Contacts of the helix formed by residues 1 - 28 (chain D) in PDB entry 4IP8
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 ARG 1 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 3.9 22.1 - - + +
18B TRP* 3.8 20.8 - - + +
0D MET* 1.3 77.6 - - - +
2D SER* 1.3 81.9 + - - +
4D PHE 3.8 0.2 - - - -
5D SER* 2.8 36.4 + - - -
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Residues in contact with SER 2 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TRP* 4.7 2.2 + - - -
57C ALA* 6.0 0.9 - - - +
1D ARG* 1.3 96.6 - - - +
3D PHE* 1.3 67.9 + - - +
5D SER* 3.7 6.9 - - - -
6D PHE* 2.9 27.4 + - - +
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Residues in contact with PHE 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 5.2 4.7 - + - -
10C ALA* 4.7 6.1 - - + -
11C PHE* 4.6 14.1 - + - -
14C ALA* 5.2 4.9 - - + -
53C TRP* 3.6 47.7 - + + +
54C ALA* 3.8 24.5 - - + -
57C ALA* 3.8 29.2 - - + -
58C ILE* 5.7 1.1 - - + -
0D MET* 3.2 33.6 + - + +
2D SER* 1.3 85.0 + - - +
4D PHE* 1.3 81.7 + + - +
6D PHE 3.6 0.2 + - - -
7D LEU* 3.4 45.7 + - + +
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Residues in contact with PHE 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 4.9 9.6 - - + -
3A PHE* 4.8 7.4 - + - -
4A PHE* 4.9 12.3 - + - -
11B PHE* 3.4 48.9 - + - +
14B ALA* 3.6 35.9 - - + -
15B ARG* 4.0 13.1 - - + +
18B TRP* 5.3 2.2 - + + -
58B ILE* 5.2 3.4 - - + -
203C P4C 6.3 0.9 - - - -
0D MET* 3.0 58.6 + - + +
3D PHE* 1.3 93.5 - + - +
5D SER* 1.3 61.4 + - - +
7D LEU* 3.4 3.6 + - - +
8D GLY* 2.9 26.5 + - - -
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Residues in contact with SER 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 3.6 23.7 + - - +
1D ARG* 2.8 27.1 + - - -
2D SER* 3.7 9.6 - - - -
3D PHE 3.3 0.2 - - - -
4D PHE* 1.3 77.6 - - - +
6D PHE* 1.3 57.1 + - - +
8D GLY* 3.3 2.4 + - - -
9D GLU* 3.0 47.6 + - - +
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Residues in contact with PHE 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 4.7 8.5 - + - -
53C TRP* 3.7 28.9 - + + -
202C P4C 4.0 26.5 - - - +
2D SER 2.9 17.9 + - - +
3D PHE 3.9 2.7 - - - +
5D SER* 1.3 77.1 - - - +
7D LEU* 1.3 61.2 + - + +
9D GLU* 3.5 9.7 + - - +
10D ALA* 3.1 23.1 + - + +
49D PRO* 3.9 13.7 - - + -
50D GLY* 3.5 31.5 - - - -
53D TRP* 3.7 38.6 - + - -
202D P4C 3.8 24.7 - - - -
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Residues in contact with LEU 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.7 35.4 - - + -
7C LEU* 3.7 30.5 - - + -
10C ALA* 5.9 0.7 - - + -
11C PHE* 4.0 11.4 - - + -
53C TRP* 4.0 18.2 - - + -
3D PHE* 3.4 46.8 + - + +
4D PHE* 3.4 5.8 + - + +
5D SER 3.3 0.4 - - - -
6D PHE* 1.3 81.0 - - + +
8D GLY* 1.3 65.1 + - - +
10D ALA* 3.2 5.3 + - + +
11D PHE* 3.0 35.0 + - + -
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Residues in contact with GLY 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY* 5.0 4.9 - - - -
11B PHE* 4.1 12.9 - - - +
12B ASP* 4.5 13.5 - - - -
15B ARG* 6.1 0.4 - - - -
4D PHE 2.9 17.8 + - - -
5D SER* 3.7 2.2 - - - -
7D LEU* 1.3 76.9 - - - +
9D GLU* 1.3 54.7 + - - +
11D PHE* 3.4 3.6 + - - +
12D ASP* 2.9 38.8 + - - +
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Residues in contact with GLU 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D SER* 3.0 35.7 + - - +
6D PHE* 3.7 8.0 - - - +
8D GLY* 1.3 76.8 - - - +
10D ALA* 1.3 52.1 + - - +
12D ASP* 3.8 3.1 - - - +
13D GLY* 2.8 32.4 + - - -
47D ARG* 3.4 31.9 - - - +
48D GLY* 4.3 0.2 - - - -
49D PRO* 3.2 18.9 - - - +
50D GLY* 3.0 29.7 + - - -
51D GLY* 3.6 11.2 + - - +
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Residues in contact with ALA 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 4.7 6.5 - - + -
6D PHE* 3.1 15.9 + - + +
7D LEU* 3.2 11.9 + - + +
