Contacts of the helix formed by residues 10 - 40 (chain F) in PDB entry 3P8C
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 GLU 10 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F GLN 5.7 0.2 - - - +
6F MET* 3.1 36.7 + - - +
8F LEU 3.6 0.6 - - - -
9F GLU* 1.3 92.1 - - + +
11F GLU* 1.3 63.8 + - + +
12F ILE 3.5 1.8 - - - -
13F PRO* 3.6 2.7 - - - +
14F GLY* 2.8 28.1 + - - -
17F ARG* 4.1 5.5 + - - +
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Residues in contact with GLU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F MET* 2.9 52.5 + - + +
7F LEU* 3.6 25.8 - - + +
10F GLU* 1.3 74.7 - - + +
12F ILE* 1.3 58.2 - - - +
14F GLY* 3.8 1.0 - - - -
15F GLY* 2.9 23.9 + - - -
68F LEU* 4.5 0.2 - - - +
71F ASN* 4.0 26.9 + - - +
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Residues in contact with ILE 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D PHE* 5.3 1.1 - - + +
56D PHE* 3.6 35.2 - - + -
7F LEU* 3.0 34.2 + - + +
8F LEU 4.6 0.2 - - - +
11F GLU* 1.3 73.5 - - - +
13F PRO* 1.4 65.1 - - + +
16F ARG* 3.0 36.0 + - - +
68F LEU* 3.7 17.1 - - + +
71F ASN* 4.1 29.8 - - + +
72F VAL* 4.7 7.2 - - + -
75F MET* 3.9 33.9 - - + -
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Residues in contact with PRO 13 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D PHE* 5.0 7.4 - - + -
7F LEU 3.7 0.9 - - - +
8F LEU 3.3 27.8 - - - +
9F GLU* 3.5 15.9 - - - +
10F GLU 3.6 12.3 - - - +
12F ILE* 1.4 93.7 - - + +
14F GLY* 1.3 55.2 + - - +
16F ARG* 3.4 10.7 + - + +
17F ARG* 2.9 44.9 + - - +
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Residues in contact with GLY 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F GLU 2.8 20.5 + - - -
11F GLU* 3.9 1.3 - - - -
13F PRO* 1.3 77.0 - - - +
15F GLY* 1.3 56.4 + - - +
17F ARG* 3.4 23.5 + - - +
18F ALA* 3.0 28.2 + - - +
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Residues in contact with GLY 15 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F GLU 2.9 18.4 + - - -
12F ILE 3.8 1.3 - - - -
13F PRO 3.4 0.2 - - - -
14F GLY* 1.3 74.6 - - - +
16F ARG* 1.3 61.2 + - - +
18F ALA* 3.6 8.0 + - - +
19F LEU* 3.2 22.9 + - - +
64F LEU* 5.1 3.8 - - - +
67F THR* 6.3 3.1 - - - -
68F LEU* 3.6 22.4 - - - +
71F ASN* 6.0 0.4 - - - -
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Residues in contact with ARG 16 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLU* 2.8 41.8 + - + +
52D PHE* 4.6 6.7 - - + -
53D GLY* 3.5 29.3 + - - +
56D PHE* 3.4 31.5 - - - -
57D ASN* 4.5 8.5 + - - +
12F ILE* 3.0 33.7 + - + +
13F PRO* 3.7 10.2 - - + +
15F GLY* 1.3 74.8 - - - +
17F ARG* 1.3 59.7 + - - +
19F LEU* 3.1 6.6 + - - +
20F PHE* 3.0 25.7 + - - +
68F LEU* 3.9 17.0 - - + -
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Residues in contact with ARG 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F GLU 5.4 0.6 + - - -
10F GLU* 4.1 7.1 + - - +
13F PRO* 2.9 23.9 + - - +
14F GLY* 3.5 36.5 + - - +
16F ARG* 1.3 76.5 - - + +
18F ALA* 1.3 56.3 + - - +
20F PHE* 3.3 6.2 + - - +
21F ASP* 2.9 40.5 + - - +
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Residues in contact with ALA 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F GLY 3.0 17.4 + - - +
15F GLY* 3.7 9.0 - - - +
16F ARG 3.3 0.2 - - - -
17F ARG* 1.3 75.4 - - - +
19F LEU* 1.3 55.9 + - - +
21F ASP* 3.7 9.5 - - - +
22F SER* 3.1 25.3 + - - -
64F LEU* 3.6 30.8 - - + +
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D SER* 3.4 43.2 - - - +
48D ALA* 3.7 12.1 - - + -
49D GLU* 3.5 29.8 - - + +
52D PHE* 3.9 5.8 - - + -
15F GLY 3.2 7.7 + - - +
16F ARG 3.1 10.2 + - - +
18F ALA* 1.3 75.9 - - - +
20F PHE* 1.3 59.6 + - - +
21F ASP 3.3 0.2 - - - -
22F SER* 3.4 1.8 + - - +
23F TYR* 3.1 20.6 + - - +
61F VAL* 5.0 2.7 - - - +
64F LEU* 3.7 32.5 - - + +
65F ILE* 4.2 15.7 - - + -
68F LEU* 3.7 24.0 - - + -
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Residues in contact with PHE 20 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D SER 5.4 0.2 - - - -
46D LYS* 4.7 17.9 - - + +
49D GLU* 4.3 22.1 - - + +
16F ARG 3.0 13.9 + - - +
17F ARG* 3.3 7.2 + - - +
19F LEU* 1.3 73.0 - - - +
21F ASP* 1.3 69.5 + - - +
