Contacts of the helix formed by residues 21 - 51 (chain A) in PDB entry 1AR4
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 GLY 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.2 27.3 - - - +
13A SER* 4.1 4.0 - - - -
16A GLU* 3.0 20.4 + - - +
19A ILE 3.8 0.2 + - - -
20A SER* 1.3 70.2 - - - +
22A GLU* 1.3 59.8 + - - +
24A MET* 3.7 0.9 - - - +
25A GLU* 3.0 40.7 + - - +
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 3.1 11.0 + - - +
21A GLY* 1.3 77.6 - - - +
23A ILE* 1.3 60.4 + - - +
25A GLU* 3.8 8.1 - - - +
26A LEU* 3.3 30.1 + - + +
169A LEU* 3.7 36.3 - - + +
172B LYS* 4.4 15.6 + - - -
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 4.6 11.0 - - + -
20A SER* 3.2 24.7 + - - +
22A GLU* 1.3 75.0 - - - +
24A MET* 1.3 55.9 + - - +
26A LEU* 3.3 3.3 + - - +
27A HIS* 2.7 48.3 + - + +
165A HIS 4.0 14.4 - - - +
166A ALA* 3.5 29.2 - - - +
167A PHE* 4.1 9.4 - - - -
169A LEU* 4.0 24.7 - - + -
170A GLN* 3.9 33.9 - - + +
171A TYR* 5.7 0.2 - - + -
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Residues in contact with MET 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.3 6.7 - - + -
10A TYR* 3.6 35.0 - - + +
12A TYR* 3.2 37.4 - - + +
15A LEU* 3.7 18.2 - - + -
19A ILE* 3.7 25.8 - - + +
20A SER 3.2 12.9 + - - +
21A GLY 3.7 2.2 - - - +
23A ILE* 1.3 78.4 - - - +
25A GLU* 1.3 56.2 - - - +
27A HIS* 3.9 5.3 - - - +
28A HIS* 2.9 35.0 + - - +
78A PHE* 5.9 0.7 - - - -
79A TRP* 4.0 26.9 - - + -
82A MET* 4.3 3.4 - - + -
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.5 38.3 - - + +
21A GLY 3.0 23.9 + - - +
22A GLU* 3.8 7.5 - - - +
23A ILE 3.2 0.2 - - - -
24A MET* 1.3 75.8 - - - +
26A LEU* 1.3 59.3 + - + +
29A ASP* 2.9 43.2 + - - +
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU* 3.3 17.4 + - + +
23A ILE* 3.3 3.9 + - - +
25A GLU* 1.3 80.6 - - + +
27A HIS* 1.3 63.6 + - - +
30A LYS* 3.0 41.5 + - + +
31A HIS* 3.2 7.6 + - + +
169A LEU* 3.7 23.8 - - + -
168B TYR* 3.9 17.9 - - + +
172B LYS* 3.7 29.2 - - + -
173B ASN* 3.5 23.3 - - - +
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Residues in contact with HIS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 2.7 33.7 + - + +
24A MET* 3.9 4.7 - - - +
26A LEU* 1.3 73.9 - - - +
28A HIS* 1.3 56.9 + - - +
31A HIS* 3.4 9.4 - - + +
32A HIS* 3.1 26.2 + - - +
75A HIS* 3.1 11.5 + + - -
78A PHE* 3.7 22.7 - + - -
79A TRP* 3.5 19.5 - + + -
161A ASP* 3.0 14.4 - - - -
165A HIS* 3.3 17.6 + + + +
166A ALA* 3.8 17.8 + - + -
202A MN 2.1 31.7 + - - -
168B TYR* 5.1 0.2 + - - -
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Residues in contact with HIS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.6 24.2 - - + +
6A PRO 2.6 31.9 + - - -
7A GLU* 4.1 13.1 + - - -
8A LEU* 3.4 39.6 + - + +
12A TYR* 3.9 8.2 + - + -
24A MET 2.9 19.0 + - - +
27A HIS* 1.3 76.6 - - - +
29A ASP* 1.3 87.7 + - - +
30A LYS 3.4 0.7 + - - -
32A HIS* 3.3 19.5 - - - +
33A LYS 3.5 5.5 + - - -
79A TRP* 3.4 27.2 + + + -
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Residues in contact with ASP 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.9 4.6 - - - +
12A TYR* 2.7 34.5 + - - -
25A GLU* 2.9 29.9 + - - +
28A HIS* 1.3 85.3 - - - +
30A LYS* 1.3 71.6 + - - +
33A LYS* 3.0 32.0 + - - +
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Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU 6.3 0.2 - - - -
26A LEU* 3.0 36.0 + - + +
29A ASP* 1.3 95.2 + - + +
31A HIS* 1.3 64.1 + - - +
32A HIS 3.5 0.2 - - - -
