Contacts of the helix formed by residues 13 - 42 (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 HIS 13 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ARG* 3.7 2.8 + - - -
11F ASN 4.0 2.8 + - - -
12F TYR* 1.3 76.5 - - - +
14F GLN* 1.3 73.2 + - + +
15F ASP* 3.0 47.6 + - - +
16F SER* 3.0 29.8 + - - +
17F GLU* 3.1 9.9 + - - +
124F LYS* 3.6 41.9 + - + -
126F ASP* 4.8 1.0 + - - +
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Residues in contact with GLN 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ARG* 3.7 13.9 - - - +
12F TYR 3.7 0.4 + - - -
13F HIS* 1.3 82.6 + - + +
15F ASP* 1.3 60.2 + - - +
17F GLU* 3.3 11.6 + - - +
18F LYS* 3.0 63.9 + - + +
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Residues in contact with ASP 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F HIS* 3.0 25.3 + - + +
14F GLN* 1.3 79.8 + - - +
16F SER* 1.3 56.9 + - - +
18F LYS* 3.4 12.5 + - - +
19F ALA* 3.0 28.8 + - - +
22F ARG* 4.9 1.6 + - - -
120F LEU* 3.6 24.3 - - + +
124F LYS* 3.6 17.5 + - - -
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Residues in contact with SER 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F TYR* 4.2 12.1 - - - -
13F HIS* 3.0 25.9 + - - +
15F ASP* 1.3 76.1 - - - +
17F GLU* 1.3 59.0 + - - +
19F ALA* 3.2 3.0 + - - +
20F ILE* 2.9 34.8 + - - +
117F LEU* 4.6 1.0 - - - +
120F LEU* 3.9 14.7 - - - +
121F ALA* 4.7 3.3 - - - -
124F LYS* 4.1 14.0 - - - +
126F ASP* 4.7 3.3 + - - +
129F LEU* 3.9 25.7 - - - +
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Residues in contact with GLU 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ARG* 2.8 27.1 + - - +
12F TYR* 3.6 19.2 + - + -
13F HIS 3.1 11.5 + - - +
14F GLN* 3.5 17.5 - - - +
16F SER* 1.3 76.9 - - - +
18F LYS* 1.3 63.9 + - + +
20F ILE 3.4 1.0 + - - -
21F ASN* 3.1 12.5 + - - +
73F GLN* 3.0 37.5 + - - +
78F GLY* 3.5 10.6 - - - -
79F ARG* 2.9 33.0 + - - +
81F PHE* 5.4 2.4 - - - -
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Residues in contact with LYS 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F GLN* 3.0 49.6 + - + +
15F ASP* 3.7 11.9 - - - +
17F GLU* 1.3 78.4 - - + +
19F ALA* 1.3 62.2 + - - +
21F ASN* 3.3 11.2 + - - +
22F ARG* 3.0 39.8 + - - +
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Residues in contact with ALA 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ASP 3.0 17.5 + - - +
16F SER 3.2 2.9 + - - +
18F LYS* 1.3 78.1 - - - +
20F ILE* 1.3 56.3 + - - +
22F ARG* 3.2 29.4 + - - +
23F GLN* 3.0 26.9 + - - +
117F LEU* 3.5 26.3 - - + +
120F LEU* 3.8 11.7 - - + -
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Residues in contact with ILE 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F TYR* 3.5 14.8 - - - +
16F SER 2.9 20.2 + - - +
17F GLU 3.7 4.7 - - - +
19F ALA* 1.3 74.1 - - - +
21F ASN* 1.3 60.9 + - - +
23F GLN* 3.1 4.5 + - - +
24F ILE* 2.9 33.7 + - + +
69F LEU* 3.8 43.5 - - + +
72F LEU* 4.3 7.4 - - + -
73F GLN* 3.7 19.7 - - + +
117F LEU* 3.8 22.7 - - + -
129F LEU* 4.0 22.4 - - + -
132F PHE* 5.2 0.7 - - + -
