Contacts of the helix formed by residues 0 - 28 (chain A) 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 MET 0 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ARG* 1.3 67.9 + - - +
2A SER* 3.5 2.5 - - - -
3A PHE* 3.3 29.6 + - + +
4A PHE* 2.9 63.5 + - + -
57B ALA* 3.8 19.4 + - - +
58B ILE* 3.9 24.5 - - + -
60B ASP* 6.3 0.2 - - - +
61B ALA* 3.6 33.1 - - + +
18C TRP* 3.6 35.6 - - + +
203C P4C 3.8 22.0 - - - +
4D PHE* 4.9 7.0 - - + -
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Residues in contact with ARG 1 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 1.3 79.2 - - - +
2A SER* 1.3 78.6 + - - +
4A PHE* 3.7 3.2 - - - +
5A SER* 2.8 41.9 + - - +
15C ARG* 4.6 13.8 - - + -
18C TRP* 3.8 26.1 - - + +
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Residues in contact with SER 2 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 5.2 0.3 - - - -
1A ARG* 1.3 99.7 + - - +
3A PHE* 1.3 63.3 + - - +
5A SER* 3.8 7.4 - - - -
6A PHE* 3.0 30.8 + - - +
202B P4C 3.5 31.2 - - - +
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Residues in contact with PHE 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 3.5 26.6 - - + +
1A ARG 3.2 0.2 - - - -
2A SER* 1.3 85.2 + - - +
4A PHE* 1.3 92.9 + + - +
7A LEU* 3.3 43.6 + - + +
10B ALA* 4.8 4.9 - - + -
11B PHE* 4.5 14.8 - + - -
14B ALA* 5.2 2.5 - - + -
53B TRP* 3.5 46.5 - + - -
54B ALA* 4.1 22.2 - - + -
57B ALA* 3.7 31.4 - - + -
58B ILE* 5.7 1.3 - - + -
202B P4C 4.6 1.3 - - - -
4D PHE* 4.8 6.5 - + - -
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Residues in contact with PHE 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 2.9 57.6 + - + +
1A ARG 4.1 2.0 - - - +
3A PHE* 1.3 99.1 - + - +
5A SER* 1.3 59.3 + - - +
7A LEU* 3.8 4.9 - - + +
8A GLY* 2.8 25.6 + - - -
11C PHE* 3.7 40.9 - + - +
14C ALA* 3.6 40.6 - - + -
15C ARG* 4.2 9.9 + - + +
18C TRP* 5.1 2.7 - - + -
58C ILE* 5.1 6.1 - - + -
203C P4C 4.5 8.7 - - - -
0D MET* 5.4 4.5 - - + -
3D PHE* 5.2 3.6 - + - -
4D PHE* 4.9 13.7 - + - -
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Residues in contact with SER 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ARG* 2.8 28.6 + - - +
2A SER* 3.8 8.7 - - - -
4A PHE* 1.3 74.9 - - - +
6A PHE* 1.3 61.3 + - - +
8A GLY* 3.1 1.9 + - - -
9A GLU* 2.8 46.1 + - - +
15C ARG* 3.1 31.9 + - - +
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Residues in contact with PHE 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 3.0 18.9 + - - +
3A PHE 4.0 3.4 - - - +
5A SER* 1.3 75.8 - - - +
7A LEU* 1.3 63.5 + - + +
9A GLU* 3.3 11.5 + - - +
10A ALA* 2.9 24.8 + - + +
49A PRO* 3.8 15.9 - - + -
50A GLY* 3.6 26.0 - - - -
53A TRP* 3.7 46.9 - + + -
204A P4C 4.3 14.8 - - + -
6B PHE* 4.9 5.6 - + - -
53B TRP* 3.8 25.6 - + + -
202B P4C 3.7 34.1 - - - +
