* 3.6 39.7 - - + +
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A MET* 3.4 33.6 - - - +
25A GLY 3.9 0.3 - - - -
26A THR* 2.6 32.6 + - - +
29A PHE* 4.0 13.2 - - + -
47A ALA 3.3 12.9 + - - +
48A ALA* 3.1 9.7 + - - -
50A VAL* 1.3 76.7 - - - +
52A PHE* 1.3 55.6 + - - +
54A ALA* 3.4 0.4 + - - -
55A ALA* 2.8 25.6 + - - +
225A LYS* 4.2 13.7 - - + -
226A VAL* 4.0 26.0 - - + -
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 3.1 14.3 + - + -
48A ALA 2.9 19.5 + - - +
49A LEU* 3.4 16.2 - - + +
51A THR* 1.3 78.6 - - - +
53A VAL* 1.3 67.1 + - + +
55A ALA* 3.0 14.4 + - - +
56A ILE* 3.1 39.9 + - + +
309A LFA 3.9 39.0 - - + -
52B PHE* 3.8 23.6 - + - -
56B ILE* 4.2 7.9 - - + -
303B LFA 4.0 22.2 - - + -
314B LFA 3.8 33.2 - - + -
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 2.9 25.4 + - + +
50A VAL* 3.1 6.9 + - - +
52A PHE* 1.3 80.2 - - + +
54A ALA* 1.3 63.2 + - - +
56A ILE* 3.2 10.6 + - + +
57A HIS* 3.0 19.6 + - - +
85A ASP* 4.1 20.4 - - - +
88A VAL* 4.2 10.1 - - + -
89A THR* 3.7 19.5 - - + -
92A LEU* 5.5 0.2 - - + -
305A LFA 3.7 53.1 - - + +
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A MET* 3.7 31.6 - - + -
50A VAL 2.9 14.4 + - - +
51A THR 3.8 0.2 - - - +
53A VAL* 1.3 77.1 - - - +
55A ALA* 1.3 57.2 + - - +
57A HIS* 3.2 1.0 + - - +
58A TYR* 2.8 41.6 + - + -
85A ASP* 3.5 19.2 - - - +
225A LYS* 3.7 17.3 - - + +
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.2 22.9 - - + +
22A MET* 3.8 15.7 - - + -
23A ALA 4.1 10.5 - - - +
51A THR 2.8 14.6 + - - +
52A PHE* 3.0 12.3 + - - +
54A ALA* 1.3 77.6 - - - +
56A ILE* 1.3 57.6 + - - +
58A TYR 3.2 0.7 + - - -
59A TYR* 2.8 26.0 + - - +
309A LFA 4.3 21.3 - - + -
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.1 34.4 + - + +
53A VAL* 3.6 7.2 - - - +
55A ALA* 1.3 73.5 - - - +
57A HIS* 1.3 65.4 + - - +
59A TYR* 3.4 6.7 + - - +
60A PHE* 3.1 50.1 + - + -
305A LFA 3.8 26.0 - - + -
309A LFA 4.0 20.2 - - + -
52B PHE* 3.6 32.1 - - + -
303B LFA 4.3 12.8 - - + -
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Residues in contact with HIS 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 6.1 0.2 - - - -
53A VAL 3.0 10.3 + - - +
54A ALA 3.4 6.5 - - - +
55A ALA 3.2 0.2 - - - -
56A ILE* 1.3 75.6 - - - +
58A TYR* 1.3 88.7 + + - +
60A PHE* 3.1 11.8 + - - -
61A MET* 3.2 27.2 + - + +
81A ILE* 3.3 28.6 - - + +
82A ARG* 3.9 34.0 - - + +
85A ASP* 2.6 38.7 + - + +
86A TRP* 5.2 1.3 - - - -
214A GLU* 5.7 1.6 + - - -
221A ASP* 4.5 5.2 - - - -
305A LFA 4.1 8.9 - - + +
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.7 50.9 - + - +
16A TRP* 5.7 1.2 - - - -
18A GLY* 4.3 7.6 - - - -
19A PHE* 3.6 27.8 - - - +
22A MET* 4.5 9.2 - - + -
54A ALA* 2.8 35.7 + - + +
55A ALA 3.9 0.2 - - - +
57A HIS* 1.3 89.0 - + - +
59A TYR* 1.3 68.2 + - - +
61A MET* 3.3 19.2 + - + +
62A LYS* 3.9 2.6 + - - +
214A GLU 4.9 0.8 + - - -
217A TYR* 4.0 2.6 - - - +
218A ASN* 3.2 41.0 + - + -
221A ASP* 2.5 35.9 + - + -
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 4.4 13.0 - + - -