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Residues in contact with ASN 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F GLU* 3.1 15.4 + - - +
18F LYS* 3.3 11.3 + - - +
20F ILE* 1.3 75.6 - - - +
22F ARG* 1.3 60.9 + - + +
24F ILE* 3.4 15.5 + - - +
25F ARG* 3.2 21.1 + - - +
73F GLN* 3.0 19.3 + - - +
79F ARG 3.0 22.2 + - - -
80F ILE* 3.6 5.9 - - - +
81F PHE* 3.5 46.4 + - + +
83F GLN* 6.0 1.2 - - - +
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Residues in contact with ARG 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ASP 4.9 1.6 + - - -
18F LYS* 3.0 34.9 + - - +
19F ALA* 3.2 32.9 + - - +
21F ASN* 1.3 75.7 - - + +
23F GLN* 1.3 62.6 + - - +
25F ARG* 3.3 11.0 + - - +
26F LEU* 3.1 21.4 + - - +
120F LEU* 5.3 3.4 - - - +
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Residues in contact with GLN 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ALA 3.0 12.7 + - - +
20F ILE* 3.1 11.2 + - - +
22F ARG* 1.3 76.4 - - - +
24F ILE* 1.3 64.5 + - - +
26F LEU* 3.1 13.3 + - - +
27F GLU* 2.8 48.3 + - - +
69F LEU* 3.6 21.5 - - + -
110F VAL* 3.9 10.3 + - - +
113F SER* 2.7 35.7 + - - +
114F LEU* 3.6 28.3 - - + +
117F LEU* 4.4 13.8 - - + +
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Residues in contact with ILE 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ILE* 2.9 28.6 + - + +
21F ASN* 3.7 24.7 - - - +
23F GLN* 1.3 77.0 - - - +
25F ARG* 1.3 63.0 + - - +
27F GLU* 3.3 3.8 + - - +
28F LEU* 3.1 40.6 + - + +
66F ALA* 4.2 4.9 - - + +
69F LEU* 3.6 24.0 - - + +
70F MET* 3.7 42.8 - - + +
73F GLN* 4.7 3.8 - - + -
80F ILE* 4.8 5.8 - - + -
82F LEU* 4.0 15.0 - - + -
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Residues in contact with ARG 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ASN 3.2 10.0 + - - +
22F ARG* 3.5 11.7 - - - +
23F GLN 3.3 0.2 - - - -
24F ILE* 1.3 81.7 - - - +
26F LEU* 1.3 57.6 + - - +
28F LEU* 3.4 10.3 + - - +
29F TYR* 2.9 27.4 + - - +
82F LEU* 6.3 0.2 - - - -
83F GLN* 3.5 44.4 + - + +
84F ASP* 2.8 37.8 + - - +
85F ILE* 4.8 4.9 - - + +
86F GLN* 3.5 35.1 + - - +
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Residues in contact with LEU 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ARG 3.1 12.5 + - - +
23F GLN* 3.1 16.2 + - - +
25F ARG* 1.3 73.8 - - - +
27F GLU* 1.3 60.7 + - - +
29F TYR* 3.2 18.7 + - + +
30F ALA* 2.9 26.5 + - - +
106F LEU* 5.4 0.2 - - + -
109F LYS* 3.9 30.5 - - + +
110F VAL* 3.9 29.8 - - + -
113F SER* 3.4 35.9 - - - +
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Residues in contact with GLU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLN* 2.8 45.3 + - - +
24F ILE 3.8 4.3 - - - +
26F LEU* 1.3 75.3 - - - +
28F LEU* 1.3 58.0 + - - +
30F ALA* 3.3 5.9 + - - +
31F SER* 3.0 24.1 + - - -
62F GLU* 2.7 20.8 - - - +
65F HIS* 3.3 11.1 - - + +
66F ALA* 3.8 18.6 - - + +
69F LEU* 3.6 20.0 - - + -
110F VAL* 3.5 11.4 - - - +
114F LEU* 4.4 0.5 - - - +
137F TYR* 4.2 12.4 - - - -
201F FE 2.0 34.1 - - - -
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Residues in contact with LEU 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ILE* 3.1 35.2 + - + +
25F ARG* 3.7 7.0 - - - +