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 3.3 53.0 + - + +
4A PHE* 3.8 4.0 - - + +
5A SER 3.1 0.8 - - - -
6A PHE* 1.3 79.9 - - + +
8A GLY* 1.3 63.4 + - - +
10A ALA* 3.3 4.1 + - + +
11A PHE* 3.0 36.9 + - + -
7B LEU* 3.6 31.0 - - + -
10B ALA* 5.8 0.7 - - + -
11B PHE* 3.8 21.1 - - + -
53B TRP* 4.0 17.7 - - + -
11C PHE* 3.9 22.4 - - + -
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Residues in contact with GLY 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE 2.8 21.0 + - - -
5A SER* 3.1 2.2 + - - -
7A LEU* 1.3 73.7 - - - +
9A GLU* 1.3 58.3 + - - +
11A PHE* 3.5 2.9 + - - +
12A ASP* 3.0 38.2 + - - +
8C GLY* 5.1 3.4 - - - -
11C PHE* 3.9 10.2 - - - +
12C ASP* 3.9 17.7 - - - -
15C ARG* 5.0 1.1 - - - -
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Residues in contact with GLU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER* 2.8 30.7 + - - +
6A PHE* 3.6 9.7 - - - +
7A LEU 3.2 0.2 - - - -
8A GLY* 1.3 76.5 - - - +
10A ALA* 1.3 64.8 + - - +
11A PHE 3.2 0.2 - - - -
12A ASP* 4.6 2.2 - - - +
13A GLY 3.0 18.7 + - - -
47A ARG* 3.3 35.8 - - + +
48A GLY* 3.9 4.1 - - - -
49A PRO* 3.6 13.6 - - - +
50A GLY* 3.4 22.6 + - - +
51A GLY* 3.4 16.5 + - - +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 2.9 14.8 + - + +
7A LEU* 3.6 13.0 - - + +
9A GLU* 1.3 75.0 - - - +
11A PHE* 1.3 65.1 + - + +
14A ALA* 2.9 24.9 + - - +
50A GLY* 3.3 20.1 - - - +
53A TRP* 4.0 25.4 - - + -
54A ALA* 3.2 13.6 - - + +
3B PHE* 4.7 6.2 - - + -
7B LEU* 5.6 0.4 - - + -
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Residues in contact with PHE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.0 36.4 + - + +
8A GLY 4.3 0.2 - - - +
9A GLU 3.2 0.2 - - - -
10A ALA* 1.3 80.3 - - + +
12A ASP* 1.3 65.4 + - - +
13A GLY 3.3 0.7 - - - -
14A ALA* 3.9 2.9 - - + +
15A ARG* 3.1 25.3 + - - +
3B PHE* 4.7 5.6 - + - -
7B LEU* 3.9 17.3 - - + -
4C PHE* 3.3 46.9 - + - +
7C LEU* 3.5 22.7 - - + -
8C GLY* 4.0 11.2 - - - +
11C PHE* 3.3 34.5 - + - -
11D PHE* 3.4 31.0 - + - -
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Residues in contact with ASP 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY 3.0 25.0 + - - +
9A GLU* 4.1 2.9 - - - +
11A PHE* 1.3 75.7 - - - +
13A GLY* 1.3 58.6 + - - +
15A ARG* 3.2 26.3 + - - +
16A ASP* 2.9 32.9 + - - +
47A ARG* 3.6 38.5 + - + +
201A SO4 4.8 3.4 + - - -
8C GLY* 4.7 10.7 - - - -
12C ASP* 4.3 16.6 - - - +
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Residues in contact with GLY 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU 3.0 17.6 + - - -
10A ALA 3.8 1.3 - - - -
12A ASP* 1.3 74.7 - - - +
14A ALA* 1.3 58.0 + - - +
16A ASP* 3.0 3.6 + - - +
17A MET* 2.9 34.0 + - - +
44A ALA* 3.5 29.0 - - - +
47A ARG* 3.9 1.9 - - - +
51A GLY* 4.3 4.0 - - - -
