Contacts of the helix formed by residues 54 - 81 (chain C) in PDB entry 4GCK
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 54 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C TYR* 4.0 5.4 - - - -
52C PHE* 3.3 12.5 - - - +
53C PRO* 1.3 82.9 - - - +
55C LYS* 1.3 65.1 + - - +
56C THR* 3.6 13.0 - - - -
57C ARG* 3.1 37.9 + - - +
58C MET* 3.7 2.5 + - - -
9W C 3.2 25.8 - - - -
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Residues in contact with LYS 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 6.0 1.1 - - + -
31C ARG* 3.8 7.3 - - - +
32C ILE* 3.1 26.3 + - + +
34C THR* 4.6 15.3 - - + +
37C LEU* 4.8 4.9 - - + -
49C TYR* 4.7 0.6 + - - -
54C SER* 1.3 70.3 - - - +
56C THR* 1.3 67.2 + - - +
58C MET* 2.8 43.9 + - + +
59C PHE* 3.3 35.4 + - + -
117C GLU* 2.6 29.2 + - - +
8W A 2.9 41.3 + - - -
9W C 3.0 18.0 + - - +
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Residues in contact with THR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C SER* 3.6 12.5 - - - -
55C LYS* 1.3 79.0 - - - +
57C ARG* 1.3 61.4 + - - +
59C PHE* 3.3 10.8 + - - +
60C ASP* 2.9 25.1 + - - +
117C GLU* 4.7 8.1 + - - -
118C GLN* 3.7 30.4 + - + +
120C ARG* 3.0 31.0 - - - +
121C LEU* 4.2 10.2 - - + +
9W C 5.2 2.5 + - - -
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Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ARG* 5.8 3.4 - - - +
52C PHE* 4.1 8.7 - - + -
53C PRO* 3.5 34.5 - - + +
54C SER* 3.1 17.3 + - - +
55C LYS 3.0 1.0 - - - -
56C THR* 1.3 83.5 - - - +
58C MET* 1.3 60.7 + - - +
60C ASP* 2.8 39.7 + - - +
61C SER* 2.8 31.9 + - - +
120C ARG* 3.3 14.7 - - - +
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Residues in contact with MET 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 4.1 7.4 - - + -
16C LEU* 3.7 15.1 - - + +
19C LEU* 3.8 19.1 - - + -
34C THR* 5.6 3.4 - - + -
37C LEU* 3.4 28.9 - - + -
48C LEU* 4.2 29.4 - - + +
49C TYR* 5.7 3.8 - - + -
52C PHE* 3.7 44.4 - - + -
54C SER 4.0 2.2 - - - +
55C LYS* 2.8 34.3 + - + +
57C ARG* 1.3 77.0 - - - +
59C PHE* 1.3 56.1 + - - +
61C SER* 3.0 4.9 + - - -
62C LEU* 2.9 27.9 + - - +
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Residues in contact with PHE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 4.1 24.5 - - + -
23C LEU* 4.3 15.0 - - + -
32C ILE* 4.8 7.6 - - + -
55C LYS* 3.3 29.6 + - + -
56C THR* 3.7 6.5 - - - +
58C MET* 1.3 77.3 - - - +
60C ASP* 1.3 58.0 + - - +
62C LEU* 3.1 6.6 + - - +
63C ILE* 2.9 36.4 + - + +
108C ILE* 4.1 26.0 - - + -
113C ALA* 4.5 13.7 - - + -
114C LEU* 3.9 17.7 - - + -
117C GLU* 3.7 42.4 - - + -
121C LEU* 3.8 15.9 - - + -
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Residues in contact with ASP 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C THR 2.9 12.8 + - - +
57C ARG* 2.8 32.4 + - - +
58C MET 3.2 0.2 - - - -
59C PHE* 1.3 76.9 - - - +
61C SER* 1.3 62.2 + - - +
63C ILE* 3.3 3.1 + - - -
64C GLU* 3.0 37.3 + - - +
120C ARG* 2.4 47.6 + - - -
121C LEU* 3.4 10.6 - - - +
124C ARG* 3.5 19.4 + - - -
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Residues in contact with SER 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ARG* 3.1 30.0 + - - -
16C LEU* 3.7 26.1 - - - +
52C PHE* 3.8 1.7 - - - -
57C ARG* 2.8 19.2 + - - -
58C MET 3.0 8.0 + - - -
60C ASP* 1.3 72.5 - - - +
62C LEU* 1.3 65.0 + - - +
64C GLU* 3.2 13.3 + - - +
