Contacts of the helix formed by residues 36 - 62 (chain A) in PDB entry 6GA6
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 ASP 36 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.7 1.2 - - - +
35A SER* 1.3 79.3 + - - +
37A PRO* 1.3 72.5 - - - +
38A ASP* 3.3 13.8 + - - +
39A ALA* 2.9 23.7 + - - +
40A LYS* 2.9 29.6 + - - +
230A PHE* 3.7 27.8 - - + -
231A GLY* 3.4 23.8 + - - +
233A ALA* 5.7 3.6 - - - +
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Residues in contact with PRO 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER 3.2 6.7 - - - +
36A ASP* 1.3 93.2 - - - +
38A ASP* 1.3 65.2 + - - +
40A LYS* 3.5 18.0 + - - +
41A LYS* 2.9 40.2 + - - +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASP* 3.3 12.2 + - - +
37A PRO* 1.3 79.4 - - - +
39A ALA* 1.3 66.1 + - - +
41A LYS* 3.1 31.5 + - - +
42A PHE* 3.3 21.9 - - + -
229A ILE 3.5 11.9 - - - +
230A PHE 4.7 0.2 - - - -
231A GLY* 3.8 20.1 - - - +
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.5 21.5 - - + -
36A ASP* 2.9 11.9 + - - +
38A ASP* 1.3 75.6 - - - +
40A LYS* 1.3 56.4 + - - +
42A PHE* 3.2 4.5 + - - +
43A TYR* 2.9 36.4 + - + -
229A ILE* 3.1 22.6 + - + +
230A PHE* 3.5 28.3 - - + -
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Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.9 27.4 - - + +
35A SER* 3.4 19.1 + - - +
36A ASP 2.9 15.8 + - - +
37A PRO* 3.7 18.6 - - - +
38A ASP 3.2 0.4 - - - -
39A ALA* 1.3 76.4 - - - +
41A LYS* 1.3 56.9 + - + +
43A TYR* 3.4 5.7 + - - +
44A ALA* 2.9 32.1 + - - +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO* 2.9 32.7 + - - +
38A ASP* 3.1 22.5 + - - +
40A LYS* 1.3 78.5 - - - +
42A PHE* 1.3 59.9 + - + +
44A ALA* 3.2 5.7 + - - +
45A ILE* 2.9 37.5 + - + +
99A LEU* 4.6 23.3 - - + -
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Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 3.3 27.3 + - + -
39A ALA 3.2 5.4 + - - +
41A LYS* 1.3 80.5 - - + +
43A TYR* 1.3 58.5 + - - +
45A ILE* 5.2 1.6 - - + -
46A THR* 2.7 35.8 + - - -
96A ASP* 3.4 42.0 - - - +
99A LEU* 3.9 18.6 - - + -
100A LEU* 3.7 35.0 - - + -
223A LEU* 4.0 10.8 - - + -
224A LEU* 4.3 7.6 - - + -
228A ALA 4.7 1.8 - - - -
229A ILE* 3.5 44.4 - - + -
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Residues in contact with TYR 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE 3.8 11.4 - - - -
30A LYS* 2.7 42.2 + - + +
31A GLY* 3.5 34.8 - - - +
34A VAL* 3.7 25.2 - - + +
39A ALA* 2.9 28.3 + - + +
40A LYS* 3.8 6.1 - - - +
42A PHE* 1.3 75.5 - - - +
44A ALA* 1.3 57.8 + - - +
46A THR* 4.7 0.4 - - - -
47A THR* 2.7 38.4 + - - +
224A LEU* 3.6 33.2 + - + -
229A ILE* 3.8 20.1 - - + +
230A PHE* 5.1 4.1 - + - -
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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
----------------------------------------------------------
40A LYS 2.9 18.8 + - - +
41A LYS* 3.5 7.2 - - - +
43A TYR* 1.3 77.2 - - - +
45A ILE* 1.3 64.3 + - + +
47A THR* 4.0 2.6 - - - -
48A LEU* 3.1 34.9 + - + +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 2.9 20.7 + - + +
42A PHE* 4.0 0.4 - - - +
44A ALA* 1.3 79.8 - - + +
46A THR* 1.3 62.5 + - - +
