Contacts of the helix formed by residues 47 - 74 (chain A) in PDB entry 3GHG
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 SER 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A CYS 3.8 2.2 + - - -
46A PRO* 1.3 72.3 - - - +
48A GLY* 1.3 65.7 + - - +
49A CYS* 2.9 6.1 + - - +
50A ARG* 3.1 41.7 + - - +
51A MET* 3.3 8.4 + - - +
76B CYS* 4.0 17.6 - - - -
22C THR* 4.7 0.4 - - - -
47D SER* 5.4 12.6 - - - +
74E VAL 4.5 2.9 + - - -
76E CYS* 6.0 6.3 - - - +
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Residues in contact with GLY 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO 3.3 3.8 + - - -
47A SER* 1.3 70.7 - - - +
49A CYS* 1.3 50.8 + - - +
51A MET* 3.2 4.1 - - - +
52A LYS* 2.3 39.7 + - - +
76B CYS* 4.2 5.4 - - - +
77B PRO* 3.8 19.2 + - - -
82B LEU* 3.3 26.2 - - - +
22C THR* 3.9 6.2 - - - +
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Residues in contact with CYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 3.1 3.8 - - - +
48A GLY* 1.3 76.7 - - - +
50A ARG* 1.3 58.6 + - - +
52A LYS 3.3 0.2 + - - -
53A GLY 2.8 12.5 + - - -
61B ASP* 4.3 4.3 - - - +
62B ALA 2.8 36.4 + - - +
63B GLY 4.1 11.0 - - - +
74B VAL* 5.4 2.0 - - - -
75B LEU 3.7 7.6 - - - -
76B CYS* 2.0 53.3 - - - -
77B PRO* 3.7 7.7 - - - +
33D TRP* 4.8 17.3 - - + -
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 3.7 23.4 - - - +
47A SER* 3.1 27.1 + - - +
49A CYS* 1.3 77.2 - - - +
51A MET* 1.3 61.2 + - - +
53A GLY 3.2 1.2 + - - -
54A LEU* 2.9 37.5 + - + +
59B ALA* 3.9 11.9 - - - +
60B PRO 3.2 12.6 - - - +
61B ASP* 3.3 22.3 + - - +
71E ASP 3.1 25.1 - - - +
72E LEU* 3.8 7.9 - - - +
73E GLY* 3.2 26.0 - - - +
74E VAL* 3.5 24.9 + - - +
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Residues in contact with MET 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 3.7 34.5 - - + +
47A SER 3.3 11.6 + - - +
48A GLY* 3.1 9.1 + - - +
50A ARG* 1.3 76.4 - - - +
52A LYS* 1.3 57.6 + - - +
54A LEU* 2.9 13.7 + - + +
55A ILE* 2.5 44.6 + - + +
82B LEU* 3.7 16.8 - - + -
22C THR* 4.5 5.8 - - + +
25C ILE* 4.1 11.9 - - + -
26C ALA* 3.6 31.0 - - + +
29C LEU* 4.6 17.0 - - + -
72E LEU* 3.9 14.1 - - + -
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLY 2.3 30.9 + - - +
51A MET* 1.3 67.8 - - - +
53A GLY* 1.3 61.4 + - - +
54A LEU 3.5 0.2 + - - -
55A ILE* 3.9 3.0 - - + +
56A ASP* 2.9 44.2 + - - +
62B ALA* 3.3 33.2 - - + +
63B GLY* 3.6 12.3 - - - +
77B PRO* 3.7 13.0 - - + +
81B GLN* 4.2 20.6 + - - +
82B LEU* 3.4 22.1 - - + +
85B ALA* 4.8 9.6 - - + +
44D LYS* 5.1 4.6 - - - +
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Residues in contact with GLY 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A CYS 2.8 11.1 + - - -
50A ARG 3.5 4.7 - - - -
51A MET 3.1 0.4 - - - -
52A LYS* 1.3 77.4 - - - +
54A LEU* 1.3 59.0 + - - +
56A ASP* 4.0 2.5 + - - +
57A GLU* 3.4 16.8 + - - +
60B PRO* 3.5 30.9 - - - +
61B ASP 3.9 0.2 - - - -
62B ALA* 3.4 20.1 - - - +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 2.9 28.1 + - + +
51A MET* 3.7 20.4 - - + +
53A GLY* 1.3 75.2 - - - +
55A ILE* 1.3 65.8 + - - +
56A ASP 3.0 3.6 + - - -
57A GLU* 3.0 18.4 + - + +
58A VAL* 3.2 15.4 + - - +
60B PRO* 4.3 18.8 - - + +
29C LEU* 4.4 16.8 - - + +
71E ASP* 3.2 55.9 - - + +
72E LEU* 4.7 4.0 - - + +