65C PHE* 3.1 22.2 + - - +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.7 39.0 - - + +
19C LEU* 3.2 39.5 - - + -
20C ALA* 4.4 4.3 - - + +
23C LEU* 4.4 5.2 - - + -
58C MET 2.9 6.7 + - - +
59C PHE* 3.1 8.3 + - - +
61C SER* 1.3 79.7 - - - +
63C ILE* 1.3 61.1 + - - +
65C PHE* 3.3 10.4 + - + +
66C ILE* 3.0 26.9 + - - +
105C LEU* 3.6 23.0 - - + +
108C ILE* 3.9 25.4 - - + -
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Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PHE* 2.9 20.5 + - - +
60C ASP* 3.8 4.7 - - - +
62C LEU* 1.3 73.3 - - + +
64C GLU* 1.3 60.0 + - - +
66C ILE* 3.2 7.4 + - + +
67C GLU* 2.8 37.9 + - + +
108C ILE* 4.0 22.4 - - + -
114C LEU* 4.6 3.8 - - + -
121C LEU* 3.8 46.4 - - + +
124C ARG* 4.0 30.3 - - + +
125C ILE* 3.7 24.0 - - + -
128C LEU* 5.5 0.9 - - + -
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Residues in contact with GLU 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASP* 3.0 24.5 + - - +
61C SER* 3.2 13.6 + - - +
63C ILE* 1.3 76.0 - - - +
65C PHE* 1.3 58.6 + - - +
67C GLU* 3.4 5.3 - - - +
68C ASP* 2.9 42.1 + - - +
124C ARG* 2.9 31.5 + - - +
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Residues in contact with PHE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C SER 3.1 12.0 + - - +
62C LEU* 3.4 14.4 - - + +
63C ILE 3.2 0.2 - - - -
64C GLU* 1.3 74.9 - - - +
66C ILE* 1.3 64.7 + - - +
68C ASP* 3.9 6.0 - - + +
69C SER* 2.6 52.9 + - - -
98C PHE* 4.0 11.0 - + - -
102C ASN* 4.5 6.3 - - - -
105C LEU* 3.7 31.0 - - + -
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU 3.0 21.9 + - - +
63C ILE* 3.6 11.0 - - + +
65C PHE* 1.3 74.5 - - - +
67C GLU* 1.3 65.4 + - - +
69C SER* 3.8 1.6 - - - -
70C LEU* 3.0 44.6 + - + +
98C PHE* 3.9 19.1 - - + -
105C LEU* 3.8 47.3 - - + +
108C ILE* 4.0 21.8 - - + -
109C LEU* 4.1 12.8 - - + +
125C ILE* 4.9 3.8 - - + -
128C LEU* 3.8 13.2 - - + -
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Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ILE* 2.8 25.9 + - + +
64C GLU* 3.4 8.5 - - - +
66C ILE* 1.3 78.4 - - - +
68C ASP* 1.3 61.8 - - - +
70C LEU* 3.7 0.7 - - - +
71C ILE* 2.8 37.5 + - - +
124C ARG* 4.9 7.0 - - - +
127C GLN* 5.0 3.1 - - - +
128C LEU* 3.5 46.6 + - + +
131C ARG* 3.5 29.6 + - - +
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Residues in contact with ASP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLU* 2.9 29.9 + - - +
65C PHE* 3.9 6.0 - - + +
67C GLU* 1.3 75.0 - - - +
69C SER* 1.3 69.7 + - - +
71C ILE* 4.9 2.7 - - - -
72C THR* 2.9 35.4 + - - +
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Residues in contact with SER 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C PHE* 2.6 46.8 + - - -
66C ILE 3.8 1.1 - - - -
68C ASP* 1.3 76.6 - - - +
70C LEU* 1.3 64.6 + - - +
72C THR* 4.0 1.9 - - - -
73C ARG* 3.1 41.3 + - - +
98C PHE* 3.6 26.0 - - - -
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 3.0 37.3 + - + +
67C GLU* 3.8 3.1 - - - +
69C SER* 1.3 80.2 - - - +
71C ILE* 1.3 62.9 + - + +
73C ARG 3.8 0.3 - - - -
74C ILE* 2.9 37.5 + - + +
94C LEU* 3.8 19.2 - - + +
95C ILE* 4.8 15.3 - - + +
98C PHE* 3.7 39.9 - - + -
109C LEU* 4.7 10.5 - - + -
128C LEU* 4.2 7.2 - - + -
132C ILE* 4.2 25.6 - - + -
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Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLU* 2.8 31.6 + - - +
68C ASP* 4.3 2.2 - - - +
70C LEU* 1.3 75.0 - - + +
72C THR* 1.3 63.6 + - - +
