Contacts of the helix formed by residues 39 - 67 (chain A) in PDB entry 1J30
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 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 2.9 15.0 + - + +
35A ASP* 5.6 0.2 - - - -
37A GLU* 3.6 38.5 + - + -
38A GLY* 1.3 81.2 - - - +
40A PRO* 1.3 60.2 - - - +
41A GLU* 3.3 3.4 - - - -
42A ILE* 3.3 23.7 + - + -
43A ALA* 2.9 27.1 + - - +
81B LEU* 3.5 21.1 - - + -
139B GLN* 3.8 37.4 - - + -
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Residues in contact with PRO 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP* 5.6 2.0 - - - +
38A GLY* 3.1 15.7 - - - +
39A TYR* 1.3 84.7 - - - +
41A GLU* 1.3 58.7 + - + +
43A ALA* 3.9 6.2 - - + +
44A GLY* 2.8 26.9 + - - -
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR 3.3 1.2 - - - -
40A PRO* 1.3 81.6 - - + +
42A ILE* 1.3 60.4 + - + +
44A GLY* 3.4 1.4 + - - -
45A LEU* 3.0 29.2 + - + +
136B VAL* 5.9 5.6 - - + -
139B GLN* 3.3 27.5 + - - +
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 4.1 8.5 - - + -
39A TYR* 3.3 29.7 + - + +
41A GLU* 1.3 76.9 - - + +
43A ALA* 1.3 59.1 + - - +
45A LEU* 3.3 8.3 + - + +
46A LEU* 2.9 43.8 + - + +
81B LEU* 4.8 11.0 - - + -
85B ILE* 4.2 12.6 - - + -
136B VAL* 3.3 40.6 - - + +
139B GLN* 3.6 33.0 - - + +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 3.8 15.7 - - - +
34A ALA* 3.8 9.4 - - + +
35A ASP* 3.2 27.1 - - - +
39A TYR 2.9 16.1 + - - +
40A PRO* 3.9 7.4 - - + +
42A ILE* 1.3 76.4 - - - +
44A GLY* 1.3 62.9 + - - +
46A LEU* 3.3 3.3 + - - +
47A ARG* 3.0 38.2 + - - +
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO 2.8 18.9 + - - -
41A GLU* 3.8 1.3 - - - -
43A ALA* 1.3 78.9 - - - +
45A LEU* 1.3 55.9 + - - +
47A ARG* 3.4 8.9 + - - +
48A SER* 3.0 28.8 + - - -
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU* 3.0 17.8 + - + +
42A ILE* 3.6 6.1 - - + +
43A ALA 3.2 0.2 - - - -
44A GLY* 1.3 72.7 - - - +
46A LEU* 1.3 61.1 + - - +
48A SER* 3.2 5.8 + - - +
49A ILE* 2.8 56.7 + - + +
132B LYS* 3.9 39.7 - - + +
133B PHE* 4.3 11.2 - - + -
136B VAL* 3.4 32.8 - - + -
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.7 38.4 - - + +
30A PHE* 3.7 17.9 - - + +
31A ALA* 3.5 29.6 - - + +
34A ALA* 4.7 1.8 - - + -
42A ILE* 2.9 34.3 + - + +
43A ALA* 3.3 5.1 + - - +
45A LEU* 1.3 77.9 - - + +
47A ARG* 1.3 57.8 + - - +
49A ILE* 3.5 0.9 + - - +
50A ALA* 2.9 29.2 + - - +
81B LEU* 5.1 1.3 - - + -
85B ILE* 4.3 13.7 - - + -
88B ALA* 5.3 0.2 - - + -
133B PHE* 3.5 32.1 - - + -
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 4.1 18.4 + - + +
31A ALA* 3.9 18.3 - - + +
32A LYS* 4.6 8.7 - - - +
35A ASP* 2.6 43.8 + - - -
43A ALA* 3.0 31.6 + - - +
44A GLY* 3.7 8.0 - - - +
45A LEU 3.2 0.2 - - - -
46A LEU* 1.3 77.1 - - - +
48A SER* 1.3 60.8 + - - +
50A ALA* 3.3 8.5 + - - +
51A GLU* 3.2 25.6 + - - +
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY 3.0 17.8 + - - -
45A LEU* 3.8 8.1 - - - -
47A ARG* 1.3 73.4 - - - +
49A ILE* 1.3 68.3 + - - +
51A GLU* 3.1 21.3 + - - +
52A GLY* 3.3 8.1 + - - -
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.6 25.6 - - + -
45A LEU* 2.8 38.1 + - + +
46A LEU 4.0 2.5 - - - +
48A SER* 1.3 76.1 - - - +
50A ALA* 1.3 57.9 + - - +
52A GLY* 2.8 17.8 + - - +
53A GLU* 3.0 12.2 + - - +
129B HIS* 3.5 50.8 - - + +
132B LYS* 4.3 7.0 - - + -
133B PHE* 3.4 34.1 - - + -
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN* 3.0 27.8 + - - +
27A TYR* 4.2 11.4 - - + -