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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 MET* 2.5 26.6 + - + +
52A LYS* 3.9 4.9 - - + +
54A LEU* 1.3 72.4 - - - +
56A ASP* 1.3 68.6 + - - +
58A VAL* 4.0 2.0 - - - +
59A ASN* 3.0 27.8 + - - +
82B LEU* 3.1 55.6 - - + +
85B ALA* 4.6 8.7 - - + -
86B LEU* 3.0 38.7 - - + +
89B GLN* 4.7 0.2 - - - +
25C ILE* 3.9 18.8 - - + -
29C LEU* 4.2 13.4 - - + +
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Residues in contact with ASP 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS* 2.9 36.7 + - - +
53A GLY* 4.3 3.1 - - - +
54A LEU 3.0 0.8 - - - -
55A ILE* 1.3 86.0 - - - +
57A GLU* 1.3 56.2 + - - +
58A VAL 3.0 2.6 + - - -
59A ASN* 3.1 4.7 + - - +
60A GLN* 2.7 39.6 + - + +
62B ALA* 4.3 7.0 - - + +
85B ALA* 5.4 2.4 - - - +
89B GLN* 4.4 8.8 - - - +
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLY 3.4 16.9 + - - +
54A LEU* 3.0 14.4 + - - +
56A ASP* 1.3 77.8 - - - +
58A VAL* 1.3 56.2 + - - +
60A GLN* 4.1 4.7 - - - -
61A ASP* 3.3 46.4 + - - +
60B PRO* 3.2 28.7 - - + +
71E ASP* 5.0 3.8 - - - +
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU 3.2 11.5 + - - +
55A ILE 4.0 5.8 - - - +
56A ASP 3.1 0.4 - - - -
57A GLU* 1.3 75.4 - - - +
59A ASN* 1.3 77.5 + - - +
60A GLN 3.1 4.2 + - - -
61A ASP* 3.2 3.9 + - - +
62A PHE* 2.9 64.3 + - + -
86B LEU* 5.4 1.3 - - + -
29C LEU* 4.7 17.5 - - + -
32C TYR* 4.4 8.5 - - + -
33C GLN* 3.9 20.9 - - + -
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Residues in contact with ASN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.0 13.2 + - - +
56A ASP* 3.1 5.8 + - - +
58A VAL* 1.3 93.0 - - - +
60A GLN* 1.3 57.0 + - - +
62A PHE* 4.1 6.3 - - - +
63A THR* 3.3 26.3 + - - +
86B LEU* 2.9 30.3 - - - +
89B GLN* 3.1 42.4 + - + +
93B ILE* 3.9 9.3 - - + +
32C TYR* 3.3 22.0 + - - -
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP* 2.7 20.1 + - + +
57A GLU* 4.3 4.5 - - - +
59A ASN* 1.3 75.8 - - - +
61A ASP* 1.3 75.7 + - - +
62A PHE 3.1 4.5 - - - -
63A THR* 2.6 36.5 + - - +
64A ASN* 2.8 36.2 + - - +
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 3.3 33.4 + - - +
58A VAL* 3.2 4.7 + - - +
60A GLN* 1.3 93.9 - - - +
62A PHE* 1.3 59.9 - - + +
63A THR 3.3 0.2 - - - -
64A ASN* 3.9 11.4 + - - +
65A ARG* 3.1 28.2 + - - +
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Residues in contact with PHE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 2.9 59.2 + - + +
59A ASN* 4.2 8.1 - - - +
60A GLN 3.1 0.2 - - - -
61A ASP* 1.3 81.9 - - + +
63A THR* 1.3 59.0 + - - +
65A ARG* 4.1 10.2 - - - +
66A ILE* 3.1 29.7 + - - +
93B ILE* 4.5 17.0 - - + +
32C TYR* 4.5 11.4 - + - -
33C GLN* 3.7 30.1 - - + -
36C VAL* 3.3 33.7 - - + -
37C ASP* 3.4 19.3 - - - -
40C LEU* 4.1 12.7 - - + +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASN 3.3 14.6 - - - +
60A GLN* 2.6 35.0 + - - +
62A PHE* 1.3 79.2 - - - +
64A ASN* 1.3 58.9 + - - +
65A ARG 3.4 0.2 - - - -
66A ILE* 3.2 23.0 - - + +
67A ASN* 3.1 28.9 + - - -
93B ILE* 4.6 17.5 - - + -
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Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 2.8 38.7 + - - +
61A ASP* 4.2 13.4 + - + +
63A THR* 1.3 75.8 + - - +
65A ARG* 1.3 64.8 + - - +
67A ASN* 3.6 8.2 + - - +
68A LYS* 3.4 33.8 + - - +
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP 3.1 19.2 + - - +
62A PHE* 4.1 13.3 - - - +
