Contacts of the helix formed by residues 54 - 81 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TYR* 3.8 5.6 - - - -
52B PHE* 3.2 13.2 - - - +
53B PRO* 1.3 85.1 - - - +
55B LYS* 1.3 63.0 + - - +
56B THR* 3.4 13.4 + - - -
57B ARG* 3.4 26.7 + - - +
58B MET* 3.3 14.2 + - - +
118B GLN* 4.8 2.7 + - - -
13W C 3.3 26.0 - - - -
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 5.9 0.4 - - + -
31B ARG* 4.0 6.9 - - - +
32B ILE* 2.6 29.0 + - + +
34B THR* 4.0 15.5 - - + +
37B LEU* 5.3 5.8 - - + -
54B SER* 1.3 73.1 - - - +
56B THR* 1.3 66.3 + - - +
57B ARG 3.1 0.7 - - - -
58B MET* 2.9 40.0 + - + +
59B PHE* 3.2 28.4 + - + -
117B GLU* 3.3 35.4 + - - +
12W A 2.5 41.5 + - - -
13W C 2.9 14.9 + - - +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B SER* 3.4 11.1 + - - -
55B LYS* 1.3 77.3 - - - +
57B ARG* 1.3 55.1 + - - +
59B PHE* 3.1 4.0 + - - +
60B ASP* 2.7 33.4 + - - +
117B GLU* 4.5 7.0 + - - +
118B GLN* 2.6 49.2 + - + +
120B ARG* 3.6 18.4 - - - +
121B LEU* 3.5 30.0 - - + +
13W C 4.8 1.6 + - - -
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 4.9 12.1 - - - +
52B PHE* 3.9 8.0 - - + -
53B PRO* 3.4 35.6 - - + +
54B SER* 3.4 20.6 + - - +
55B LYS 3.1 0.2 - - - -
56B THR* 1.3 85.0 - - - +
58B MET* 1.3 61.9 + - - +
60B ASP* 2.6 37.8 + - - +
61B SER* 3.0 27.3 + - - -
120B ARG* 4.2 12.1 - - - +
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Residues in contact with MET 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.9 12.8 - - + -
16B LEU* 3.7 15.5 - - + +
19B LEU* 3.9 18.2 - - + -
34B THR* 5.0 6.1 - - + -
37B LEU* 3.4 30.5 - - + -
48B LEU* 5.2 9.2 - - + +
49B TYR* 5.3 4.9 - - + +
52B PHE* 3.6 31.6 - - + -
54B SER 3.3 7.9 - - - +
55B LYS* 2.9 48.7 + - + +
57B ARG* 1.3 77.2 - - - +
59B PHE* 1.3 58.6 + - - +
61B SER* 3.0 6.6 + - - -
62B LEU* 2.9 24.3 + - - +
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Residues in contact with PHE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.1 26.9 - - + -
23B LEU* 4.0 17.3 - - + -
32B ILE* 5.0 6.1 - - + -
55B LYS* 3.2 25.0 + - + -
56B THR 3.1 7.0 + - - +
58B MET* 1.3 76.9 - - - +
60B ASP* 1.3 60.5 + - - +
62B LEU* 3.1 7.3 + - + +
63B ILE* 2.8 36.3 + - + +
108B ILE* 3.7 30.7 - - + -
113B ALA* 4.6 13.7 - - + -
114B LEU* 3.8 20.4 - - + -
117B GLU* 3.5 33.7 - - + -
121B LEU* 3.8 17.0 - - + -
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Residues in contact with ASP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR 2.7 15.1 + - - +
57B ARG* 2.6 45.0 + - - +
58B MET 3.2 0.2 - - - -
59B PHE* 1.3 72.4 - - - +
61B SER* 1.3 58.0 + - - +
63B ILE* 3.3 1.0 + - - -
64B GLU* 2.9 22.3 + - - +
120B ARG* 2.4 40.2 + - - -
121B LEU* 3.5 12.4 - - - +
124B ARG* 2.6 38.8 + - - +
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 3.7 22.2 + - - -
16B LEU* 3.8 26.7 - - - +
52B PHE* 3.8 4.0 - - - -
57B ARG* 3.0 15.3 + - - -
58B MET 3.0 9.2 + - - -
60B ASP* 1.3 77.9 - - - +
62B LEU* 1.3 57.3 + - - +