27F GLU* 1.3 77.0 - - - +
29F TYR* 1.4 61.5 + - - +
31F SER* 3.2 7.8 + - - -
32F TYR* 3.0 22.7 + - - +
63F ARG* 4.1 27.6 - - - +
66F ALA* 3.6 20.6 - - + -
70F MET* 5.5 4.3 - - - -
82F LEU* 4.4 14.4 - - + -
83F GLN 6.0 0.7 - - - +
85F ILE* 3.9 35.1 - - + +
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Residues in contact with TYR 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F ARG 2.9 14.1 + - - +
26F LEU* 3.2 25.3 + - + +
28F LEU* 1.4 76.1 - - - +
30F ALA* 1.3 59.8 + - - +
32F TYR* 3.0 5.9 + - + +
33F VAL* 2.9 52.2 + - + +
85F ILE* 3.7 9.3 - - + +
86F GLN* 3.2 51.4 - - + +
87F LYS 3.7 12.3 - - - -
88F PRO* 4.1 1.1 - - + -
89F ASP* 3.7 30.3 + - - -
106F LEU* 3.9 16.2 - - + -
109F LYS* 4.8 11.7 - - + -
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Residues in contact with ALA 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU 2.9 16.3 + - - +
27F GLU* 3.3 10.1 + - - +
29F TYR* 1.3 72.2 - - - +
31F SER* 1.3 63.0 + - - +
33F VAL* 3.3 2.4 + - - +
34F TYR* 3.0 27.5 + - - -
62F GLU* 3.8 25.1 - - + +
106F LEU* 4.1 31.2 - - + -
107F GLU* 5.9 0.9 - - - +
110F VAL* 4.4 10.5 - - + -
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Residues in contact with SER 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F GLU 3.0 9.6 + - - -
28F LEU* 3.5 14.1 - - - -
29F TYR 3.2 0.2 - - - -
30F ALA* 1.3 77.5 - - - +
32F TYR* 1.3 57.8 + - - +
35F LEU* 3.0 15.3 + - - +
59F SER* 2.7 54.7 + - - +
60F HIS* 5.9 0.2 - - - -
62F GLU* 3.6 16.3 - - - +
63F ARG* 3.9 16.1 + - - +
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Residues in contact with TYR 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LEU 3.0 12.1 + - - +
29F TYR* 3.0 11.5 + - - +
31F SER* 1.3 76.4 - - - +
33F VAL* 1.3 64.9 + - - +
35F LEU* 3.3 23.7 + - + +
36F SER* 3.0 20.4 + - - -
85F ILE* 4.0 19.7 - - + -
86F GLN 3.5 17.9 - - - +
87F LYS* 3.9 13.4 - - + +
88F PRO* 3.7 26.0 - - + +
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Residues in contact with VAL 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F TYR* 2.9 59.6 + - + +
30F ALA 3.7 5.8 - - - +
32F TYR* 1.3 71.4 - - - +
34F TYR* 1.3 58.6 + - - +
36F SER* 3.2 4.0 + - - -
37F MET* 2.9 52.8 + - + +
88F PRO* 3.7 15.5 - - + -
93F TRP* 3.9 13.7 - - + -
106F LEU* 3.9 19.5 - - + -
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Residues in contact with TYR 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ALA* 3.0 22.7 + - + +
33F VAL* 1.3 79.3 - - - +
35F LEU* 1.3 56.4 - - - +
37F MET* 3.3 9.0 + - - +
38F SER* 2.9 29.6 + - - -
54F TYR* 5.6 0.2 - + - -
55F PHE* 3.5 46.4 - + - +
58F GLN* 3.7 29.2 + - + +
59F SER* 3.6 12.3 - - - +
62F GLU* 3.8 21.5 - - + -
103F ALA* 3.8 17.5 - - + +
106F LEU* 4.1 16.6 - - + -
107F GLU* 2.5 39.9 + - - +
148F LEU* 3.8 12.2 - - + +
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Residues in contact with LEU 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F SER 3.0 18.0 + - - +
32F TYR* 3.5 26.5 - - + +
34F TYR* 1.3 76.7 - - - +
36F SER* 1.3 63.3 + - - +
38F SER* 3.3 6.3 + - - -
39F TYR* 3.2 49.6 + - + +
56F LEU* 3.9 14.6 - - + -
