Contacts of the helix formed by residues 28 - 61 (chain A) in PDB entry 3P0G
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 28 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 3.3 39.6 + - - +
24A VAL* 3.7 18.6 - - - +
25A THR* 3.5 27.0 + - - +
27A GLN* 1.4 75.4 - - - +
29A ASP* 1.3 82.0 + - - +
31A VAL* 3.9 11.9 - - - +
32A TRP* 3.8 30.2 + - - +
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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
----------------------------------------------------------
24A VAL* 5.3 1.0 - - - +
25A THR 2.9 21.7 - - - +
26A GLN* 3.0 29.7 - - - +
28A ARG* 1.3 91.1 + - - +
30A GLU* 1.4 55.2 + - - +
31A VAL 2.9 10.6 + - - -
32A TRP* 3.2 5.4 + - - +
33A VAL* 3.2 30.5 + - + +
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLN 4.9 4.6 - - - +
27A GLN* 2.9 35.5 + - - +
29A ASP* 1.4 75.6 + - - +
31A VAL* 1.3 59.7 + - - +
33A VAL* 4.3 15.3 - - + -
34A VAL* 3.4 24.1 - - + +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 3.8 27.1 - - - +
28A ARG* 3.9 13.7 - - - +
29A ASP 2.9 0.4 + - - -
30A GLU* 1.3 80.7 - - - +
32A TRP* 1.4 56.6 + - - +
33A VAL 3.1 1.6 - - - -
34A VAL* 3.1 5.0 + - - +
35A GLY* 2.8 32.4 + - - -
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Residues in contact with TRP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.8 23.5 + - - +
29A ASP* 3.2 6.8 + - - +
31A VAL* 1.4 77.8 - - - +
33A VAL* 1.4 68.9 + - + +
35A GLY* 3.8 2.9 - - - +
36A MET* 2.9 72.6 + - + +
94A ILE* 6.1 6.3 - - + -
95A LEU* 6.1 1.8 - - + -
97A LYS* 5.8 6.1 - - - -
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASP* 3.2 20.1 + - + +
30A GLU* 4.3 12.1 - - + +
31A VAL 3.1 0.2 - - - -
32A TRP* 1.4 89.7 - - + +
34A VAL* 1.4 57.8 + - + +
36A MET* 3.4 0.4 + - - -
37A GLY* 2.7 30.8 + - - -
95A LEU* 3.3 45.3 - - + +
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 3.4 20.6 - - + +
31A VAL* 3.1 8.3 + - - +
33A VAL* 1.4 78.0 - - + +
35A GLY* 1.3 59.5 + - - +
37A GLY* 3.8 2.6 - - - +
38A ILE* 3.1 40.6 + - + +
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Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL 2.8 15.7 + - - -
32A TRP* 3.8 3.8 - - - -
34A VAL* 1.3 76.3 - - - +
36A MET* 1.4 64.3 + - - +
38A ILE* 4.0 6.4 - - - +
39A VAL* 3.2 27.7 + - - +
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Residues in contact with MET 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TRP* 2.9 66.7 + - + +
33A VAL* 3.9 3.8 - - - +
35A GLY* 1.4 75.4 - - - +
37A GLY* 1.3 53.9 + - - +
39A VAL* 3.0 18.2 + - + +
40A MET* 2.9 50.8 + - + +
94A ILE* 6.4 0.2 - - + -
95A LEU* 4.3 10.3 - - + -
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Residues in contact with GLY 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL 2.7 22.1 + - - -
34A VAL* 3.8 3.8 - - - -
35A GLY 3.4 0.2 - - - -
36A MET* 1.3 73.0 - - - +
38A ILE* 1.3 59.8 + - - +
40A MET* 4.0 4.6 - - - +
41A SER* 3.4 22.2 + - - -
91A ALA* 6.0 0.2 - - - +
95A LEU* 3.7 24.6 - - - +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.1 29.1 + - + +
35A GLY* 4.0 8.5 - - - +
36A MET 3.3 0.2 - - - -
37A GLY* 1.3 75.8 - - - +
39A VAL* 1.4 67.0 + - + +
40A MET 3.2 0.7 - - - -
41A SER* 3.1 9.0 + - - +
42A LEU* 3.0 44.3 + - + +
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY 3.2 17.7 + - - +
36A MET* 3.0 20.7 + - + +
38A ILE* 1.4 79.4 - - + +
40A MET* 1.4 62.0 + - + +
42A LEU* 3.2 29.9 + - + +
43A ILE* 3.0 33.7 + - + +