74C ILE* 3.3 11.1 + - + +
75C ASN* 3.0 45.3 + - - +
128C LEU* 4.2 12.6 - - + -
131C ARG* 3.7 62.4 - - + +
132C ILE* 4.6 11.0 - - + +
135C GLN* 6.1 3.4 - - + -
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Residues in contact with THR 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ASP* 2.9 28.3 + - - +
69C SER* 4.0 3.1 - - - -
71C ILE* 1.3 78.0 - - - +
73C ARG* 1.3 64.6 + - + +
75C ASN* 3.5 9.7 + - - +
76C LEU* 3.2 35.2 + - + +
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Residues in contact with ARG 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C SER* 3.1 26.6 + - - +
72C THR* 1.3 80.8 - - + +
74C ILE* 1.3 65.4 + - - +
76C LEU* 3.6 13.6 - - + +
77C ILE* 3.0 27.0 + - + +
94C LEU* 3.5 30.6 - - + +
98C PHE* 4.8 6.2 - - - -
101C ARG* 2.6 49.6 - - - +
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LEU* 2.9 29.2 + - + +
71C ILE* 3.7 11.2 - - + +
73C ARG* 1.3 75.2 - - - +
75C ASN* 1.3 65.6 + - - +
77C ILE* 3.0 10.5 + - - +
78C LEU* 2.9 33.8 + - + +
91C ILE* 3.9 42.0 - - + -
94C LEU* 3.7 14.6 - - + -
95C ILE* 5.3 2.0 - - + -
132C ILE* 4.3 29.4 - - + -
135C GLN* 4.3 18.4 - - + +
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Residues in contact with ASN 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ILE* 3.0 35.9 + - - +
72C THR* 3.7 8.8 - - - +
74C ILE* 1.3 76.8 - - - +
76C LEU* 1.3 62.6 + - + +
78C LEU* 3.1 17.7 + - - +
79C LYS* 3.1 26.5 + - - +
135C GLN* 3.7 20.3 + - - -
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C THR* 3.2 28.8 + - + +
73C ARG* 3.6 17.9 - - + +
74C ILE 3.2 0.2 - - - -
75C ASN* 1.3 75.7 - - + +
77C ILE* 1.3 68.2 + - + +
79C LYS* 3.1 12.6 + - + +
80C ASP* 3.0 25.5 + - + +
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Residues in contact with ILE 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ARG* 3.0 20.7 + - + +
74C ILE* 3.0 8.0 + - - +
76C LEU* 1.3 78.3 - - + +
78C LEU* 1.3 59.3 + - + +
79C LYS 3.1 0.2 + - - -
80C ASP* 4.7 3.6 - - - -
81C GLU* 2.9 30.1 + - + +
87C ARG* 4.2 22.7 - - + +
90C LEU* 3.8 56.1 - - + +
91C ILE* 4.0 15.5 - - + +
94C LEU* 4.2 16.4 - - + -
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ILE* 2.9 24.1 + - + +
75C ASN* 3.1 12.3 + - - +
77C ILE* 1.3 76.8 - - + +
79C LYS* 1.3 59.8 + - + +
81C GLU 3.6 2.3 - - - +
87C ARG* 2.8 50.7 + - + +
91C ILE* 4.5 7.4 - - + -
135C GLN* 3.2 39.0 - - - +
138C GLN* 5.3 3.6 - - - +
139C VAL* 3.5 27.1 - - + -
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Residues in contact with LYS 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ASN* 3.1 18.4 + - - +
76C LEU* 3.1 15.0 + - + +
78C LEU* 1.3 79.7 - - + +
80C ASP* 1.3 59.5 + - - +
81C GLU 3.6 1.0 - - - -
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LEU 3.0 15.6 + - - +
77C ILE* 4.1 4.3 - - - +
79C LYS* 1.3 77.2 - - - +
81C GLU* 1.3 64.5 + - + +
82C LYS 4.1 1.4 + - - -
----------------------------------------------------------
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Residues in contact with GLU 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ILE 2.9 14.1 + - - +
78C LEU 3.6 1.9 - - - +
79C LYS 5.2 0.7 - - - -
80C ASP* 1.3 84.1 - - + +
82C LYS* 1.3 56.9 + - - +
83C ASP* 2.9 39.0 + - - +
86C ALA* 3.4 28.8 - - + +
87C ARG* 2.8 48.3 + - + +
90C LEU* 4.2 20.4 - - + +
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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