48A LEU* 3.3 7.5 + - - +
49A VAL* 3.3 21.8 + - + +
92A LEU* 3.2 44.6 - - + +
95A LEU* 3.8 25.1 - - + -
96A ASP* 3.3 27.6 - - - +
99A LEU* 3.6 31.0 - - + -
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.6 7.3 - - + -
42A PHE 2.7 22.1 + - - -
43A TYR 4.2 0.2 - - - -
45A ILE* 1.3 77.6 - - - +
47A THR* 1.3 58.4 + - - +
49A VAL* 3.7 6.3 + - + +
50A PRO* 2.9 23.2 - - - +
93A LEU* 6.3 1.1 - - + -
96A ASP* 2.7 27.3 + - - +
216A LYS 5.1 1.7 - - - +
219A PHE* 5.3 2.2 - - + -
220A GLY* 3.6 31.2 - - - -
223A LEU* 3.4 9.0 - - + +
224A LEU* 3.7 24.0 - - + -
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Residues in contact with THR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.9 28.8 + - + +
27A PHE* 3.4 25.4 + - + +
28A LEU* 4.0 25.0 - - + +
43A TYR* 2.7 27.4 + - - +
44A ALA* 4.1 2.7 - - - -
46A THR* 1.3 75.6 - - - +
48A LEU* 1.3 65.7 + - - +
49A VAL 3.2 0.4 - - - -
50A PRO* 3.3 13.0 - - - +
51A ALA* 3.3 13.5 + - + +
224A LEU* 5.0 0.2 - - - +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 3.1 27.4 + - + +
45A ILE* 3.3 8.3 + - - +
47A THR* 1.3 78.4 - - - +
49A VAL* 1.3 56.9 + - - +
51A ALA* 3.5 8.5 - - + +
52A ILE* 2.9 46.5 + - + +
92A LEU* 4.1 20.6 - - + -
311A L2P 5.1 14.6 - - + -
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.3 16.8 + - + +
46A THR* 3.9 7.4 - - + +
47A THR 3.2 1.0 - - - -
48A LEU* 1.3 76.7 - - - +
50A PRO* 1.3 70.0 - - + +
52A ILE 3.4 0.2 + - - -
53A ALA* 3.1 18.4 + - - +
89A THR* 3.4 23.4 - - - +
92A LEU* 3.7 28.0 - - + -
93A LEU* 4.2 21.8 - - + +
216A LYS* 3.5 41.3 - - + +
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Residues in contact with PRO 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 3.7 26.1 - - - +
24A THR* 3.1 22.1 + - - +
27A PHE* 3.9 22.9 - - + -
46A THR 2.9 27.4 - - - +
47A THR 3.3 11.4 - - - +
49A VAL* 1.3 83.8 - - + +
51A ALA* 1.3 57.4 + - - -
53A ALA* 3.7 7.8 - - + -
54A PHE* 2.7 28.1 + - - +
216A LYS* 4.8 4.0 - - + +
217A VAL* 4.5 10.1 - - + -
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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
----------------------------------------------------------
24A THR* 3.1 24.5 + - + -
47A THR* 3.3 13.6 + - + +
48A LEU* 3.2 17.6 + - + +
50A PRO* 1.3 75.7 - - - +
52A ILE* 1.3 64.4 + - + +
54A PHE* 3.3 8.4 + - - +
55A THR* 3.2 26.3 + - - +
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 2.9 29.6 + - + +
51A ALA* 1.3 74.3 - - + +
53A ALA* 1.3 64.8 + - - +
55A THR* 2.7 25.4 + - - -
56A MET* 3.1 7.9 + - + +
85A ASP* 4.2 18.4 - - - +
88A PHE* 4.1 8.5 - - + -
89A THR* 3.6 19.5 - - + -
92A LEU* 4.0 24.2 - - + -
311A L2P 3.4 58.3 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 3.8 18.4 - - + -
49A VAL 3.1 17.6 + - - +
50A PRO 3.8 3.4 - - - +
52A ILE* 1.3 77.3 - - - +
54A PHE* 1.3 56.3 + - - +
56A MET* 3.2 1.2 + - - +
57A TYR* 2.8 37.4 + - + -
85A ASP* 3.4 24.5 - - - +
89A THR* 4.4 0.2 - - - +
216A LYS* 3.7 22.4 - - + -
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Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.4 38.8 - - + +
20A MET* 3.7 13.4 - - + +
21A GLY* 3.7 19.1 - - - +
24A THR* 4.6 1.6 - - - +
50A PRO 2.7 22.2 + - - +