23F TYR* 3.2 31.7 + + + +
24F THR* 3.2 35.0 + - + +
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Residues in contact with ASP 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F ARG* 2.9 27.0 + - - +
18F ALA* 3.7 9.0 - - - +
20F PHE* 1.3 79.3 - - - +
22F SER* 1.3 59.9 + - - +
24F THR* 3.1 10.1 + - - -
25F ASN* 2.8 47.0 + - - +
----------------------------------------------------------
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Residues in contact with SER 22 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D SER* 2.9 22.4 + - - -
18F ALA 3.1 19.4 + - - -
19F LEU* 3.4 8.3 - - - -
20F PHE 3.3 0.2 - - - -
21F ASP* 1.3 75.1 - - - +
23F TYR* 1.3 61.0 + - - +
25F ASN* 4.7 4.9 - - - +
26F LEU* 3.0 45.6 + - - +
60F SER* 4.8 4.2 + - - -
61F VAL* 3.7 7.3 - - - +
64F LEU* 3.9 17.1 - - - +
----------------------------------------------------------
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Residues in contact with TYR 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D SER* 2.6 61.8 + - - +
43D SER* 5.0 2.9 - - - -
45D SER* 3.7 0.4 - - - -
46D LYS* 3.6 46.2 + - + +
19F LEU 3.1 12.4 + - - +
20F PHE* 3.3 36.1 - + - +
21F ASP 3.2 0.4 - - - -
22F SER* 1.3 79.3 - - - +
24F THR* 1.3 79.6 + - + +
27F GLU* 3.5 24.9 + - - +
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Residues in contact with THR 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F PHE* 3.2 27.1 + - + +
21F ASP* 3.1 17.8 + - - -
23F TYR* 1.3 93.7 - - + +
25F ASN* 1.3 70.3 + - - +
27F GLU* 3.4 10.6 + - - +
28F ARG* 3.4 33.2 + - - +
----------------------------------------------------------
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Residues in contact with ASN 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ASP* 2.8 35.4 + - - +
22F SER* 4.3 4.8 - - - +
24F THR* 1.3 78.2 + - - +
26F LEU* 1.3 59.3 + - + +
28F ARG* 3.0 35.3 + - - +
29F VAL* 2.8 33.9 + - + +
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Residues in contact with LEU 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ILE* 3.4 13.2 - - + +
41D LEU* 3.8 23.1 - - + +
42D SER* 3.9 12.3 - - - -
22F SER* 3.0 43.0 + - - +
25F ASN* 1.3 75.9 - - + +
27F GLU* 1.3 59.5 + - - +
29F VAL* 3.7 13.5 - - + -
30F ALA* 2.9 29.3 + - - +
57F SER* 3.2 32.3 - - - +
60F SER* 6.0 2.9 - - - +
61F VAL* 3.7 21.5 - - + -
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Residues in contact with GLU 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ARG* 5.2 10.9 + - + +
42D SER* 4.0 10.0 + - - +
23F TYR* 3.5 35.6 + - - +
24F THR* 3.4 13.9 + - - +
25F ASN 3.2 0.4 - - - -
26F LEU* 1.3 79.6 - - - +
28F ARG* 1.3 57.9 + - + +
30F ALA* 3.8 5.2 - - - +
31F ASP* 3.1 39.6 + - - +
----------------------------------------------------------
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Residues in contact with ARG 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F THR* 3.4 20.2 + - - +
25F ASN* 3.0 38.5 + - - +
27F GLU* 1.3 75.4 - - + +
29F VAL* 1.3 60.9 + - + +
31F ASP* 3.3 10.9 + - - +
32F TYR* 2.9 29.8 + - - +
----------------------------------------------------------
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Residues in contact with VAL 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ILE* 3.8 15.5 - - + -
25F ASN* 2.8 23.5 + - + +
26F LEU* 3.8 14.1 - - + +
27F GLU 3.4 0.2 - - - -
28F ARG* 1.3 77.4 - - + +
30F ALA* 1.3 57.6 + - - +
32F TYR* 3.4 6.3 + - - +
33F CYS* 3.0 31.2 + - - -
53F TYR* 3.7 46.4 - - + -
57F SER* 4.3 6.1 - - - +
----------------------------------------------------------
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Residues in contact with ALA 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ALA* 3.4 28.1 - - - +
38D ILE* 3.9 11.2 - - + -
39D ARG* 3.6 25.4 - - + -
26F LEU 2.9 18.6 + - - +
27F GLU 3.8 3.4 - - - +
29F VAL* 1.3 74.3 - - - +
31F ASP* 1.3 64.4 + - - +
33F CYS* 3.4 5.8 + - - +
34F GLU* 3.0 25.1 + - - +
----------------------------------------------------------
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Residues in contact with ASP 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ARG* 2.8 25.9 + - - +