54A ALA* 4.5 3.4 - - - -
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA 2.9 17.6 + - - +
11A PHE* 3.9 3.6 - - + +
12A ASP 3.4 0.2 - - - -
13A GLY* 1.3 74.6 - - - +
15A ARG* 1.3 62.5 + - - +
17A MET* 3.6 2.3 + - - +
18A TRP* 3.1 23.6 + - - +
54A ALA* 4.0 3.2 - - + +
58A ILE* 3.7 25.8 - - + +
3B PHE* 5.2 2.5 - - + -
4C PHE* 3.5 42.4 - - + -
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Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE 3.1 15.1 + - - +
12A ASP* 3.3 35.2 + - - +
14A ALA* 1.3 77.5 - - - +
16A ASP* 1.3 59.8 + - - +
18A TRP* 3.4 6.1 + - - +
19A ARG* 2.8 30.9 + - - +
47A ARG* 4.5 2.3 - - - +
201A SO4 3.2 38.9 + - - -
1C ARG* 4.1 21.1 - - + +
4C PHE* 3.8 17.5 - - + +
5C SER* 3.7 34.1 + - - +
8C GLY* 6.2 1.3 - - - -
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Residues in contact with ASP 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP 2.9 13.9 + - - +
13A GLY 3.0 7.2 + - - +
15A ARG* 1.3 75.7 + - - +
17A MET* 1.3 64.9 + - - +
19A ARG* 2.9 30.5 + - - +
20A ALA* 3.0 22.7 + - - +
39A ARG* 4.8 1.4 + - - -
40A GLY* 4.1 4.9 - - - +
43A ASP* 3.4 34.3 - - + +
44A ALA 3.9 6.5 - - - +
47A ARG* 2.7 43.1 + - - +
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Residues in contact with MET 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY 2.9 19.1 + - - +
14A ALA 3.8 4.5 - - - +
16A ASP* 1.3 75.0 - - - +
18A TRP* 1.3 63.0 + - - +
20A ALA* 3.2 6.7 + - + +
21A TYR* 3.2 19.1 + - - +
37A HIS* 5.3 1.6 - - - +
40A GLY* 3.4 31.4 - - - +
41A ASN* 3.6 26.9 - - - +
44A ALA* 4.4 0.9 - - + -
55A ALA* 4.1 21.1 - - - +
58A ILE* 3.9 39.7 - - + -
59A SER* 3.7 13.5 - - - +
62A ARG* 4.5 9.9 - - + +
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Residues in contact with TRP 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 3.1 18.8 + - - +
15A ARG* 3.8 6.7 - - - +
17A MET* 1.3 72.5 - - - +
19A ARG* 1.3 61.4 + - - +
21A TYR* 3.1 35.6 + + + +
22A SER* 2.9 44.2 + - - -
58A ILE* 5.7 0.2 - - - +
202A P4C 4.6 17.3 - - - -
0C MET* 3.5 45.1 - - + +
1C ARG* 3.9 26.5 - - + +
4C PHE* 5.3 1.8 - + + -
61D ALA* 3.8 30.1 - - + -
64D ASN* 4.6 13.2 - - + -
65D ILE* 4.5 12.6 - - + -
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Residues in contact with ARG 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 2.8 18.9 + - - +
16A ASP* 2.9 32.5 + - - +
18A TRP* 1.3 78.4 - - - +
20A ALA* 1.3 57.2 + - - +
22A SER* 3.7 7.1 - - - -
23A ASP* 2.9 40.1 + - - +
39A ARG* 3.6 20.4 - - - +
43A ASP* 3.4 24.2 + - - +
47A ARG* 5.0 2.6 - - - +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP 3.0 6.4 + - - +
17A MET* 3.4 10.5 - - + +
19A ARG* 1.3 77.9 - - - +
21A TYR* 1.3 56.2 + - - +
23A ASP 3.6 0.2 + - - -
24A MET* 2.9 29.9 + - - +
36A PHE* 3.5 34.0 - - + +
39A ARG* 3.4 16.5 - - - +