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Residues in contact with MET 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A MET* 2.9 28.1 + - + +
37A GLY 4.0 5.2 - - - +
39A VAL* 1.4 74.4 - - + +
41A SER* 1.3 56.8 + - - +
43A ILE* 3.0 16.4 + - + +
44A VAL* 3.0 29.8 + - - +
87A VAL* 5.0 1.9 - - + +
91A ALA* 3.6 36.1 - - + +
94A ILE* 3.8 38.6 - - + -
95A LEU* 4.1 20.2 - - + -
313A TRP* 3.6 25.8 - - + -
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY 3.4 14.9 + - - -
38A ILE* 3.1 12.5 + - - -
40A MET* 1.3 76.6 - - - +
42A LEU* 1.4 58.9 + - - +
44A VAL* 3.5 17.7 - - - +
45A LEU* 3.4 28.3 - - - +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 3.0 28.3 + - + +
39A VAL* 3.3 30.3 - - + +
40A MET 3.1 0.4 + - - -
41A SER* 1.4 73.5 - - - +
43A ILE* 1.4 56.9 + - + +
45A LEU* 3.1 6.7 + - - +
46A ALA* 2.9 35.9 + - - +
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.0 37.9 - - + +
40A MET* 3.3 12.3 - - + +
42A LEU* 1.4 75.0 - - + +
44A VAL* 1.3 53.3 + - - +
45A LEU 3.2 0.2 + - - -
46A ALA* 3.3 7.1 + - - +
47A ILE* 2.9 56.2 + - + +
87A VAL* 4.4 11.4 - - + -
313A TRP* 4.7 17.3 - - + -
316A TYR* 5.2 0.9 - - + -
317A VAL* 3.5 36.1 - - + +
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET 3.0 10.9 + - - +
41A SER* 3.5 28.0 - - - +
43A ILE* 1.3 75.2 - - - +
45A LEU* 1.3 64.8 + - + +
47A ILE* 4.1 4.7 - - - +
48A VAL* 3.4 30.1 + - - +
83A GLY 3.2 25.6 - - - +
87A VAL* 3.8 15.5 - - + -
88A PRO* 3.6 33.9 - - + -
91A ALA* 6.2 0.7 - - + -
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 3.4 18.6 - - - +
42A LEU* 3.1 10.9 + - - +
44A VAL* 1.3 81.5 - - + +
46A ALA* 1.4 58.5 + - - +
47A ILE 3.3 0.2 - - - -
48A VAL* 3.3 4.0 + - + +
49A PHE* 2.7 46.8 + - + +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU 2.9 17.0 + - - +
43A ILE* 3.6 7.4 - - - +
45A LEU* 1.4 71.6 - - - +
47A ILE* 1.4 65.5 + - + +
49A PHE* 4.4 4.4 - - - +
50A GLY* 3.3 20.8 + - - -
320A GLY* 4.4 14.5 - - - +
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 2.9 40.5 + - + +
44A VAL 4.2 0.9 - - - +
46A ALA* 1.4 76.9 - - + +
48A VAL* 1.4 60.6 + - - +
51A ASN* 2.8 30.2 + - - +
79A ASP 2.9 29.7 - - - +
80A LEU* 4.8 0.2 - - - -
82A MET* 5.1 0.2 - - + -
83A GLY* 3.5 20.4 - - - +
87A VAL* 4.0 19.1 - - + -
316A TYR 3.2 24.5 - - - +
317A VAL* 4.7 1.3 - - - +
319A SER* 4.2 8.1 - - - -
320A GLY* 3.9 24.0 - - - +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL 3.4 18.2 + - - +
45A LEU* 3.3 5.6 + - - +
47A ILE* 1.4 74.3 - - - +
49A PHE* 1.4 57.0 + - - +
51A ASN 3.2 1.7 + - - -
52A VAL* 2.8 43.2 + - + +
80A LEU* 3.8 19.6 - - + +
83A GLY 3.4 20.4 - - - +
84A LEU* 3.7 28.7 - - + -
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Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 2.7 31.3 + - + +
46A ALA* 4.4 3.6 - - - +
48A VAL* 1.4 73.3 - - - +
50A GLY* 1.3 62.0 + - - +
52A VAL* 3.5 7.9 + - + +
53A LEU* 3.1 69.7 + - + +
340A LEU* 3.7 21.3 - - + -
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Residues in contact with GLY 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 3.3 15.2 + - - -
47A ILE 4.4 0.2 - - - -
49A PHE* 1.3 83.2 - - - +
51A ASN* 1.3 56.6 + - - +
53A LEU* 3.9 4.3 - - - +
54A VAL* 3.0 32.9 + - - +
320A GLY 5.6 0.7 - - - -
323A PRO* 3.5 21.1 - - - +
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Residues in contact with ASN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 2.8 25.6 + - - +
48A VAL 3.2 2.6 + - - +
50A GLY* 1.3 74.8 - - - +
52A VAL* 1.3 58.7 + - - +
53A LEU 3.2 1.6 - - - -
54A VAL* 4.0 4.1 - - - +
55A ILE* 3.0 38.8 + - - +
