Contacts of the helix formed by residues 27 - 54 (chain F) in PDB entry 3PJV
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 LEU 27 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ILE* 4.7 17.0 - - + -
144D LEU* 4.2 27.4 - - + +
147D SER* 3.7 29.4 - - - +
148D ALA* 4.5 10.3 - - + -
24F MSE 3.7 31.4 - - + +
25F VAL* 3.1 2.0 - - - +
26F SER* 1.3 87.0 - - - +
28F GLU* 1.3 59.0 + - - +
29F SER 3.3 2.7 - - - -
30F SER* 3.2 17.8 + - - +
31F ARG* 2.8 31.5 + - + +
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Residues in contact with GLU 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F MSE 4.9 3.2 + - - +
25F VAL* 3.0 36.8 + - + +
27F LEU* 1.3 76.9 - - - +
29F SER* 1.3 60.7 + - - +
31F ARG* 3.3 25.0 + - - +
32F THR* 2.8 34.4 + - - +
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Residues in contact with SER 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F VAL 4.8 0.2 + - - -
26F SER 4.4 8.7 + - - -
28F GLU* 1.3 75.7 - - - +
30F SER* 1.3 69.6 + - - +
32F THR* 3.4 7.3 + - - -
33F GLN* 3.2 24.8 + - - +
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Residues in contact with SER 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 4.1 15.0 - - - -
147D SER* 5.0 4.4 + - - -
26F SER 5.3 0.5 + - - -
27F LEU* 3.2 23.3 + - - +
29F SER* 1.3 82.5 + - - +
31F ARG* 1.3 62.8 + - - +
33F GLN* 3.4 7.1 + - - +
34F TYR* 3.1 49.5 + - - -
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Residues in contact with ARG 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D LEU 4.8 1.6 + - - -
110D ILE* 2.6 46.0 + - + +
111D GLY 3.1 18.6 + - - -
112D LEU* 3.9 22.6 - - + +
113D GLU 5.0 1.0 - - - +
144D LEU* 4.4 13.2 - - + +
24F MSE 5.5 4.6 + - - -
27F LEU* 2.8 17.3 + - + +
28F GLU* 3.5 26.0 + - - +
29F SER 3.2 0.2 - - - -
30F SER* 1.3 74.2 - - - +
32F THR* 1.3 69.2 + - - +
34F TYR* 3.3 4.5 + - - +
35F VAL* 2.9 28.3 + - + +
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Residues in contact with THR 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F GLU* 2.8 24.6 + - - +
29F SER* 3.4 10.1 + - - -
30F SER 3.4 0.2 - - - -
31F ARG* 1.3 82.9 - - - +
33F GLN* 1.3 56.8 + - - +
35F VAL* 3.4 9.6 + - + +
36F ASN* 2.9 43.0 + - - +
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Residues in contact with GLN 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ASP* 3.9 33.9 + - - +
143D LYS* 4.9 1.2 - - - +
29F SER 3.2 17.4 + - - +
30F SER* 3.6 6.0 - - - +
32F THR* 1.3 78.0 - - - +
34F TYR* 1.3 85.6 + - + +
36F ASN* 3.3 10.8 + - - +
37F GLN* 3.1 21.6 + - + +
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Residues in contact with TYR 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ASP 5.0 1.8 - - - -
112D LEU* 5.3 4.7 - - + -
140D ALA* 3.9 32.5 - - + -
143D LYS* 3.5 48.1 + - + +
144D LEU* 3.5 41.7 - - + -
147D SER* 4.7 5.4 + - - -
30F SER* 3.1 32.1 + - - +
31F ARG* 3.9 3.1 - - - +
33F GLN* 1.3 94.4 - - + +
35F VAL* 1.3 60.6 + - - +
37F GLN* 3.2 9.0 + - + +
38F LEU* 2.9 34.2 + - - +
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Residues in contact with VAL 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D LEU* 3.5 26.2 - - + -
113D GLU* 3.8 41.5 - - + +
115D ALA* 3.6 6.6 - - + +
31F ARG* 2.9 27.1 + - + +
32F THR* 3.7 9.9 - - + +
34F TYR* 1.3 77.6 - - - +
36F ASN* 1.3 58.7 + - - +
38F LEU* 3.3 6.4 + - - -
39F ARG* 2.9 45.4 + - - +
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Residues in contact with ASN 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F THR* 2.9 29.8 + - - +
33F GLN* 3.5 9.1 - - - +