28A LEU* 3.9 23.1 - - + -
46A LEU 2.9 19.0 + - - +
47A ARG 3.4 7.9 - - - +
48A SER 3.1 0.2 - - - -
49A ILE* 1.3 78.8 - - - +
51A GLU* 1.3 61.1 + - - +
53A GLU* 3.1 10.8 + - - +
54A THR 3.0 17.7 + - - -
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN* 5.0 0.2 - - - +
47A ARG 3.2 15.5 + - - +
48A SER* 3.1 14.4 + - - +
50A ALA* 1.3 75.9 - - - +
52A GLY* 1.3 62.7 + - - +
54A THR* 3.2 15.6 + - - +
55A ALA* 3.1 20.8 + - - +
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Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER 3.3 5.1 + - - -
49A ILE 2.8 10.2 + - - -
51A GLU* 1.3 80.2 - - - +
53A GLU* 1.3 59.3 + - - +
55A ALA* 3.1 8.4 + - - +
56A HIS* 3.0 36.8 + - - -
129B HIS* 4.7 9.6 - - - -
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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
----------------------------------------------------------
20A GLU* 3.5 26.0 - - - +
23A ALA* 3.9 10.7 - - + +
24A ASN* 4.1 7.6 - - + +
27A TYR* 3.3 16.8 - - + -
49A ILE 3.0 11.6 + - - +
50A ALA* 3.1 9.8 + - - +
52A GLY* 1.3 74.0 - - - +
54A THR* 1.3 60.7 + - - +
56A HIS* 3.2 4.2 + - - +
57A ALA* 3.0 28.9 + - - +
401A FE 2.1 29.1 - - - -
25B ARG* 4.9 0.7 - - - -
92B GLU* 3.2 4.2 - - - +
129B HIS* 3.5 6.2 - - - -
402B ZN 2.2 32.5 - - - -
403B OXY 2.6 9.7 + - - -
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN* 3.0 14.2 + - - -
50A ALA 3.0 5.1 + - - -
51A GLU* 3.4 21.3 + - - +
52A GLY 3.1 0.2 - - - -
53A GLU* 1.3 75.4 - - - +
55A ALA* 1.3 67.2 + - - +
57A ALA* 3.2 2.2 + - - +
58A PHE* 2.9 57.7 + - + -
25B ARG* 2.8 32.4 + - - +
28B LEU* 6.0 0.7 - - + -
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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
----------------------------------------------------------
51A GLU 3.1 10.1 + - - +
52A GLY* 3.1 11.9 + - - +
54A THR* 1.3 79.8 - - - +
56A HIS* 1.3 63.4 + - + +
58A PHE* 3.9 6.4 - - - +
59A GLY* 3.0 26.0 + - - -
118B TRP* 3.9 6.4 - - + -
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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
----------------------------------------------------------
20A GLU* 3.2 22.1 + - + +
52A GLY* 3.0 17.1 + - - -
53A GLU* 3.2 8.1 + - - +
54A THR 3.1 0.2 - - - -
55A ALA* 1.3 79.9 - - + +
57A ALA* 1.3 65.5 + - - +
59A GLY 3.2 1.7 + - - -
60A HIS* 3.0 28.6 + - - -
401A FE 2.1 24.7 - - - -
118B TRP* 3.5 11.6 - + - -
121B THR* 6.0 0.4 - - - +
122B LEU* 3.6 30.4 - - + +
125B ALA* 3.7 28.0 - - + +
126B GLU* 2.9 18.0 + - - -
129B HIS* 4.2 7.0 - + - -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 3.5 23.1 - - + -
20A GLU* 3.8 17.4 - - + +
21A SER* 4.4 1.6 - - - +
53A GLU 3.0 18.0 + - - +
54A THR 3.7 3.4 - - - +
56A HIS* 1.3 78.3 - - - +
58A PHE* 1.3 65.1 + - + +
60A HIS* 3.2 7.3 + - - +
61A LEU* 3.0 18.0 + - - +
25B ARG* 3.9 28.0 - - + -
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Residues in contact with PHE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 2.9 44.3 + - + +
55A ALA* 4.0 6.1 - - - +
57A ALA* 1.3 79.7 - - + +
59A GLY* 1.3 57.9 + - - +
61A LEU* 3.2 7.6 + - + +
62A ASP* 2.9 34.7 + - - +
25B ARG* 3.4 32.1 - - + -
28B LEU* 3.9 25.4 - - + -
29B TYR* 3.7 28.1 - + + -
32B LYS* 3.7 36.8 - - + +
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Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA 3.0 12.7 + - - -
56A HIS 3.2 0.6 + - - -
58A PHE* 1.3 76.6 - - - +