27F GLU* 3.1 25.7 + - - +
28F ARG* 3.3 12.6 + - - +
30F ALA* 1.3 78.4 - - - +
32F TYR* 1.3 57.1 + - - +
34F GLU* 3.3 2.5 + - - +
35F ASN* 2.8 45.8 + - - +
----------------------------------------------------------
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Residues in contact with TYR 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ARG 2.9 17.6 + - - +
29F VAL* 3.6 5.6 - - - +
30F ALA 3.3 0.2 - - - -
31F ASP* 1.3 75.7 - - - +
33F CYS* 1.3 63.1 + - - +
35F ASN* 3.2 4.0 + - - +
36F ASN* 2.6 67.6 + - + +
49F GLU* 2.6 36.0 + - + -
53F TYR* 4.1 23.8 - + - -
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Residues in contact with CYS 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ASN* 3.0 18.4 + - - -
35D ALA* 4.7 3.1 - - + -
38D ILE* 4.0 11.9 - - + -
29F VAL 3.0 25.0 + - - +
30F ALA 3.8 4.9 - - - +
32F TYR* 1.3 81.9 - - - +
34F GLU* 1.3 60.6 + - - +
36F ASN* 4.4 3.6 + - - +
37F TYR* 3.5 12.6 + - - +
49F GLU 5.0 0.2 - - - -
50F THR* 3.7 33.9 + - + +
53F TYR* 3.7 41.3 - - - -
----------------------------------------------------------
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Residues in contact with GLU 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ASN* 4.1 8.0 + - - +
32D ILE* 4.8 20.7 - - + +
35D ALA* 4.0 10.7 - - + +
39D ARG* 2.8 34.4 + - - +
30F ALA 3.0 16.6 + - - +
31F ASP 3.7 3.6 - - - +
33F CYS* 1.3 79.2 - - - +
35F ASN* 1.3 70.0 + - - +
37F TYR* 3.6 2.8 + - - +
38F ILE* 3.3 43.2 + - + +
----------------------------------------------------------
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Residues in contact with ASN 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F ASP* 2.8 35.4 + - - +
32F TYR* 4.0 2.6 - - - +
34F GLU* 1.3 82.4 - - - +
36F ASN* 1.3 54.7 + - - +
38F ILE* 3.1 12.0 + - - +
39F GLN* 2.7 60.9 + - - +
----------------------------------------------------------
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Residues in contact with ASN 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F TYR* 2.6 56.5 + - + +
33F CYS* 4.4 3.5 + - - +
35F ASN* 1.3 71.3 - - - +
37F TYR* 1.3 57.7 + - - +
39F GLN* 3.8 5.5 - - - -
40F SER* 3.0 46.6 + - - -
46F ALA* 3.6 28.3 + - - +
49F GLU* 4.0 15.8 + - - +
----------------------------------------------------------
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Residues in contact with TYR 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLU* 5.9 0.5 - - - +
27D GLU* 2.9 47.5 + - - +
28D CYS* 3.5 27.3 + - + +
31D ASN* 3.3 46.0 - - + +
32D ILE* 6.3 1.3 - - + -
33F CYS 3.5 6.3 + - - +
34F GLU 3.8 2.5 - - - +
35F ASN 3.2 1.0 - - - -
36F ASN* 1.3 80.5 - - - +
38F ILE* 1.3 70.4 - - + +
40F SER* 3.5 5.5 - - - +
43F LYS* 3.1 73.9 + - + +
46F ALA* 3.8 14.6 - - + -
47F LEU* 4.1 4.3 - - + -
50F THR* 5.1 0.2 - - - +
----------------------------------------------------------
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Residues in contact with ILE 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D CYS* 6.1 4.3 - - - -
32D ILE* 5.7 9.0 - - + -
34F GLU* 3.3 37.9 - - + +
35F ASN* 3.1 14.3 + - - +
37F TYR* 1.3 82.5 - - + +
39F GLN* 1.3 65.7 + - + +
40F SER 3.6 1.6 + - - +
43F LYS* 4.0 13.7 + - - +
----------------------------------------------------------
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Residues in contact with GLN 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ASN* 2.7 46.4 + - - +
36F ASN* 4.1 5.2 - - - +
38F ILE* 1.3 78.1 - - + +
40F SER* 1.3 60.5 + - - +
41F ALA 4.1 0.9 + - - -
----------------------------------------------------------
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Residues in contact with SER 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F ASN* 3.0 32.4 + - - -
37F TYR 3.5 12.1 - - - +
38F ILE 3.4 2.0 - - - +
39F GLN* 1.3 80.0 - - - +
41F ALA* 1.3 60.8 + - - +
42F ASP* 3.9 21.5 - - - -
43F LYS* 3.6 15.6 + - - +
46F ALA* 4.6 4.7 - - - -
----------------------------------------------------------
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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