Contacts of the helix formed by residues 48 - 77 (chain F) in PDB entry 5JKL
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 LEU 48 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F PHE* 3.0 38.8 + - + +
46F VAL* 3.5 14.6 - - + +
47F ALA* 1.3 80.9 - - - +
49F LYS* 1.3 59.7 + - - +
50F ASN 3.3 3.9 + - - -
51F PHE* 3.3 23.9 + - + -
52F ALA* 3.0 22.7 + - - +
164F GLY 5.8 0.4 - - - +
167F GLU* 4.1 21.1 - - + +
168F TYR* 4.0 23.6 - - + +
171F ASP* 3.3 28.3 - - + +
172F LYS* 4.5 4.5 - - - +
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Residues in contact with LYS 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F PHE 5.1 0.9 - - - -
42F ASP* 6.0 2.2 - - - +
47F ALA* 3.8 6.8 + - - +
48F LEU* 1.3 72.2 - - - +
50F ASN* 1.3 64.7 + - - +
52F ALA* 3.4 8.4 + - - +
53F LYS* 3.0 38.8 + - - +
171F ASP* 3.5 3.8 + - - +
172F LYS* 5.8 0.2 - - - +
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Residues in contact with ASN 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F LYS* 1.3 81.1 - - - +
51F PHE* 1.4 57.2 + - - -
52F ALA 3.2 0.9 - - - -
53F LYS* 3.9 20.7 + - - +
54F TYR* 2.9 30.3 + - - +
171F ASP* 2.9 46.6 + - - +
172F LYS* 4.3 8.9 - - - +
175F LEU* 3.7 17.5 - - + +
176F GLY* 3.5 20.7 - - - -
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Residues in contact with PHE 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F PHE* 3.5 21.3 - + + -
48F LEU* 3.5 22.4 - - + +
50F ASN* 1.4 73.4 - - - +
52F ALA* 1.3 61.9 + - - +
54F TYR* 3.3 2.3 + - - +
55F PHE* 3.1 39.2 + + - -
96F GLY* 3.5 34.8 - - - -
100F MET* 3.8 24.2 - - + -
155F LEU* 4.1 10.1 - - + -
167F GLU* 3.7 23.6 - - + -
170F PHE* 3.6 22.2 - + - -
171F ASP* 3.0 29.3 + - + -
175F LEU* 3.6 17.4 - - + +
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F SER* 2.7 48.4 + - - +
41F PHE* 3.7 6.4 - - + +
42F ASP* 4.1 15.3 - - + +
48F LEU 3.0 13.7 + - - +
49F LYS* 3.5 11.9 - - - +
50F ASN 3.2 0.2 - - - -
51F PHE* 1.3 77.4 - - - +
53F LYS* 1.3 62.7 + - + +
56F LEU* 3.0 11.1 + - - +
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Residues in contact with LYS 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F LYS* 3.0 27.7 + - - +
50F ASN* 3.9 20.9 + - - +
51F PHE 3.4 0.4 - - - -
52F ALA* 1.3 76.5 - - + +
54F TYR* 1.3 64.0 + - - +
56F LEU* 3.3 7.4 + - - +
57F HIS* 3.0 25.1 + - - +
175F LEU 6.1 0.2 - - - +
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Residues in contact with TYR 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F ASN 2.9 18.8 + - - +
51F PHE* 3.6 6.1 - - - +
53F LYS* 1.3 76.8 - - - +
55F PHE* 1.3 93.1 + + - +
57F HIS* 3.2 9.0 + + + +
58F GLN* 3.0 50.2 + - + +
100F MET* 3.8 19.3 - - + -
144F ALA 5.5 0.2 + - - -
147F GLU* 2.6 32.6 + - - +
148F LEU* 3.7 19.4 - - + +
151F HIS* 3.8 17.9 - + - -
175F LEU* 4.0 19.3 - - + +
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Residues in contact with PHE 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F TYR* 3.5 53.3 - + - +
37F MET* 3.9 17.9 - - + -