60A HIS* 1.3 62.0 + - - +
62A ASP* 3.2 12.0 + - - +
63A PHE* 3.2 29.0 + - - -
118B TRP* 3.5 28.9 - - - -
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Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.0 26.2 - - + +
16A GLY* 3.4 30.1 - - - -
17A PHE* 3.5 12.1 - - + -
20A GLU* 3.8 5.8 - - + +
56A HIS 3.0 17.8 + - - -
57A ALA* 3.2 6.3 + - - +
59A GLY* 1.3 77.4 - - - +
61A LEU* 1.3 61.0 + - - +
63A PHE* 3.3 4.2 + - - +
64A ILE* 3.0 27.9 + - - +
100B TYR* 3.0 23.5 + + - -
118B TRP* 3.0 32.0 + - - +
119B PHE* 3.7 19.5 - + - -
122B LEU* 3.4 16.4 - - + +
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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
----------------------------------------------------------
17A PHE* 3.4 44.2 - - + -
57A ALA 3.0 8.9 + - - +
58A PHE* 3.2 12.1 + - + +
60A HIS* 1.3 78.2 - - - +
62A ASP* 1.3 56.4 + - - +
64A ILE* 3.6 6.4 - - + +
65A ARG* 2.8 32.7 + - - +
71A ASP* 5.4 0.2 - - - +
72A PRO* 3.9 26.9 - - + -
78A ILE* 4.4 14.1 - - + +
25B ARG 4.7 0.2 - - - +
26B ARG* 4.6 10.5 - - + -
29B TYR* 3.6 46.3 + - + -
30B PHE* 5.7 1.1 - - + -
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Residues in contact with ASP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 2.9 18.7 + - - +
59A GLY* 3.5 13.9 - - - +
60A HIS 3.2 0.4 - - - -
61A LEU* 1.3 76.6 - - - +
63A PHE* 1.3 58.9 + - + +
65A ARG* 3.4 13.1 + - - +
66A GLN* 2.8 50.9 + - - +
29B TYR* 2.6 33.7 + - - -
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Residues in contact with PHE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.0 8.8 - - + +
13A LEU* 4.0 21.1 - - + -
59A GLY* 3.2 21.0 + - - -
60A HIS 3.3 5.6 + - - +
62A ASP* 1.3 81.4 - - + +
64A ILE* 1.3 58.1 + - - +
66A GLN* 3.8 15.1 - - + +
67A GLY* 3.0 26.3 + - - -
114B GLU* 3.7 37.9 - - + -
115B VAL* 3.8 24.2 - - + -
118B TRP* 3.4 50.0 - + + -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA 5.4 0.2 - - - +
13A LEU* 3.9 38.8 - - + +
14A LYS* 4.2 2.9 - - + +
17A PHE* 4.8 1.1 - - + -
60A HIS 3.0 25.1 + - - +
61A LEU* 3.6 8.7 - - + +
62A ASP 3.2 0.2 - - - -
63A PHE* 1.3 77.2 - - - +
65A ARG* 1.3 61.3 + - - +
67A GLY 3.3 1.2 + - - -
68A GLY 3.3 2.9 + - - -
69A LEU* 2.9 55.3 + - + +
70A THR 3.3 24.7 - - - +
72A PRO* 3.8 28.0 - - + -
78A ILE* 4.6 9.4 - - + -
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU 2.8 20.1 + - - +
62A ASP* 3.4 21.0 + - - +
64A ILE* 1.3 75.8 - - - +
66A GLN* 1.3 85.8 + - - +
67A GLY 3.0 0.2 - - - -
68A GLY* 3.0 19.2 + - - -
69A LEU 4.7 4.7 - - - -
78A ILE* 3.3 35.2 - - + +
79A GLY* 4.0 19.2 + - - -
84A MET* 4.0 13.2 - - - +
29B TYR* 2.9 20.2 + - - +
33B ARG* 3.9 19.6 - - - +
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Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP* 2.8 40.3 + - - +
63A PHE* 4.1 19.2 - - - +
65A ARG* 1.3 98.2 + - - +
67A GLY* 1.3 58.0 + - - +
68A GLY 3.4 0.6 + - - -
114B GLU* 5.6 2.0 + - - -
----------------------------------------------------------
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 4.4 12.6 - - - +
4A LEU* 4.3 19.9 + - - +
5A LYS* 5.8 0.3 - - - +
63A PHE 3.0 17.0 + - - -
64A ILE 3.7 0.7 - - - -
65A ARG 3.0 0.4 - - - -
66A GLN* 1.3 77.3 - - - +
68A GLY* 1.3 62.8 + - - +
69A LEU* 3.2 10.4 + - - +
----------------------------------------------------------
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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