64B GLU* 3.4 7.9 + - - +
65B PHE* 3.0 26.7 + - - +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.7 41.1 - - + +
19B LEU* 3.7 36.6 - - + -
20B ALA* 4.7 4.3 - - + +
23B LEU* 4.1 5.8 - - + -
58B MET 2.9 8.5 + - - +
59B PHE* 3.1 9.6 + - + +
61B SER* 1.3 79.1 - - - +
63B ILE* 1.3 56.7 + - - +
65B PHE* 3.2 12.7 + - + +
66B ILE* 3.0 31.6 + - - +
105B LEU* 3.7 19.9 - - + +
108B ILE* 3.8 26.9 - - + -
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PHE* 2.8 20.5 + - - +
60B ASP* 3.6 4.3 - - - +
62B LEU* 1.3 74.0 - - + +
64B GLU* 1.3 66.8 + - - +
66B ILE* 2.9 10.7 + - - +
67B GLU* 2.8 28.8 + - + +
108B ILE* 3.9 24.2 - - + -
114B LEU* 4.6 3.1 - - + -
121B LEU* 3.7 47.8 - - + +
124B ARG* 3.6 33.9 - - + +
125B ILE* 4.0 19.5 - - + -
128B LEU* 5.6 2.6 - - + +
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ASP 2.9 16.7 + - - +
61B SER* 3.7 8.5 - - - +
63B ILE* 1.3 76.8 - - - +
65B PHE* 1.3 63.1 + - - +
67B GLU* 3.4 6.0 + - - +
68B ASP* 3.0 45.2 + - - +
124B ARG* 3.5 22.4 + - - +
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B SER 3.0 15.2 + - - +
62B LEU* 3.3 14.1 - - + +
63B ILE 3.1 0.2 - - - -
64B GLU* 1.3 78.3 - - - +
66B ILE* 1.3 56.0 + - - +
68B ASP* 3.4 6.3 + - + +
69B SER* 2.5 50.0 + - - -
73B ARG* 6.0 2.2 - - - -
98B PHE* 4.2 8.7 - + - -
102B ASN* 4.8 5.8 - - - -
105B LEU* 3.7 33.4 - - + -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU 3.0 16.7 + - - +
63B ILE* 2.9 11.5 + - + +
65B PHE* 1.3 77.1 - - - +
67B GLU* 1.3 62.4 + - - +
69B SER* 3.8 2.4 - - - -
70B LEU* 2.8 47.2 + - + +
98B PHE* 4.0 12.3 - - + -
105B LEU* 3.7 45.3 - - + +
108B ILE* 4.2 19.3 - - + -
109B LEU* 4.3 17.9 - - + -
125B ILE* 4.8 3.6 - - + -
128B LEU* 4.0 17.5 - - + -
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 2.8 17.7 + - + +
64B GLU* 3.8 7.5 - - - +
66B ILE* 1.3 78.2 - - - +
68B ASP* 1.3 63.0 + - - +
70B LEU* 4.8 0.2 - - - -
71B ILE* 2.8 48.4 + - + +
124B ARG* 5.1 13.9 + - - +
127B GLN* 6.2 0.2 - - - +
128B LEU* 3.9 36.3 + - + +
131B ARG* 2.7 32.8 + - - +
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU* 3.0 36.4 + - - +
65B PHE* 4.0 6.3 - - + +
67B GLU* 1.3 76.8 - - - +
69B SER* 1.3 68.3 + - - +
71B ILE* 4.9 1.8 - - - -
72B THR* 2.8 37.9 + - - +
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Residues in contact with SER 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 2.5 46.6 + - - -
66B ILE 3.8 1.8 - - - -
68B ASP* 1.3 78.4 - - - +
70B LEU* 1.3 57.9 + - - +
72B THR* 4.8 0.2 - - - -
73B ARG* 2.7 55.1 + - - +
98B PHE* 3.4 28.6 - - - -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 2.8 46.3 + - + +
67B GLU* 4.0 3.4 - - - +
69B SER* 1.3 78.6 - - - +
71B ILE* 1.3 62.0 + - + +
73B ARG* 3.3 2.1 + - - -
74B ILE* 2.9 41.1 + - + +
94B LEU* 3.8 31.1 - - + +
95B ILE* 4.4 13.0 - - + -
98B PHE* 3.6 38.6 - - + -
109B LEU* 5.5 3.8 - - + -
128B LEU* 5.1 3.4 - - + -
132B ILE* 4.9 17.0 - - + -
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 2.8 41.1 + - + +