76A ALA* 3.3 35.6 - - - +
79A ASP* 3.3 23.2 - - - +
80A LEU* 4.0 11.0 - - + -
319A SER 3.2 23.0 + - - -
322A ASN* 5.2 0.5 - - - +
323A PRO* 3.5 17.7 - - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 2.8 23.6 + - + +
49A PHE* 4.0 11.4 - - + +
51A ASN* 1.3 75.7 - - - +
53A LEU* 1.3 66.8 - - + +
55A ILE* 4.6 4.1 - - - +
56A THR* 2.8 32.0 + - - +
80A LEU* 3.9 25.7 - - + +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.1 51.9 + - + +
50A GLY* 3.9 6.1 - - - +
51A ASN 3.2 0.2 - - - -
52A VAL* 1.3 84.4 - - + +
54A VAL* 1.3 59.6 + - - +
56A THR* 3.6 2.4 + - - -
57A ALA* 3.0 31.0 + - - +
336A PHE* 3.3 27.7 - - + +
339A LEU* 4.0 12.2 - - + +
340A LEU* 3.7 36.3 - - + -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLY 3.0 23.8 + - - +
51A ASN* 3.4 6.5 + - - +
53A LEU* 1.3 77.0 - - - +
55A ILE* 1.4 61.6 + - - +
57A ALA* 3.4 3.3 + - - +
58A ILE* 3.2 33.8 + - + +
72A ILE* 3.9 11.7 - - + -
76A ALA* 3.9 19.3 - - + -
323A PRO* 3.7 13.9 - - + -
327A CYS* 3.3 37.0 - - - -
332A PHE* 4.4 0.9 - - + -
336A PHE* 3.6 18.4 - - + -
----------------------------------------------------------
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASN 3.0 22.5 + - - +
52A VAL* 4.6 4.0 - - - +
54A VAL* 1.4 75.7 - - - +
56A THR* 1.4 56.3 + - - +
58A ILE* 3.5 5.2 + - - +
59A ALA* 3.0 30.5 + - + +
73A THR* 4.6 16.3 - - + +
76A ALA* 3.5 34.8 - - + +
77A CYS* 3.9 21.5 - - - -
80A LEU* 4.0 21.5 - - + -
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Residues in contact with THR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 2.8 23.1 + - - +
53A LEU* 4.0 2.9 - - - -
55A ILE* 1.4 74.6 - - - +
57A ALA* 1.4 56.4 + - - +
59A ALA* 4.1 5.6 - - - -
60A LYS* 2.7 57.5 + - + +
339A LEU* 3.9 22.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU 3.0 19.7 + - - +
54A VAL 3.4 6.5 - - - +
56A THR* 1.4 74.1 - - - +
58A ILE* 1.4 57.4 + - - +
61A PHE* 2.9 35.4 + - - -
64A LEU* 3.5 19.9 - - + +
332A PHE* 4.4 1.6 - - + -
335A ALA* 4.2 5.6 - - + -
336A PHE* 3.7 21.1 - - + -
339A LEU* 3.7 16.5 - - + +
----------------------------------------------------------
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.2 27.6 + - + +
55A ILE* 4.1 3.6 - - - +
57A ALA* 1.4 73.2 - - - +
59A ALA* 1.3 57.5 + - - +
61A PHE 3.3 4.3 - - - +
64A LEU* 3.8 29.2 - - + +
65A GLN* 2.4 41.1 + - + +
69A ASN* 3.5 25.6 - - + +
70A TYR* 6.0 0.7 - - + -
72A ILE* 4.3 4.9 - - + -
73A THR* 3.8 23.8 - - + +
332A PHE* 3.8 29.6 - - + -
----------------------------------------------------------
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.0 23.4 + - + +
56A THR* 3.3 8.7 + - - +
58A ILE* 1.3 77.5 - - - +
60A LYS* 1.4 63.0 + - + +
65A GLN* 4.7 3.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 2.7 41.9 + - + +
59A ALA* 1.4 79.1 - - + +
61A PHE* 1.3 72.7 + - + +
62A GLU 3.9 1.4 + - - -
339A LEU* 4.4 10.8 - - + -
----------------------------------------------------------
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Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 2.9 20.4 + - - +
58A ILE 3.3 16.3 - - - +
59A ALA 5.3 0.2 - - - -
60A LYS* 1.3 81.7 - - + +
62A GLU* 1.3 64.7 + - - +
63A ARG* 3.5 5.4 - - + +
64A LEU* 3.5 21.9 + - + +
65A GLN* 3.5 4.1 + - - -
331A ASP 5.7 0.2 - - - +
334A ILE* 5.9 3.1 - - + -
335A ALA* 3.4 37.7 - - + -
338A GLU* 3.2 47.8 - - + -
339A LEU* 3.6 23.6 - - + -
----------------------------------------------------------
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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