9D GLU* 1.3 78.1 - - - +
11D PHE* 1.3 63.7 + - + +
14D ALA* 2.8 25.8 + - - +
50D GLY 3.3 20.4 - - - +
53D TRP* 3.9 25.1 - - + -
54D ALA* 3.3 12.2 - - + +
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Residues in contact with PHE 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.4 35.4 - + - -
4B PHE* 3.7 42.0 - + - +
7B LEU* 3.9 15.5 - - + -
8B GLY* 3.9 9.0 - - - +
11B PHE* 3.1 40.4 - + - -
3C PHE* 4.7 8.1 - + - -
7C LEU* 4.0 23.8 - - + -
11C PHE* 5.2 0.2 - + - -
7D LEU* 3.0 33.2 + - + +
8D GLY 4.1 0.2 - - - +
10D ALA* 1.3 79.0 - - + +
12D ASP* 1.3 63.3 + - - +
14D ALA* 3.5 5.3 + - + +
15D ARG* 3.0 26.7 + - - +
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Residues in contact with ASP 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY* 4.2 13.0 - - - -
12B ASP* 4.4 14.5 - - - +
8D GLY 2.9 22.3 + - - +
9D GLU* 3.8 3.0 - - - +
11D PHE* 1.3 75.7 - - - +
13D GLY* 1.3 57.9 + - - +
15D ARG* 2.8 31.7 + - - +
16D ASP* 2.9 33.4 + - - +
47D ARG* 3.5 37.2 + - + +
201D SO4 4.0 3.5 + - - -
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Residues in contact with GLY 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLU 2.8 18.1 + - - -
10D ALA 3.7 1.3 - - - -
12D ASP* 1.3 74.8 - - - +
14D ALA* 1.3 64.7 + - - +
16D ASP* 3.0 6.1 + - - +
17D MET* 3.0 25.5 + - - +
44D ALA* 3.6 27.2 - - - +
47D ARG* 4.0 2.6 - - - +
51D GLY* 4.2 4.9 - - - -
54D ALA* 4.3 3.8 - - - -
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Residues in contact with ALA 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 3.6 36.3 - - + -
3C PHE* 5.2 4.5 - - + -
10D ALA 2.8 18.1 + - - +
11D PHE* 3.6 8.3 - - + +
13D GLY* 1.3 74.5 - - - +
15D ARG* 1.3 57.9 + - - +
17D MET* 3.2 3.6 + - - +
18D TRP* 3.0 28.9 + - - +
54D ALA* 3.9 2.8 - - + +
58D ILE* 3.6 23.3 - - + +
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Residues in contact with ARG 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ARG* 4.5 14.6 - - + +
4B PHE* 4.1 12.9 + - + -
5B SER* 3.2 35.8 + - - +
8B GLY* 5.5 0.8 - - - -
11D PHE 3.0 14.6 + - - +
12D ASP* 2.8 50.6 + - - +
14D ALA* 1.3 77.6 - - - +
16D ASP* 1.3 58.1 + - - +
18D TRP* 3.5 4.6 + - - +
19D ARG* 2.9 32.6 + - + +
47D ARG* 3.8 4.6 - - - +
201D SO4 2.5 50.1 + - - -
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Residues in contact with ASP 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ASP 2.9 13.5 + - - +
13D GLY 3.0 7.2 + - - +
15D ARG* 1.3 77.2 - - - +
17D MET* 1.3 65.5 + - - +
19D ARG* 3.2 28.4 + - - +
20D ALA* 3.0 22.5 + - - +
39D ARG* 4.9 0.3 + - - -
40D GLY* 4.3 4.2 - - - -
43D ASP* 3.0 42.5 - - + +
44D ALA* 3.5 6.2 + - - +
47D ARG* 2.9 41.5 + - - +
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Residues in contact with MET 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLY 3.0 16.8 + - - +
14D ALA 3.5 6.5 - - - +
16D ASP* 1.3 77.0 - - - +
18D TRP* 1.3 63.2 + - - +
20D ALA* 3.1 7.5 + - - +
21D TYR 3.1 17.2 + - - -
40D GLY* 3.3 29.4 - - - +
41D ASN* 3.5 15.0 - - - +
44D ALA* 4.2 2.2 - - + -
55D ALA* 4.0 22.0 - - - +
58D ILE* 3.9 27.6 - - + -
59D SER* 3.6 33.0 - - - +
203D P4C 3.4 33.0 - - - +
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Residues in contact with TRP 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 3.9 28.3 - - + -
64A ASN* 4.4 16.1 - - + +
65A ILE* 4.3 15.0 - - + -
0B MET* 3.5 43.1 - - + +
1B ARG* 3.8 29.2 - - + +
4B PHE* 4.9 5.2 - + + -
14D ALA 3.0 15.8 + - - +
15D ARG* 4.0 6.5 - - - +
17D MET* 1.3 77.2 - - - +
19D ARG* 1.3 54.2 + - - +
21D TYR* 3.2 35.1 + + - +
22D SER* 2.7 46.3 + - - -
203D P4C 4.2 19.7 - - - -
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Residues in contact with ARG 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ARG* 2.9 22.2 + - + +
16D ASP* 3.2 29.3 + - - +
17D MET 3.2 0.2 - - - -