33A LYS* 3.7 24.2 + - - +
34A ALA* 3.1 23.7 + - - +
173B ASN* 3.9 34.1 - - + +
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Residues in contact with HIS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU 3.2 14.4 + - - -
27A HIS* 3.4 23.1 - - + +
30A LYS* 1.3 75.9 - - - +
32A HIS* 1.3 66.1 + - - +
34A ALA* 3.2 17.1 + - - +
35A TYR* 3.1 32.2 - + + -
75A HIS* 5.1 0.2 - - - +
165A HIS* 3.7 33.2 + + + +
164B GLU* 4.0 5.2 + - - -
168B TYR* 2.7 42.9 + + - -
173B ASN* 3.8 20.6 - - + +
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Residues in contact with HIS 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.5 9.6 - - + +
6A PRO* 3.7 17.9 - - + +
27A HIS 3.1 13.7 + - - +
28A HIS* 3.3 16.4 + - - +
30A LYS 3.5 0.2 - - - -
31A HIS* 1.3 72.6 - - - +
33A LYS* 1.3 67.4 + - - +
35A TYR* 3.0 17.6 + + - +
36A VAL* 3.1 10.9 + - + +
71A GLY 4.4 1.3 - - - -
72A HIS* 3.0 41.7 + + - -
75A HIS* 3.7 13.8 - - + +
76A SER* 3.5 24.5 - - - -
79A TRP* 2.9 31.1 + - + -
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Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.0 25.3 - - + +
28A HIS 3.5 3.8 + - - -
29A ASP 3.0 27.9 + - - +
30A LYS* 3.9 27.2 - - - +
31A HIS 3.3 0.4 - - - -
32A HIS* 1.3 76.9 - - - +
34A ALA* 1.3 57.7 + - - +
36A VAL* 3.2 4.8 + - + +
37A ASP* 3.0 45.9 + - - +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LYS 3.1 14.0 + - - +
31A HIS* 3.3 13.0 - - + +
32A HIS 3.1 0.6 - - - -
33A LYS* 1.3 79.7 - - - +
35A TYR* 1.3 63.1 + - + +
37A ASP* 3.6 7.2 + - - +
38A GLY* 2.9 24.9 + - - -
68A ASN* 3.9 3.2 - - - +
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Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 3.1 34.6 + + + -
32A HIS* 3.0 8.5 + + - +
34A ALA* 1.3 77.4 - - + +
36A VAL* 1.3 60.0 + - - +
38A GLY 3.3 0.3 + - - -
39A ALA* 2.9 29.8 + - - +
67A PHE* 3.9 17.3 - + - -
68A ASN* 3.4 42.9 - - - +
71A GLY* 4.0 6.3 - - - -
72A HIS* 3.9 9.2 - - - +
75A HIS* 3.3 36.1 - + - -
146A HIS* 3.1 28.6 + + - -
163A TRP* 4.0 8.0 - - - -
165A HIS* 3.9 17.5 - - - -
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 3.5 34.7 - - + +
4A THR* 3.9 7.4 - - - -
5A LEU* 4.0 21.1 - - + +
32A HIS* 3.1 18.7 + - + +
33A LYS* 3.2 7.8 + - - +
35A TYR* 1.3 76.7 - - - +
37A ASP* 1.3 67.6 + - - +
39A ALA* 3.3 4.9 + - - +
40A ASN* 3.1 30.7 + - - +
72A HIS* 3.7 32.3 - - + +
----------------------------------------------------------
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Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS* 3.0 41.0 + - - +
34A ALA* 3.9 6.7 - - - +
36A VAL* 1.3 80.8 - - - +
38A GLY* 1.3 57.8 + - - +
40A ASN* 3.5 8.4 + - - +
41A THR* 2.9 33.1 + - - +
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA 2.9 13.8 + - - -
36A VAL 3.3 0.2 - - - -
37A ASP* 1.3 76.3 - - - +
39A ALA* 1.3 58.7 + - - +
41A THR* 3.5 6.2 + - - -
42A ALA* 3.1 27.7 + - - +
64A ASP* 5.2 0.7 - - - +
68A ASN* 3.7 28.9 + - - -
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 3.5 27.0 - - + -
35A TYR 2.9 17.4 + - - +
36A VAL* 3.7 3.4 - - - +
38A GLY* 1.3 73.4 - - - +
40A ASN* 1.3 65.9 + - - +
42A ALA* 3.4 7.6 + - - +
43A LEU* 3.2 26.2 + - - +
65A LEU* 4.3 3.8 - - + +
68A ASN* 3.4 5.1 - - - +
69A LEU* 4.0 26.2 - - + +
72A HIS* 5.4 1.3 - - + -
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Residues in contact with ASN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA* 3.3 18.5 - - + +
2A VAL* 3.4 10.0 + - - +
