Contacts of the helix formed by residues 1 - 28 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 4.1 20.2 - - + +
18A TRP* 3.9 22.9 - - + +
0C MET* 1.3 78.4 - - - +
2C SER* 1.3 70.9 + - - +
4C PHE* 3.3 2.0 + - - +
5C SER* 2.7 42.4 + - - +
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Residues in contact with SER 2 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C MET 5.3 0.2 - - - -
1C ARG* 1.3 93.8 - - - +
3C PHE* 1.3 59.0 + - - +
5C SER* 3.5 8.0 - - - -
6C PHE* 2.9 31.5 + - - +
57D ALA* 5.9 1.4 - - - +
202D P4C 3.1 27.4 + - - -
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Residues in contact with PHE 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 5.2 6.1 - + - -
0C MET* 3.2 36.0 + - + +
1C ARG 3.2 0.4 - - - -
2C SER* 1.3 85.0 + - - +
4C PHE* 1.3 75.7 + + - +
6C PHE* 3.5 3.1 + - - +
7C LEU* 3.3 46.9 + - + +
10D ALA* 4.7 7.6 - - + -
11D PHE* 4.7 12.8 - + - -
14D ALA* 5.2 4.5 - - + -
53D TRP* 3.5 44.7 - + - -
54D ALA* 3.9 24.0 - - + -
57D ALA* 3.7 29.4 - - + -
58D ILE* 5.8 1.3 - - + -
202D P4C 4.4 1.3 - - - -
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Residues in contact with PHE 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.3 44.7 - + - +
14A ALA* 3.5 35.9 - - + -
15A ARG* 3.8 20.5 - - + +
18A TRP* 5.3 3.1 - + + -
58A ILE* 5.1 3.1 - - + -
0B MET* 4.8 17.5 - - + -
3B PHE* 4.7 8.3 - + - -
4B PHE* 5.0 5.4 - + - -
0C MET* 3.1 58.4 + - + +
1C ARG* 5.2 0.4 - - - -
3C PHE* 1.3 89.3 - + - +
5C SER* 1.3 59.7 + - - +
7C LEU* 3.7 3.8 - - - +
8C GLY* 2.9 27.0 + - - -
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Residues in contact with SER 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.7 22.6 + - - +
1C ARG* 2.7 30.0 + - - +
2C SER* 3.5 11.4 - - - -
3C PHE 3.2 0.2 - - - -
4C PHE* 1.3 72.7 - - - +
6C PHE* 1.3 62.4 + - - +
8C GLY* 3.3 2.1 + - - -
9C GLU* 3.0 40.7 + - - +
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Residues in contact with PHE 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER 2.9 17.0 + - - +
3C PHE 3.9 4.0 - - - +
5C SER* 1.3 76.0 - - - +
7C LEU* 1.3 66.9 + - + +
9C GLU* 3.4 12.3 + - - +
10C ALA* 3.1 20.1 + - + +
49C PRO* 3.9 12.3 - - + -
50C GLY* 3.3 28.9 - - - -
53C TRP* 3.7 39.3 - + + -
202C P4C 4.0 23.3 - - - -
6D PHE* 4.7 8.5 - + - -
53D TRP* 3.8 26.2 - + + -
202D P4C 3.9 31.9 - - - +
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Residues in contact with LEU 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.5 40.8 - - + -
3C PHE* 3.3 42.5 + - + +
4C PHE 3.7 6.1 - - - +
5C SER 3.2 0.4 - - - -
6C PHE* 1.3 78.6 - - + +
8C GLY* 1.3 65.8 + - - +
10C ALA* 3.2 5.7 + - + +
11C PHE* 3.1 34.0 + - + -
7D LEU* 3.7 30.7 - - + -
10D ALA* 5.9 0.7 - - + -
11D PHE* 4.0 12.3 - - + -
53D TRP* 4.1 17.9 - - + -
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Residues in contact with GLY 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY 5.1 3.1 - - - -
11A PHE* 4.0 13.6 - - - +
12A ASP* 4.7 12.6 - - - -
15A ARG* 6.2 0.4 - - - -
4C PHE 2.9 16.8 + - - -
5C SER* 3.3 1.8 + - - -
7C LEU* 1.3 76.0 - - - +
9C GLU* 1.3 56.7 + - - +
11C PHE* 3.3 4.4 + - - +
12C ASP* 2.9 39.2 + - - +
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Residues in contact with GLU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C SER* 3.0 31.1 + - - +
6C PHE* 3.6 14.2 - - - +
7C LEU 3.2 0.2 - - - -
8C GLY* 1.3 76.9 - - - +
10C ALA* 1.3 51.9 + - - +
12C ASP* 3.7 2.3 - - - +
13C GLY* 2.7 33.8 + - - -
47C ARG* 3.2 34.4 - - + +
48C GLY* 4.1 0.3 - - - -
49C PRO* 3.5 17.1 - - - +
50C GLY* 3.1 25.7 + - - -
51C GLY* 3.7 10.0 - - - +
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Residues in contact with ALA 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE 3.1 13.8 + - - +
7C LEU* 3.2 11.0 + - + +
9C GLU* 1.3 75.4 - - - +