40A GLY* 3.6 22.0 - - - +
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Residues in contact with TYR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET 3.2 9.3 + - - +
18A TRP* 3.1 47.6 + + + +
20A ALA* 1.3 76.1 - - - +
22A SER* 1.3 70.5 + - - +
24A MET* 3.1 15.9 + - + +
25A ARG* 2.9 32.5 + - + +
202A P4C 3.7 43.3 - - - +
64D ASN* 2.8 32.0 + - - -
65D ILE* 3.3 22.7 - - + -
68D PHE* 3.6 24.0 - + - +
----------------------------------------------------------
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 2.9 42.7 + - - -
19A ARG* 3.7 7.6 - - - -
21A TYR* 1.3 81.2 - - - +
23A ASP* 1.3 61.5 + - - +
25A ARG* 3.4 6.6 + - - +
26A GLU* 3.0 30.0 + - - +
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 2.9 28.9 + - - +
20A ALA 3.9 1.6 - - - +
22A SER* 1.3 76.0 - - - +
24A MET* 1.3 57.0 + - - +
26A GLU* 3.1 9.7 + - - +
27A ALA* 2.7 37.6 + - - +
36A PHE* 3.8 19.3 - - + -
39A ARG* 2.9 30.0 + - - +
103A LYS 4.8 3.4 - - - +
104A TYR* 3.8 20.1 - - + -
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Residues in contact with MET 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 2.9 19.6 + - - +
21A TYR* 3.4 15.5 - - + +
23A ASP* 1.3 75.7 - - - +
25A ARG* 1.3 63.0 + - - +
27A ALA* 3.8 1.6 - - - +
28A ASN* 3.1 20.6 + - - -
29A TYR 4.6 1.7 + - - -
32A SER* 5.1 3.0 + - - +
33A ASP* 3.6 34.5 - - + -
36A PHE* 3.7 31.6 - - + -
37A HIS* 4.6 16.6 - - + -
66A GLN* 5.0 5.8 - - - +
202A P4C 4.1 19.7 - - - +
68D PHE* 4.2 26.2 - - + -
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 2.9 29.0 + - + +
22A SER* 3.8 6.3 - - - +
24A MET* 1.3 77.3 - - - +
26A GLU* 1.3 63.2 + - - +
28A ASN* 3.6 13.2 + - - +
64D ASN* 2.8 57.1 + - - +
67D ARG* 3.8 27.3 - - - +
68D PHE* 3.5 48.2 - - + +
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER 3.0 18.0 + - - +
23A ASP* 3.6 10.8 - - - +
25A ARG* 1.3 78.2 - - - +
27A ALA* 1.3 64.3 + - - +
28A ASN* 3.4 4.2 + - - +
103A LYS* 2.7 35.8 + - - -
104A TYR* 2.8 14.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP 2.7 20.6 + - - +
24A MET 3.8 4.5 - - - +
26A GLU* 1.3 73.4 - - - +
28A ASN* 1.3 70.4 + - - +
29A TYR* 3.1 18.3 + - + +
36A PHE* 4.0 17.9 - - + -
100A LEU* 4.4 1.6 - - + -
101A PRO* 5.7 0.2 - - + -
104A TYR* 3.6 31.6 + - + -
----------------------------------------------------------
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Residues in contact with ASN 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A MET 3.1 13.0 + - - -
25A ARG* 3.6 12.1 + - - +
26A GLU 3.2 5.2 - - - +
27A ALA* 1.3 78.3 - - - +
29A TYR* 1.3 58.5 + - - +
30A ILE* 4.1 4.8 + - - +
68D PHE* 6.3 1.3 - - - -
----------------------------------------------------------
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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