35F VAL* 1.3 77.0 - - - +
37F GLN* 1.3 57.6 + - - +
39F ARG* 3.4 22.1 + - - +
40F SER* 3.0 30.1 + - - -
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Residues in contact with GLN 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D SER 5.9 1.8 - - - +
72D ASP* 4.5 7.6 + - + +
73D SER* 3.5 42.4 + - - +
75D TYR* 3.5 19.1 + - - -
140D ALA* 5.7 2.6 - - - +
33F GLN* 3.1 14.1 + - + +
34F TYR* 3.2 10.6 + - + +
36F ASN* 1.3 75.8 - - - +
38F LEU* 1.3 83.3 + - - +
40F SER* 3.3 8.6 + - - +
41F HIS* 2.9 35.2 + - - +
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Residues in contact with LEU 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D TYR* 4.9 5.4 - - + +
112D LEU* 4.2 24.7 - - + -
113D GLU 4.9 9.2 - - - +
114D PRO 4.8 4.7 - - - +
115D ALA* 4.0 9.9 - - + -
135D SER* 3.1 29.2 + - - +
136D HIS 3.7 23.6 - - - +
137D PRO* 4.3 14.8 - - + -
140D ALA* 4.3 10.5 - - + +
34F TYR 2.9 22.5 + - - +
35F VAL* 3.8 7.2 - - - +
37F GLN* 1.3 90.2 - - - +
39F ARG* 1.3 57.3 + - - +
41F HIS* 4.4 0.7 - - - -
42F ALA* 3.0 26.7 + - - +
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Residues in contact with ARG 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D GLU* 2.7 33.1 + - - -
115D ALA* 3.2 23.7 + - + +
116D GLY 4.2 10.0 + - - +
117D GLY* 4.9 1.0 - - - -
35F VAL* 2.9 28.3 + - - +
36F ASN* 3.6 26.0 + - - +
38F LEU* 1.3 78.5 - - - +
40F SER* 1.3 57.6 + - - +
42F ALA* 3.3 2.4 + - - +
43F GLN* 2.8 36.2 + - + +
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Residues in contact with SER 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F ASN 3.0 15.1 + - - -
37F GLN* 3.3 13.2 + - - +
39F ARG* 1.3 77.6 - - - +
41F HIS* 1.3 60.1 + - - +
43F GLN* 3.8 6.2 - - - +
44F ASP* 2.8 42.6 + - - +
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Residues in contact with HIS 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D TYR* 3.4 38.0 + + - +
135D SER* 2.8 19.7 + - - +
37F GLN* 2.9 27.9 + - - +
38F LEU* 3.7 4.3 - - - +
40F SER* 1.3 79.2 + - - +
42F ALA* 1.3 60.6 + - - +
44F ASP* 3.5 9.3 + - + +
45F ALA* 3.3 21.0 + - - +
74F GLY* 6.0 0.4 - - - -
75F TYR* 3.9 18.2 + - - -
76F TYR* 3.5 32.7 + + - -
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Residues in contact with ALA 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ALA 4.1 4.5 - - - +
117D GLY* 3.7 9.6 - - - +
133D VAL* 3.5 39.1 - - + +
135D SER* 3.2 22.1 + - - +
38F LEU 3.0 14.1 + - - +
39F ARG 3.7 3.4 - - - +
41F HIS* 1.3 73.6 - - - +
43F GLN* 1.3 61.3 + - - +
45F ALA* 3.2 1.6 + - - +
46F ALA* 2.9 29.8 + - - +
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Residues in contact with GLN 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D GLY* 3.6 9.3 - - - -
118D ASP* 3.0 40.8 + - - +
119D ALA* 4.4 0.4 - - - +
39F ARG* 2.8 25.0 + - + +
40F SER* 3.8 7.6 - - - +
42F ALA* 1.3 71.5 - - - +
44F ASP* 1.3 68.5 + - - +
46F ALA* 3.3 1.6 + - - +
47F THR* 3.0 53.1 + - - +
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Residues in contact with ASP 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F SER* 2.8 33.1 + - - +
41F HIS* 3.7 8.6 - - + +
43F GLN* 1.3 74.8 - - - +
45F ALA* 1.3 59.3 + - - +
47F THR* 3.5 5.3 + - - -
48F ALA* 3.1 28.1 + - - +
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Residues in contact with ALA 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D VAL* 4.2 8.5 - - + -
41F HIS 3.3 8.6 + - - +
42F ALA 3.2 7.5 + - - +
43F GLN 3.2 0.6 - - - -
44F ASP* 1.3 78.6 - - - +
46F ALA* 1.3 59.8 + - - +
48F ALA* 3.8 4.7 - - - +