11C PHE* 1.3 63.3 + - + +
14C ALA* 2.8 25.8 + - - +
50C GLY 3.2 22.6 - - - +
53C TRP* 3.9 25.8 - - + -
54C ALA* 3.2 12.0 - - + +
3D PHE* 4.7 6.0 - - + -
7D LEU* 5.9 0.4 - - + -
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Residues in contact with PHE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.7 42.4 - + - +
7A LEU* 3.9 15.7 - - + -
8A GLY* 3.9 8.1 - - - +
11A PHE* 3.3 39.5 - + - -
11B PHE* 3.3 39.5 - + - -
7C LEU* 3.1 29.7 + - + +
8C GLY 4.0 2.0 - - - +
10C ALA* 1.3 81.0 - - + +
12C ASP* 1.3 63.3 + - - +
14C ALA* 4.2 2.5 - - + -
15C ARG* 3.0 26.7 + - - +
3D PHE* 4.6 8.7 - + - -
7D LEU* 4.0 21.1 - - + -
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Residues in contact with ASP 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY* 3.9 12.8 - - - -
12A ASP* 4.3 15.6 - - - +
8C GLY* 2.9 22.3 + - - +
9C GLU* 3.9 2.2 - - - +
11C PHE* 1.3 74.0 - - - +
13C GLY* 1.3 60.7 + - - +
15C ARG* 3.1 33.2 + - - +
16C ASP* 2.9 32.7 + - - -
47C ARG* 3.5 37.4 + - - +
201C SO4 4.2 1.6 + - - -
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Residues in contact with GLY 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLU 2.7 22.5 + - - -
10C ALA 3.7 1.8 - - - -
12C ASP* 1.3 71.1 - - - +
14C ALA* 1.3 64.0 + - - +
16C ASP* 3.1 4.5 + - - +
17C MET* 3.0 25.9 + - - +
44C ALA* 3.6 26.9 - - - +
47C ARG* 4.0 2.4 - - - +
51C GLY* 4.3 6.1 - - - -
54C ALA* 4.3 4.3 - - - -
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Residues in contact with ALA 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.6 40.8 - - + -
10C ALA 2.8 21.2 + - - +
11C PHE* 3.7 5.2 - - + +
13C GLY* 1.3 72.2 - - - +
15C ARG* 1.3 62.7 + - - +
17C MET* 3.2 3.5 + - - +
18C TRP* 3.1 22.7 + - - +
54C ALA* 3.9 3.2 - - + +
58C ILE* 3.6 23.1 - - + +
3D PHE* 5.2 3.8 - - + -
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Residues in contact with ARG 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ARG* 4.6 17.0 - - + +
4A PHE* 4.2 14.3 + - + -
5A SER* 3.1 38.7 + - - +
8A GLY* 5.0 1.8 - - - -
11C PHE 3.0 15.0 + - - +
12C ASP* 3.1 33.9 + - - +
13C GLY 3.2 0.2 - - - -
14C ALA* 1.3 75.4 - - - +
16C ASP* 1.3 58.9 + - - +
18C TRP* 3.4 5.9 + - - +
19C ARG* 3.0 29.9 + - + +
47C ARG* 3.7 8.1 - - - +
201C SO4 3.1 38.6 + - - -
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Residues in contact with ASP 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASP 2.9 13.6 + - - +
13C GLY 3.1 8.5 + - - +
15C ARG* 1.3 77.1 + - - +
17C MET* 1.3 64.2 + - - +
19C ARG* 3.0 27.9 + - - +
20C ALA* 3.1 20.8 + - - +
39C ARG* 4.9 0.5 + - - -
40C GLY* 4.2 5.8 - - - -
43C ASP* 3.2 40.2 - - + +
44C ALA 3.9 6.5 - - - +
47C ARG* 2.8 38.5 + - - +
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Residues in contact with MET 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLY 3.0 17.7 + - - +
14C ALA 3.2 6.9 + - - +
16C ASP* 1.3 73.5 - - - +
18C TRP* 1.3 64.4 + - - +
20C ALA* 3.2 10.7 + - - +
21C TYR 3.2 1.2 + - - -
37C HIS 5.3 0.2 - - - +
40C GLY* 3.4 29.4 - - - +
41C ASN* 3.6 14.4 - - - +
44C ALA* 4.2 2.0 - - + -
55C ALA* 4.0 20.4 - - - +
58C ILE* 3.8 40.8 - - + -
59C SER* 3.6 24.9 - - - +
62C ARG* 5.1 0.4 - - - +
204C P4C 3.2 42.3 - - - +
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Residues in contact with TRP 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 3.6 34.2 - - + +
1A ARG* 3.8 29.4 - - + +
4A PHE* 5.1 2.2 - - + -
61B ALA* 3.8 25.1 - - + -
64B ASN* 4.5 14.3 - - + +
65B ILE* 4.0 22.2 - - + -
14C ALA 3.1 15.9 + - - +
15C ARG* 3.8 6.7 - - - +
17C MET* 1.3 77.3 - - - +
19C ARG* 1.3 59.2 + - - +
21C TYR* 3.2 23.0 + + - +
22C SER* 2.8 39.5 + - - -
203C P4C 3.9 40.6 - - - -
204C P4C 4.2 4.7 + - - -
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Residues in contact with ARG 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ARG* 3.0 19.0 + - + +