38F SER* 3.7 10.3 - - - +
41F PHE* 3.6 33.4 - + - -
51F PHE* 3.1 36.7 + + - +
54F TYR* 1.3 96.9 - + - +
56F LEU* 1.3 60.7 + - - +
58F GLN* 3.3 2.0 + - + -
59F SER* 3.0 18.9 + - - -
99F ALA* 4.1 12.3 - - + -
100F MET* 3.8 25.1 - - + -
103F ALA* 4.2 8.1 - - + -
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Residues in contact with LEU 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F LEU* 3.9 27.8 - - + -
38F SER* 3.4 19.9 - - - +
39F TYR* 4.2 19.7 - - + +
52F ALA 3.0 11.7 + - - +
53F LYS* 3.8 7.6 - - + +
54F TYR 3.3 0.2 - - - -
55F PHE* 1.3 75.4 - - - +
57F HIS* 1.3 63.2 + - - +
59F SER* 3.1 8.2 + - - -
60F HIS* 3.0 51.4 + - + +
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Residues in contact with HIS 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F LYS 3.0 13.9 + - - +
54F TYR* 3.4 11.2 - + - +
56F LEU* 1.3 77.4 - - - +
58F GLN* 1.3 80.0 + - - +
60F HIS* 3.2 10.4 + - + +
61F GLU* 2.9 53.2 + - + +
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Residues in contact with GLN 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F TYR* 3.7 33.5 - - + +
54F TYR* 3.0 64.1 + - + +
55F PHE* 3.6 7.6 - - - +
57F HIS* 1.3 92.5 - - - +
59F SER* 1.3 55.6 + - - +
61F GLU* 3.3 6.6 + - - +
62F GLU* 2.9 33.4 + - - +
147F GLU* 4.3 4.6 + - - -
148F LEU* 6.3 0.2 - - + -
203F MG 2.1 33.6 - - - -
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Residues in contact with SER 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F SER* 2.7 53.9 + - - +
34F TYR* 3.6 6.9 - - - +
35F LEU* 3.7 24.7 - - - +
55F PHE 3.0 12.7 + - - -
56F LEU* 3.1 14.6 + - - -
58F GLN* 1.3 76.8 - - - +
60F HIS* 1.3 66.9 + - - +
62F GLU 3.3 1.4 + - - -
63F ARG* 3.1 11.3 + - - +
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Residues in contact with HIS 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F SER* 5.9 0.4 - - - -
35F LEU* 6.1 0.2 - - - +
56F LEU* 3.0 48.2 + - + +
57F HIS* 3.7 11.0 - - - +
59F SER* 1.3 84.2 - - - +
61F GLU* 1.3 63.1 + - + +
63F ARG* 3.3 9.7 + - + +
64F GLU* 3.2 26.6 + - + +
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Residues in contact with GLU 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F HIS* 2.9 49.5 + - + +
58F GLN* 3.5 9.6 - - - +
60F HIS* 1.3 76.3 - - - +
62F GLU* 1.3 56.6 + - - +
64F GLU* 3.1 13.1 + - - +
65F HIS* 2.9 46.8 + - + +
140F GLU* 5.6 1.9 - - - +
203F MG 4.2 15.9 - - - -
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Residues in contact with GLU 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F GLU* 2.7 14.7 - - - +
30F ALA* 3.8 18.8 - - + +
31F SER* 3.6 24.0 - - - +
34F TYR* 3.8 18.5 - - + -
58F GLN 2.9 19.1 + - - +
61F GLU* 1.3 75.8 - - - +
63F ARG* 1.3 64.3 + - - +
65F HIS* 3.1 15.3 + - - +
66F ALA* 3.0 21.3 + - - +
107F GLU* 3.5 23.5 - - - +
110F VAL* 6.1 0.9 - - - -
201F FE 2.0 32.1 - - - -
203F MG 4.2 7.3 - - - -
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Residues in contact with ARG 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LEU* 4.1 24.0 - - - +