64A ASN* 1.3 79.5 - - - +
66A ILE* 1.3 62.2 + - - +
68A LYS* 3.1 8.6 + - - +
69A LEU* 2.9 25.4 + - + +
37C ASP* 3.1 33.9 + - - +
40C LEU* 3.8 35.1 + - + +
41C GLN* 5.0 5.1 - - - +
44C GLU* 2.7 40.1 + - - +
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE 3.1 12.8 + - - +
63A THR* 3.2 33.2 - - + +
65A ARG* 1.3 78.8 - - - +
67A ASN* 1.3 60.1 + - - +
69A LEU* 3.6 5.8 - - + +
70A LYS* 2.8 59.0 + - + +
93B ILE* 5.3 6.5 - - + +
96B SER* 4.0 21.1 - - - +
97B VAL* 4.6 15.9 - - + +
100B LEU* 3.7 26.9 - - + -
40C LEU* 5.0 11.8 - - + +
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Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.1 23.3 + - - +
64A ASN* 3.9 9.8 + - - +
65A ARG 3.2 1.0 - - - -
66A ILE* 1.3 83.5 - - - +
68A LYS* 1.3 56.7 + - - +
70A LYS* 3.4 26.2 + - - +
71A ASN* 3.2 30.9 + - - +
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN* 3.4 21.1 + - - +
65A ARG* 3.1 8.8 + - - +
67A ASN* 1.3 75.3 - - - +
69A LEU* 1.3 59.8 + - - +
71A ASN* 2.6 34.2 + - - +
72A SER* 3.2 10.3 + - - +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 2.9 18.3 + - + +
66A ILE* 3.6 8.1 - - + +
68A LYS* 1.3 76.2 - - - +
70A LYS* 1.3 64.6 + - - +
72A SER* 3.1 8.2 + - - -
73A LEU* 3.1 17.5 + - + +
100B LEU* 3.4 34.8 - - + -
104B VAL* 4.8 8.3 - - + -
40C LEU* 5.7 7.0 - - + +
43C LEU* 4.1 34.8 - - + -
44C GLU* 4.3 17.3 - - + +
47C LEU* 4.1 20.9 - - + +
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Residues in contact with LYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 2.8 38.7 + - + +
67A ASN* 3.4 28.4 + - - +
69A LEU* 1.3 74.6 - - - +
71A ASN* 1.3 57.4 + - - +
73A LEU* 2.8 25.6 + - - +
74A PHE* 3.0 36.0 + - + -
96B SER* 5.0 9.5 + - - +
99B GLU* 5.6 4.3 - - - +
100B LEU* 3.3 31.4 - - + -
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Residues in contact with ASN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASN 3.2 19.7 + - - +
68A LYS* 2.6 38.1 + - - +
70A LYS* 1.3 77.0 - - - +
72A SER* 1.3 64.7 + - - +
74A PHE* 4.4 7.5 - - - +
75A GLU* 3.2 23.2 + - - +
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Residues in contact with SER 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 3.2 7.0 + - - +
69A LEU* 3.1 8.7 + - - -
70A LYS 3.0 0.4 - - - -
71A ASN* 1.3 90.5 + - - +
73A LEU* 1.3 60.0 + - - +
74A PHE 3.2 2.5 - - - -
75A GLU* 2.9 23.6 + - - +
76A TYR* 3.1 30.5 + - - -
47C LEU* 3.8 22.9 - - - +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.1 12.6 + - + +
70A LYS* 2.8 12.0 + - - +
72A SER* 1.3 77.2 - - - +
74A PHE* 1.3 93.8 + - + +
76A TYR* 3.9 5.4 + - + +
77A GLN* 3.4 31.2 + - + +
100B LEU* 3.8 11.7 - - + +
103B ASN* 4.9 9.9 - - + +
104B VAL* 3.2 48.0 - - + +
107B VAL* 6.4 0.7 - - + -
108B SER* 5.8 3.6 - - - -
47C LEU* 4.7 5.3 - - + +
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Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 3.0 49.8 + - + +
71A ASN* 4.5 5.8 - - - +
72A SER 3.2 0.6 - - - -
73A LEU* 1.3 97.6 - - + +
75A GLU* 1.3 60.5 + - - +
76A TYR 3.4 0.2 - - - -
77A GLN* 3.6 17.1 - - + +
78A LYS* 2.9 52.2 + - - +
99B GLU* 5.5 6.3 - - - -
100B LEU* 5.2 2.7 - - + -
103B ASN* 6.3 1.1 - - - -
----------------------------------------------------------
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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