59F SER* 3.7 10.9 - - - +
60F HIS* 6.1 0.2 - - - +
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Residues in contact with SER 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F TYR* 3.0 14.2 + - - -
33F VAL 3.4 8.5 - - - -
35F LEU* 1.3 77.0 - - - +
37F MET* 1.3 65.8 + - - +
39F TYR* 3.5 2.9 + - - +
40F TYR* 3.1 21.7 + - - +
88F PRO* 3.9 16.7 - - - +
90F LYS 3.8 8.5 + - - -
91F ASP* 4.5 5.7 + - - +
93F TRP* 2.9 19.9 + - - -
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Residues in contact with MET 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F VAL* 2.9 29.1 + - + +
34F TYR* 3.6 17.5 - - - +
35F LEU 3.3 0.2 - - - -
36F SER* 1.3 76.6 - - - +
38F SER* 1.3 63.5 + - - +
40F TYR* 3.1 9.2 + - - +
41F PHE* 3.0 25.0 + - + -
55F PHE* 3.9 38.6 - - + -
93F TRP* 3.7 50.7 - - + -
99F ALA* 3.6 25.4 - - + +
102F LYS* 3.8 4.3 - - + +
103F ALA* 3.8 16.8 - - - +
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Residues in contact with SER 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F TYR 2.9 16.5 + - - -
35F LEU 3.5 6.3 - - - -
36F SER 3.3 0.4 - - - -
37F MET* 1.3 76.5 - - - +
39F TYR* 1.3 68.9 + - - +
41F PHE 3.1 15.2 + - - -
42F ASP* 3.3 1.4 + - - +
52F ALA* 2.7 47.6 + - - +
55F PHE* 3.7 8.4 - - - +
56F LEU* 3.4 27.8 - - - +
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Residues in contact with TYR 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F LEU* 3.2 41.5 + - + +
36F SER* 4.4 2.5 - - - +
38F SER* 1.3 82.7 - - - +
40F TYR* 1.3 64.0 + - - +
42F ASP* 3.3 37.4 + - + +
43F ARG* 3.4 13.5 + - - +
56F LEU* 4.2 24.8 - - + +
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Residues in contact with TYR 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F SER 3.1 12.8 + - - +
37F MET 3.1 9.0 + - - +
39F TYR* 1.3 75.5 - - - +
41F PHE* 1.3 97.1 + + - +
43F ARG* 3.2 49.1 + - - +
46F VAL* 3.5 33.5 - - + +
91F ASP 4.3 4.5 - - - +
92F ASP* 3.4 25.6 + - - -
93F TRP* 3.6 27.1 - - + -
94F GLU* 3.2 39.7 + - - -
95F SER* 4.2 3.9 - - - -
----------------------------------------------------------
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Residues in contact with PHE 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F MET* 3.0 25.3 + - + -
38F SER 3.1 6.6 + - - +
40F TYR* 1.3 98.4 - + - +
42F ASP* 1.3 54.7 + - - +
43F ARG 3.3 0.4 - - - -
46F VAL* 3.5 17.9 - - + -
47F ALA* 3.3 9.0 + - - -
48F LEU* 3.0 55.4 + - + +
51F PHE* 3.5 17.5 - + + -
52F ALA* 3.7 10.8 - - - +
55F PHE* 3.6 31.2 - + - -
95F SER 3.7 9.4 - - - -
96F GLY* 3.7 24.9 - - - -
99F ALA* 3.6 24.7 - - + -
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Residues in contact with ASP 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F SER 3.3 9.4 + - - +
39F TYR* 3.3 36.9 + - + +
40F TYR 3.2 0.4 - - - -
41F PHE* 1.3 75.7 - - - +
43F ARG* 1.4 64.1 + - - +
44F ASP 3.5 1.6 + - - -
47F ALA* 5.2 1.3 - - - +
49F LYS* 6.0 2.6 - - - +
52F ALA* 4.5 9.0 - - + -
----------------------------------------------------------
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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