31F SER* 3.9 12.3 + - - +
59F SER 3.1 12.7 + - - +
60F HIS* 3.7 11.9 - - + +
61F GLU 3.3 0.4 - - - -
62F GLU* 1.3 76.3 - - - +
64F GLU* 1.3 62.8 + - - +
66F ALA* 3.1 5.2 + - - +
67F GLU* 2.9 62.2 + - - +
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Residues in contact with GLU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F HIS* 3.2 15.4 + - + +
61F GLU* 3.1 16.9 + - - +
63F ARG* 1.3 78.1 - - - +
65F HIS* 1.3 67.9 + - + +
67F GLU* 2.7 34.6 + - - +
68F LYS* 3.0 26.7 + - - +
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Residues in contact with HIS 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F GLU* 3.3 19.3 - - - +
61F GLU* 2.9 37.8 + - + +
62F GLU* 3.1 20.4 + - - +
64F GLU* 1.3 78.6 - - + +
66F ALA* 1.3 63.8 + - - +
68F LYS* 4.6 3.8 - - + +
69F LEU* 3.2 10.7 + - - +
136F HIS 5.5 3.4 - - - -
137F TYR* 2.7 40.5 + + + -
140F GLU* 4.9 20.6 + - + +
141F GLN* 4.7 8.5 - - - -
201F FE 2.2 28.7 - - - -
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Residues in contact with ALA 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ILE* 4.2 8.3 - - + +
27F GLU* 3.8 20.1 - - + +
28F LEU* 3.6 33.0 - - + -
62F GLU 3.0 12.0 + - - +
63F ARG* 3.1 8.7 + - - +
65F HIS* 1.3 77.8 - - - +
67F GLU* 1.4 62.4 + - - +
69F LEU* 3.1 7.5 + - - +
70F MET* 3.0 28.8 + - - +
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Residues in contact with GLU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F ARG* 2.9 54.8 + - - +
64F GLU* 2.7 42.6 - - - +
66F ALA* 1.4 75.2 - - + +
68F LYS* 1.3 57.5 + - - +
70F MET* 3.2 16.2 + - - +
71F LYS* 2.9 28.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F GLU 3.0 16.8 + - - +
65F HIS* 4.4 3.7 - - + +
67F GLU* 1.3 77.5 - - - +
69F LEU* 1.3 56.8 + - - +
71F LYS* 3.4 13.0 + - + +
72F LEU* 2.9 27.0 + - - +
132F PHE* 3.9 11.9 - - + -
136F HIS* 3.3 49.2 + - + +
137F TYR* 3.3 20.2 - - + +
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ILE* 3.8 30.4 - - + +
23F GLN* 3.6 29.2 - - + -
24F ILE* 3.6 17.3 - - + +
27F GLU* 3.6 26.2 - - + -
65F HIS 3.2 13.8 + - - +
66F ALA* 3.1 4.0 + - - +
68F LYS* 1.3 76.0 - - - +
70F MET* 1.3 59.0 + - - +
72F LEU* 3.3 5.5 + - + +
73F GLN* 3.0 28.4 + - - +
114F LEU* 5.9 0.9 - - + -
117F LEU* 5.0 2.9 - - + -
132F PHE* 3.6 24.0 - - + -
133F ILE* 6.3 0.2 - - + -
137F TYR* 3.4 17.9 - - + +
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Residues in contact with MET 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ILE* 3.7 33.2 - - + -
28F LEU* 5.5 4.0 - - - -
66F ALA* 3.0 20.7 + - - +
67F GLU* 3.6 15.5 - - - +
69F LEU* 1.3 76.1 - - - +
71F LYS* 1.3 62.7 + - - +
73F GLN* 3.3 4.3 + - - +
74F ASN* 3.1 21.8 + - - +
80F ILE* 3.6 41.0 - - + +
82F LEU* 4.2 18.8 - - + -
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Residues in contact with LYS 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F GLU 2.9 13.0 + - - +
68F LYS* 3.5 16.2 - - + +
69F LEU 3.2 0.2 - - - -
70F MET* 1.3 77.3 - - - +
72F LEU* 1.3 57.6 + - - +