16C ASP* 3.0 31.7 + - - +
17C MET 3.2 0.4 - - - -
18C TRP* 1.3 76.6 - - - +
20C ALA* 1.3 60.1 + - - +
22C SER* 4.1 8.5 - - - -
23C ASP* 2.8 48.2 + - - +
39C ARG* 3.6 32.2 - - - +
43C ASP* 4.0 14.3 + - - -
47C ARG* 5.1 2.6 - - - +
201C SO4 5.4 2.6 + - - -
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Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ASP 3.1 7.2 + - - +
17C MET 3.3 10.1 - - - +
19C ARG* 1.3 76.6 - - - +
21C TYR* 1.3 57.3 + - - +
23C ASP* 3.3 2.6 + - - +
24C MET* 2.9 28.7 + - - +
36C PHE* 3.5 32.5 - - + +
39C ARG* 3.5 14.9 - - - +
40C GLY* 3.6 21.1 - - - +
204C P4C 4.1 8.5 - - - -
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Residues in contact with TYR 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASN* 3.0 28.8 + - - -
65B ILE* 3.3 26.2 - - + +
68B PHE* 3.3 37.4 - + - +
17C MET 3.2 1.4 + - - -
18C TRP* 3.2 33.8 + + - +
20C ALA* 1.3 79.5 - - - +
22C SER* 1.3 66.1 + - - +
24C MET* 3.1 10.7 + - + +
25C ARG* 2.9 32.7 + - - +
203C P4C 3.5 36.6 - - - -
204C P4C 3.5 32.8 - - - +
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Residues in contact with SER 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASN* 5.9 1.4 + - - -
18C TRP* 2.8 40.1 + - - -
19C ARG* 3.8 10.8 - - - -
20C ALA 3.3 0.2 - - - -
21C TYR* 1.3 77.6 - - - +
23C ASP* 1.3 61.4 + - - +
25C ARG* 3.3 9.6 + - - +
26C GLU* 3.0 29.6 + - - +
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Residues in contact with ASP 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ARG* 2.8 36.7 + - - +
20C ALA 3.7 1.3 - - - +
22C SER* 1.3 70.4 - - - +
24C MET* 1.3 61.4 + - - +
26C GLU* 4.4 6.6 - - - +
27C ALA* 2.9 33.1 + - - +
36C PHE* 3.6 12.8 - - + -
39C ARG* 2.8 30.5 + - - +
103C LYS 4.8 2.8 - - - +
104C TYR* 3.6 29.4 - - + -
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Residues in contact with MET 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 4.2 23.9 - - + -
20C ALA 2.9 14.3 + - - +
21C TYR* 3.1 19.7 + - + +
23C ASP* 1.3 76.2 - - - +
25C ARG* 1.3 63.8 + - - +
27C ALA* 4.0 1.2 - - - +
28C ASN* 3.2 19.8 + - - -
29C TYR 4.6 1.6 + - - -
32C SER* 4.8 3.9 + - - +
33C ASP* 3.5 41.7 - - - +
36C PHE* 3.7 27.0 - - + -
37C HIS* 5.0 3.4 - - - +
66C GLN* 5.9 2.9 - - - +
203C P4C 4.4 7.4 - - - +
204C P4C 3.3 34.3 - - - +
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Residues in contact with ARG 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASN* 3.0 45.9 + - - +
67B ARG* 3.8 29.7 - - - +
68B PHE* 3.0 59.8 - - + +
21C TYR* 2.9 24.0 + - + +
22C SER* 3.4 13.2 - - - +
23C ASP 3.3 0.2 - - - -
24C MET* 1.3 79.2 - - - +
26C GLU* 1.3 62.4 + - - +
28C ASN* 3.5 13.0 + - - +
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C SER 3.0 16.6 + - - +
23C ASP* 3.8 8.9 - - - +
25C ARG* 1.3 78.6 - - - +
27C ALA* 1.3 61.3 + - - +
28C ASN* 3.3 5.0 + - - +
103C LYS* 2.8 34.4 + - - -
104C TYR* 2.8 17.2 + - - +
----------------------------------------------------------
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Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASP 2.9 18.8 + - - +
24C MET 4.1 2.7 - - - +
26C GLU* 1.3 76.8 - - - +
28C ASN* 1.3 70.8 + - - +
29C TYR* 3.0 24.6 + - + +
36C PHE* 4.2 11.4 - - + -
100C LEU* 4.3 2.0 - - + -
101C PRO* 5.6 0.7 - - + -
104C TYR* 3.6 31.4 - - + -
----------------------------------------------------------
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Residues in contact with ASN 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C MET 3.2 14.0 + - - -
25C ARG 3.5 8.3 + - - +
26C GLU 3.2 7.5 - - - +
27C ALA* 1.3 76.8 - - - +
29C TYR* 1.3 58.5 + - - +
30C ILE* 4.1 3.7 + - - +
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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