68B ASP* 4.5 2.0 - - - +
70B LEU* 1.3 69.1 - - - +
72B THR* 1.3 67.5 + - - +
74B ILE* 3.1 11.1 + - + +
75B ASN* 3.0 40.3 + - - +
128B LEU* 4.1 13.2 - - + -
131B ARG* 3.6 52.0 - - + +
132B ILE* 4.6 12.1 - - + +
135B GLN* 6.4 1.3 - - + -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP* 2.8 29.9 + - - +
69B SER* 4.0 2.2 - - - -
71B ILE* 1.3 80.0 - - - +
73B ARG* 1.3 72.0 + - - +
75B ASN* 3.3 10.2 + - - +
76B LEU* 3.2 32.9 + - + +
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 6.0 2.6 - - - -
69B SER* 2.7 52.8 + - - +
71B ILE 3.2 0.4 - - - -
72B THR* 1.3 85.0 - - + +
74B ILE* 1.3 65.8 + - - +
76B LEU* 3.3 15.4 + - + +
77B ILE* 3.0 26.8 + - + +
94B LEU* 3.6 32.9 - - + +
98B PHE* 4.8 9.1 - - - -
101B ARG* 5.1 12.9 - - - +
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 2.9 27.1 + - + +
71B ILE* 3.1 11.8 + - + +
73B ARG* 1.3 74.6 - - - +
75B ASN* 1.3 67.9 + - - +
77B ILE* 3.1 8.8 + - - +
78B LEU* 3.0 26.0 + - + +
91B ILE* 3.8 42.8 - - + -
94B LEU* 3.6 16.2 - - + -
95B ILE* 5.4 2.7 - - + -
132B ILE* 4.2 29.8 - - + -
135B GLN* 3.9 24.0 - - + +
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.0 35.2 + - - +
72B THR* 3.6 9.7 - - - +
74B ILE* 1.3 79.1 - - - +
76B LEU* 1.3 62.8 + - + +
78B LEU* 3.1 19.9 + - - +
79B LYS* 3.1 27.2 + - - +
135B GLN* 4.3 13.9 - - - +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 3.2 28.0 + - + +
73B ARG* 3.6 17.9 - - + +
74B ILE 3.2 0.2 - - - -
75B ASN* 1.3 74.3 - - - +
77B ILE* 1.3 64.4 + - + +
79B LYS* 3.2 12.8 + - + +
80B ASP* 3.0 32.4 + - - +
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG* 3.0 20.3 + - + +
74B ILE* 3.1 8.9 + - - +
76B LEU* 1.3 77.8 - - + +
78B LEU* 1.3 57.2 + - + +
80B ASP* 4.3 4.5 - - - -
81B GLU* 2.8 30.0 + - - +
87B ARG* 4.1 22.2 - - + +
90B LEU* 3.7 59.9 - - + +
91B ILE* 3.9 15.0 - - + +
94B LEU* 4.0 20.0 - - + -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 3.0 18.7 + - + +
75B ASN* 3.1 15.2 + - - +
77B ILE* 1.3 76.6 - - - +
79B LYS* 1.3 61.8 + - + +
81B GLU 3.5 3.9 - - - +
82B LYS* 5.5 0.2 - - - -
87B ARG* 3.0 47.5 + - + +
91B ILE* 4.5 8.3 - - + -
135B GLN* 3.5 33.9 - - - +
139B VAL* 3.5 29.4 - - + -
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 3.1 25.7 + - - +
76B LEU* 3.8 12.8 - - + +
77B ILE 3.2 0.2 - - - -
78B LEU* 1.3 81.4 - - + +
80B ASP* 1.3 59.5 + - - +
81B GLU 5.2 0.2 - - - -
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.0 24.5 + - - +
77B ILE* 3.8 5.2 - - - +
79B LYS* 1.3 79.3 - - - +
81B GLU* 1.3 61.9 + - + +
82B LYS 4.3 0.3 + - - -
90B LEU* 6.2 1.1 - - + -
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE 2.8 13.1 + - - +
78B LEU 3.5 3.8 - - - +
79B LYS 5.2 0.4 - - - -
80B ASP* 1.3 82.3 - - + +
82B LYS* 1.3 57.1 + - - +
83B ASP* 2.8 36.9 + - - +
86B ALA* 3.6 30.6 - - + +
87B ARG* 2.7 45.3 + - + +
90B LEU* 4.0 19.6 - - + +
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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