19A PHE* 3.8 29.0 - + + -
55A ALA 2.8 20.9 + - - +
56A ILE* 3.5 8.1 - - - +
58A TYR* 1.3 74.2 - - - +
60A PHE* 1.3 95.7 + + - +
62A LYS* 3.1 58.3 - - + +
309A LFA 4.2 19.1 - - + -
310A LFA 4.0 37.4 - - + +
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Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 3.1 44.7 + - + +
57A HIS 3.1 3.1 + - - +
59A TYR* 1.3 100.7 - + - +
61A MET* 1.3 65.7 + - - +
62A LYS 3.1 2.5 - - - -
63A ASP* 3.1 36.9 + - - +
64A ALA 3.8 2.6 + - - -
81A ILE* 4.2 24.8 - - + +
305A LFA 4.6 12.6 - - + -
309A LFA 5.7 2.5 - - + -
30B LEU* 5.9 2.9 - - + -
303B LFA 4.1 40.8 - - + -
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Residues in contact with MET 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.4 50.1 - - + -
57A HIS* 3.2 38.6 + - + +
58A TYR* 3.3 13.8 + - + +
60A PHE* 1.3 77.7 - - - +
62A LYS* 1.3 62.9 + - - +
64A ALA* 2.9 26.3 + - + +
65A VAL* 3.4 12.1 + - - +
78A PRO* 3.8 39.5 - - + +
81A ILE* 4.3 9.0 - - - -
214A GLU* 4.9 12.1 - - + +
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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
----------------------------------------------------------
12A GLN* 6.5 0.2 - - - +
15A PHE* 5.0 4.4 - - - +
16A TRP* 3.9 34.8 - - + +
58A TYR 3.9 2.9 + - - +
59A TYR* 3.1 52.8 + - + +
60A PHE 3.1 0.6 - - - -
61A MET* 1.3 77.5 - - - +
63A ASP* 1.3 82.8 + - - +
65A VAL* 3.8 7.1 - - - +
66A GLY* 3.0 29.5 + - - +
310A LFA 3.7 33.7 - - + -
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Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 3.1 32.0 + - - +
61A MET 3.0 0.8 - - - -
62A LYS* 1.3 101.6 - - - +
64A ALA* 1.3 66.5 + - - +
66A GLY* 4.0 8.2 + - - +
75A ASP* 5.0 1.0 - - - +
76A GLY* 4.9 6.8 + - - -
310A LFA 4.9 5.7 - - - +
----------------------------------------------------------
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE 3.8 2.1 + - - +
61A MET* 2.9 26.7 + - + +
63A ASP* 1.3 79.8 - - - +
65A VAL* 1.3 64.8 + - + +
73A GLU 4.2 0.9 - - - +
74A ILE* 3.6 3.9 - - + -
75A ASP* 2.9 46.0 + - - +
76A GLY* 4.5 4.3 - - - -
77A PHE 5.3 0.2 - - - +
78A PRO* 4.2 24.2 - - + -
81A ILE* 5.5 2.5 - - + -
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.7 5.4 - - + +
11A THR* 3.7 22.0 - - - +
12A GLN* 3.8 30.4 + - + +
15A PHE* 4.2 22.0 - - + -
61A MET 3.5 15.3 - - - +
62A LYS* 3.8 7.6 - - - +
64A ALA* 1.3 79.3 - - + +
66A GLY* 1.3 65.2 + - - +
68A SER* 5.1 1.9 + - - -
69A GLY 5.6 1.2 + - - -
70A LEU 5.0 1.2 - - - +
73A GLU* 4.0 19.1 - - - +
74A ILE* 4.0 33.6 - - + +
211A LEU* 4.5 7.0 - - + -
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 2.9 23.3 + - - +
62A LYS 3.0 22.5 + - - +
63A ASP* 4.4 7.4 - - - -
64A ALA 3.5 1.4 - - - -
65A VAL* 1.3 79.2 - - - +
67A THR* 1.3 61.0 + - - -
68A SER* 3.6 1.6 - - - -
----------------------------------------------------------
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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