18D TRP* 1.3 75.4 - - - +
20D ALA* 1.3 59.5 + - - +
22D SER* 3.7 7.6 - - - -
23D ASP* 2.9 39.4 + - - +
39D ARG* 3.6 23.0 - - - +
43D ASP* 4.0 17.7 + - - -
47D ARG* 5.1 3.4 - - - +
201D SO4 5.7 1.6 + - - -
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Residues in contact with ALA 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASP 3.0 6.6 + - - +
17D MET 3.1 9.6 + - - +
19D ARG* 1.3 78.2 - - - +
21D TYR* 1.3 62.5 + - - +
23D ASP* 3.3 1.9 + - - +
24D MET* 2.9 24.9 + - - +
36D PHE* 3.5 32.0 - - + +
39D ARG* 3.5 15.7 - - - +
40D GLY* 3.5 22.2 - - - +
203D P4C 4.4 5.4 - - - -
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Residues in contact with TYR 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN* 2.8 38.5 + - - -
65A ILE* 3.5 15.6 - - + -
68A PHE* 3.6 21.5 - + - +
69A PHE* 6.3 0.4 - + - -
17D MET 3.1 3.0 + - - -
18D TRP* 3.4 42.2 - + - +
20D ALA* 1.3 79.3 - - - +
22D SER* 1.3 67.9 + - - +
24D MET* 3.1 24.6 + - + +
25D ARG* 3.0 41.5 + - + +
203D P4C 3.7 47.4 + - - +
----------------------------------------------------------
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Residues in contact with SER 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN* 5.6 2.6 + - - -
18D TRP* 2.7 41.8 + - - -
19D ARG* 3.7 9.6 - - - -
21D TYR* 1.3 78.9 - - - +
23D ASP* 1.3 60.7 + - - +
25D ARG* 3.3 7.6 + - - +
26D GLU* 3.0 28.6 + - - +
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Residues in contact with ASP 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ARG* 2.9 31.2 + - - +
20D ALA 3.7 1.8 - - - +
22D SER* 1.3 73.9 - - - +
24D MET* 1.3 59.8 + - - +
26D GLU* 3.1 9.8 + - - +
27D ALA* 2.8 34.1 + - - +
36D PHE* 3.6 19.3 - - + -
39D ARG* 2.9 28.7 + - - +
103D LYS 4.7 3.1 - - - +
104D TYR* 3.7 22.4 - - + -
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Residues in contact with MET 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 4.6 22.8 - - + -
20D ALA 2.9 12.1 + - - +
21D TYR* 3.1 25.3 + - + +
23D ASP* 1.3 76.2 - - - +
25D ARG* 1.3 63.9 + - - +
27D ALA* 3.7 1.2 + - - +
28D ASN* 3.3 18.9 + - - -
29D TYR 4.6 1.2 + - - -
32D SER* 5.1 3.7 + - - +
33D ASP* 3.8 35.7 - - - +
36D PHE* 3.5 31.0 - - + -
37D HIS* 4.5 10.3 - - + -
62D ARG* 6.0 1.3 - - + -
66D GLN* 6.0 2.5 - - - +
203D P4C 3.4 26.9 - - - +
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Residues in contact with ARG 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN* 2.9 41.4 + - - +
67A ARG* 3.5 35.6 + - - +
68A PHE* 3.2 48.1 - - + +
21D TYR* 3.0 35.1 + - + +
22D SER* 3.4 11.9 - - - +
23D ASP 3.1 0.2 - - - -
24D MET* 1.3 77.5 - - - +
26D GLU* 1.3 63.8 + - - +
28D ASN* 3.5 14.9 + - - +
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Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D SER 3.0 15.5 + - - +
23D ASP* 3.1 13.7 + - - +
25D ARG* 1.3 77.6 - - - +
27D ALA* 1.3 61.7 + - - +
28D ASN* 3.3 4.9 + - - +
103D LYS* 2.6 31.7 + - - -
104D TYR* 3.1 16.2 + - - +
----------------------------------------------------------
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ASP 2.8 21.0 + - - +
24D MET 4.2 2.5 - - - +
26D GLU* 1.3 73.3 - - - +
28D ASN* 1.3 70.4 + - - +
29D TYR* 2.9 23.4 + - + +
36D PHE* 4.1 12.8 - - + -
100D LEU* 4.3 1.8 - - + -
101D PRO* 5.6 0.2 - - + -
104D TYR* 3.5 34.5 - - + -
----------------------------------------------------------
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Residues in contact with ASN 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D MET 3.3 13.0 + - - -
25D ARG 3.5 11.6 + - - +
26D GLU 3.2 5.6 - - - +
27D ALA* 1.3 76.9 - - - +
29D TYR* 1.3 58.2 + - - +
30D ILE* 4.0 5.0 + - - +
----------------------------------------------------------
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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