51A ALA* 3.4 8.7 - - - +
52A ILE 3.2 0.2 - - - -
53A ALA* 1.3 74.4 - - - +
55A THR* 1.3 76.2 + - + +
57A TYR* 3.4 3.4 + - - +
58A LEU* 2.9 39.8 + - + +
304A D10 4.9 6.3 - - + -
305A HP6 4.1 30.3 - - + -
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA 3.2 13.7 + - - +
52A ILE* 2.7 22.6 + - - -
54A PHE* 1.3 90.3 - - + +
56A MET* 1.3 75.1 + - - +
58A LEU* 3.4 7.9 + - - +
59A SER* 3.0 26.5 + - - -
311A L2P 4.4 13.8 - - + +
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Residues in contact with MET 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 3.1 16.4 + - + +
53A ALA 4.0 2.2 - - - +
55A THR* 1.3 101.0 + - - +
57A TYR* 1.3 64.5 + - - +
59A SER* 2.8 34.6 + - - +
60A MET* 3.0 17.0 + - + +
80A TRP* 5.3 3.1 - - + -
81A ALA* 3.8 13.7 - - + +
84A ALA* 3.9 24.0 - - - -
85A ASP* 3.8 35.4 - - + +
311A L2P 3.5 35.0 - - + -
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Residues in contact with TYR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP 4.4 2.0 - - - -
13A LEU* 3.7 35.0 - - + +
16A GLY* 3.8 19.1 - - - -
17A THR* 3.4 18.4 + - - +
20A MET* 4.2 17.7 - - + -
53A ALA 2.8 27.2 + - - +
54A PHE 3.8 3.6 - - - +
56A MET* 1.3 75.7 - - - +
58A LEU* 1.3 58.8 + - - +
60A MET* 3.1 19.9 + - + +
61A LEU* 2.8 29.6 + - - +
82A ARG* 3.8 11.4 + - - -
85A ASP* 4.5 8.7 - - - -
205A THR* 5.8 0.7 - - + -
208A PHE 3.6 0.5 + - - -
209A MET* 3.3 32.0 + - + -
212A ASP* 2.6 34.6 + - + -
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.6 15.4 + - + -
54A PHE* 2.9 37.8 + - + +
55A THR* 3.6 7.2 - - - +
57A TYR* 1.3 76.6 - - - +
59A SER* 1.3 57.9 + - - +
61A LEU* 3.2 12.9 + - + +
62A LEU* 2.9 61.9 + - + +
305A HP6 4.0 37.7 - - + -
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR 3.0 14.3 + - - -
56A MET* 2.8 29.8 + - - +
58A LEU* 1.3 77.5 - - - +
60A MET* 1.3 59.1 + - - +
62A LEU* 4.0 4.2 - - - -
63A GLY 3.2 2.4 + - - -
64A TYR* 2.9 46.8 + - - -
65A GLY* 2.9 9.6 + - - -
80A TRP* 5.7 0.6 - - - -
81A ALA* 3.3 20.4 - - - +
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Residues in contact with MET 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 2.9 21.8 + - - -
13A LEU* 3.9 12.6 - - + -
56A MET* 3.0 22.9 + - + +
57A TYR* 3.1 35.4 + - + +
59A SER* 1.3 76.4 + - - +
61A LEU* 1.3 65.3 + - - +
63A GLY* 3.1 7.1 + - - -
65A GLY 4.2 3.6 - - - +
79A TYR* 3.6 47.4 - - + -
81A ALA* 3.7 14.6 - - + -
82A ARG* 3.8 43.5 - - + +
85A ASP* 5.9 0.9 - - - +
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.5 28.6 - - + +
7A ARG* 2.8 21.5 + - - +
10A TRP* 3.7 28.3 - - + +
13A LEU* 4.0 12.9 - - + +
14A ALA* 3.9 17.9 - - + +
17A THR* 4.3 5.6 - - - +
57A TYR 2.8 12.9 + - - +
58A LEU* 3.2 24.4 + - + +
60A MET* 1.3 77.4 - - - +
62A LEU* 1.3 64.6 + - + +
304A D10 4.2 29.8 - - + -
305A HP6 4.9 4.7 - - + -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.3 22.2 - - + +
7A ARG* 4.0 2.9 + - - -
58A LEU* 2.9 45.5 + - + +
59A SER* 4.4 4.5 - - - +
61A LEU* 1.3 81.0 - - + +
63A GLY* 1.3 59.9 + - - +
64A TYR* 3.4 5.6 + - + +
305A HP6 4.2 28.9 - - + -
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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