49F LEU* 2.9 32.8 + - - +
70F ILE* 4.9 9.5 - - + +
76F TYR* 3.3 37.0 - - + +
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Residues in contact with ALA 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D GLY 3.8 6.3 - - - +
118D ASP* 3.7 35.9 - - - +
119D ALA* 3.5 5.2 - - - +
131D VAL* 4.0 9.4 - - - +
133D VAL* 3.7 15.4 - - + +
42F ALA 2.9 16.0 + - - +
43F GLN* 3.3 4.5 + - - +
45F ALA* 1.3 75.4 - - - +
47F THR* 1.3 58.8 + - - +
49F LEU* 3.8 0.9 - - - +
50F ALA* 2.9 31.2 + - - +
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Residues in contact with THR 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ALA* 3.9 11.6 - - + +
43F GLN* 3.0 33.9 + - - +
44F ASP* 3.8 5.4 - - - -
46F ALA* 1.3 75.9 - - - +
48F ALA* 1.3 66.7 + - - +
50F ALA* 3.5 2.1 + - - +
51F LEU* 3.1 22.5 + - + +
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Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ASP 3.1 18.9 + - - +
45F ALA* 3.9 4.9 - - - +
47F THR* 1.3 77.0 - - - +
49F LEU* 1.3 57.8 + - - +
51F LEU* 3.3 10.7 + - - +
52F SER* 3.0 28.8 + - - -
70F ILE* 6.2 3.8 - - + -
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Residues in contact with LEU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D VAL* 3.7 24.2 - - + -
133D VAL* 5.1 1.3 - - + -
45F ALA 2.9 18.8 + - - +
46F ALA 3.9 2.7 - - - +
48F ALA* 1.3 76.2 - - - +
50F ALA* 1.3 59.6 + - - +
52F SER* 2.7 25.4 + - - +
53F LEU* 2.9 44.8 + - + +
66F LEU* 4.1 21.8 - - + +
67F VAL* 4.1 14.8 - - + +
70F ILE* 4.4 17.9 - - + +
79F ILE* 3.7 30.5 - - + -
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Residues in contact with ALA 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ALA* 3.7 15.3 - - + -
120D LEU 3.7 22.2 - - - +
121D VAL* 3.8 21.2 - - + +
131D VAL* 4.0 7.3 - - + +
46F ALA 2.9 18.9 + - - +
47F THR 3.8 3.4 - - - +
49F LEU* 1.3 75.3 - - - +
51F LEU* 1.3 55.2 + - - +
53F LEU 3.4 0.9 + - - -
54F THR* 2.8 33.1 + - - -
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Residues in contact with LEU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F THR* 3.1 15.3 + - + +
48F ALA* 3.4 12.6 - - - +
49F LEU 3.2 0.2 - - - -
50F ALA* 1.3 77.3 - - - +
52F SER* 1.3 61.8 + - - +
54F THR* 3.3 21.5 + - + +
55F PRO* 3.5 6.7 - - + +
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Residues in contact with SER 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ALA 3.0 13.8 + - - -
49F LEU* 2.7 34.7 + - - +
51F LEU* 1.3 78.3 - - - +
53F LEU* 1.3 58.6 + - - +
55F PRO* 3.5 5.0 - - - +
56F ASN* 3.0 23.7 + - - -
66F LEU* 3.5 17.4 - - - +
70F ILE* 5.7 1.0 - - - +
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Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D VAL* 4.3 11.0 - - + -
131D VAL* 3.8 25.6 - - + -
49F LEU* 2.9 35.3 + - + +
50F ALA 3.8 4.9 - - - +
52F SER* 1.3 77.1 - - - +
54F THR* 1.3 60.5 + - - +
55F PRO* 3.4 0.4 - - - -
56F ASN* 2.8 19.9 + - + -
57F ILE* 3.0 22.8 + - + +
63F VAL* 3.9 39.7 - - + +
66F LEU* 3.9 24.0 - - + -
67F VAL* 4.6 0.7 - - + -
81F VAL* 4.2 20.0 - - + -
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Residues in contact with THR 54 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D LEU 5.4 0.3 + - - -
121D VAL* 3.9 16.6 - - - +
122D SER* 4.1 19.1 + - - +
50F ALA 2.8 21.3 + - - -
51F LEU* 3.5 13.9 + - + +
52F SER 3.3 0.2 - - - -
53F LEU* 1.3 78.7 - - - +
55F PRO* 1.3 67.3 - - + +
56F ASN 3.1 4.5 + - - -
57F ILE* 3.7 14.7 + - - +
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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