74F ASN* 3.3 8.5 + - - +
75F GLN* 2.8 57.9 + - + +
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Residues in contact with LEU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F TYR* 4.0 18.8 - - + +
20F ILE* 4.3 10.3 - - + -
68F LYS 2.9 14.6 + - - +
69F LEU* 3.5 8.5 - - - +
70F MET 3.3 0.2 - - - -
71F LYS* 1.3 75.6 - - - +
73F GLN* 1.3 68.3 + - - +
75F GLN* 3.1 15.6 + - + +
76F ARG* 3.0 31.6 + - + +
128F HIS* 3.7 30.3 - - + +
129F LEU* 4.2 17.9 - - + -
132F PHE* 3.8 39.7 - - + -
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Residues in contact with GLN 73 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F TYR* 2.7 37.9 + - - -
17F GLU* 3.0 33.8 + - - +
20F ILE* 3.7 10.7 - - + +
21F ASN* 3.0 25.2 + - - +
24F ILE* 4.7 0.9 - - + -
69F LEU 3.0 13.2 + - - +
70F MET* 3.5 9.4 - - - +
72F LEU* 1.3 81.6 - - - +
74F ASN* 1.3 62.0 + - - +
76F ARG* 3.4 0.9 + - - +
77F GLY 3.2 3.3 + - - -
78F GLY* 2.9 40.7 + - - -
79F ARG 3.8 2.8 + - - +
80F ILE* 3.7 23.6 - - + -
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Residues in contact with ASN 74 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D LYS* 3.5 24.6 - - - +
8F VAL* 4.2 2.1 - - - +
70F MET 3.1 13.1 + - - +
71F LYS* 3.8 8.7 - - - +
73F GLN* 1.3 76.2 - - - +
75F GLN* 1.3 66.3 + - - +
77F GLY* 3.1 12.1 + - - -
78F GLY 3.8 6.3 - - - +
79F ARG* 3.8 20.1 + - - +
80F ILE* 3.8 26.2 + - - +
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Residues in contact with GLN 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ASN* 4.6 9.1 + - - +
142D VAL* 3.9 26.7 - - + +
143D LYS* 4.0 25.1 - - - +
145D ILE* 5.8 0.7 - - - +
146D LYS* 4.1 27.4 - - + +
8F VAL* 3.6 13.5 - - - +
71F LYS* 2.8 49.2 + - + +
72F LEU* 3.1 32.2 + - + +
74F ASN* 1.3 74.3 - - - +
76F ARG* 1.3 61.5 + - + +
77F GLY 3.6 0.3 + - - -
132F PHE* 5.3 3.3 - - - -
----------------------------------------------------------
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Residues in contact with ARG 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D VAL* 4.0 17.5 - - - +
8F VAL* 3.9 4.9 - - - +
9F ARG* 3.5 26.0 - - - +
10F GLN 3.0 28.8 + - - +
11F ASN* 3.1 22.4 + - - +
12F TYR* 3.6 34.1 - - + +
72F LEU* 3.0 35.1 + - + +
73F GLN 4.2 0.2 - - - +
75F GLN* 1.3 75.5 - - + +
77F GLY* 1.3 60.7 + - - +
78F GLY 3.3 1.0 + - - -
126F ASP* 3.0 30.6 + - - -
128F HIS* 3.1 39.6 + - - +
129F LEU* 3.8 5.9 - - - +
----------------------------------------------------------
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Residues in contact with GLY 77 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F SER* 3.5 25.7 + - - -
8F VAL* 3.5 17.7 - - - -
9F ARG* 3.7 15.1 + - - +
73F GLN 3.2 0.2 + - - -
74F ASN 3.1 13.3 + - - -
75F GLN 3.3 0.8 + - - -
76F ARG* 1.3 80.7 - - - +
78F GLY* 1.3 65.2 + - - +
79F ARG* 4.1 10.6 + - - +
----------------------------------------------------------
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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