3A TYR* 2.9 51.6 + - - -
36A VAL* 3.1 27.2 + - - +
37A ASP* 3.8 8.7 + - - +
39A ALA* 1.3 77.8 - - - +
41A THR* 1.3 61.4 + - - +
43A LEU* 3.4 6.8 + - - +
44A ASP* 3.1 32.5 + - - +
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 2.9 22.1 + - - +
38A GLY* 3.8 7.4 - - - -
40A ASN* 1.3 75.1 - - - +
42A ALA* 1.3 59.8 + - - +
44A ASP* 3.2 9.0 + - + +
45A LYS* 2.9 50.1 + - + +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY 3.1 19.0 + - - +
39A ALA 3.6 5.4 - - - +
41A THR* 1.3 77.3 - - - +
43A LEU* 1.3 56.9 + - - +
45A LYS* 3.4 7.4 + - - +
46A LEU* 3.0 34.8 + - - +
61A LEU* 4.2 9.8 - - - +
64A ASP* 4.2 8.7 - - + -
65A LEU* 3.8 38.1 - - + +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 3.8 30.5 - - + -
3A TYR* 3.4 33.4 - - + +
39A ALA 3.2 10.8 + - - +
40A ASN* 3.7 8.1 - - - +
41A THR 3.2 0.2 - - - -
42A ALA* 1.3 76.5 - - - +
44A ASP* 1.3 61.0 + - - +
46A LEU* 3.2 10.2 + - + +
47A ALA* 2.9 29.0 + - - +
50A ARG* 5.2 1.2 + - - -
65A LEU* 4.1 26.7 - - + -
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Residues in contact with ASP 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASN* 3.1 21.6 + - - +
41A THR* 3.2 11.0 + - - +
43A LEU* 1.3 77.1 - - - +
45A LYS* 1.3 63.3 + - + +
47A ALA* 3.3 9.1 + - - +
48A GLU* 3.1 27.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 2.9 36.8 + - + +
42A ALA* 3.6 3.1 - - - +
43A LEU 3.2 0.2 - - - -
44A ASP* 1.3 78.3 - - + +
46A LEU* 1.3 60.3 + - - +
48A GLU* 3.4 27.8 + - - +
49A ALA* 3.0 27.4 + - - +
61A LEU* 3.6 34.2 - - + +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA 3.0 23.7 + - - +
43A LEU* 3.6 12.6 - - + +
45A LYS* 1.3 75.2 - - - +
47A ALA* 1.3 62.9 + - - +
49A ALA* 3.3 7.6 + - + +
50A ARG* 3.2 41.0 + - - +
55A PHE* 5.0 2.2 - - + -
58A ILE* 4.0 22.2 - - + -
61A LEU* 3.8 30.7 - - + +
62A GLU* 4.8 8.7 - - - +
65A LEU* 3.8 31.4 - - + -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU 2.9 12.9 + - - +
44A ASP* 3.4 12.8 - - - +
45A LYS 3.2 0.2 - - - -
46A LEU* 1.3 77.3 - - - +
48A GLU* 1.3 61.5 + - - +
50A ARG* 3.2 27.7 + - - +
51A ASP* 3.1 30.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP 3.1 16.1 + - - +
45A LYS* 3.5 29.6 + - - +
46A LEU 3.4 0.2 - - - -
47A ALA* 1.3 76.0 - - - +
49A ALA* 1.3 63.8 + - - +
51A ASP* 3.3 9.5 + - + +
52A LYS* 3.1 58.1 + - + +
----------------------------------------------------------
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS 3.0 18.2 + - - +
46A LEU* 3.5 11.0 - - + +
47A ALA 3.2 0.4 - - - -
48A GLU* 1.3 77.8 - - - +
50A ARG* 1.3 56.6 + - - +
53A ALA* 2.9 7.6 + - - -
54A ASP* 2.9 50.4 + - - +
55A PHE* 3.9 19.6 - - + -
61A LEU* 4.6 10.8 - - + -
----------------------------------------------------------
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU 5.2 1.0 + - - -
46A LEU* 3.2 28.7 + - - +
47A ALA* 3.5 30.9 + - - +
48A GLU 3.2 0.2 - - - -
49A ALA* 1.3 75.5 - - - +
51A ASP* 1.3 67.7 + - - +
53A ALA* 3.2 12.5 + - - +
55A PHE* 3.8 26.3 - - + -
----------------------------------------------------------
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Residues in contact with ASP 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 3.1 24.0 + - - +
48A GLU* 3.3 11.7 + - + +
50A ARG* 1.3 80.0 - - - +
52A LYS* 1.3 63.5 + - + +
53A ALA* 3.7 0.9 + - - +
----------------------------------------------------------
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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