Contacts of the helix formed by residues 13 - 42 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J ARG* 3.7 1.8 + - - -
11J ASN 4.0 3.4 + - - -
12J TYR* 1.3 76.3 - - - +
14J GLN* 1.3 74.8 + - + +
15J ASP* 3.0 43.5 + - - +
16J SER* 2.9 29.9 + - - +
17J GLU* 3.1 10.0 + - - +
124J LYS* 3.7 43.6 + - + -
126J ASP* 4.7 0.8 + - - -
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Residues in contact with GLN 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J ARG* 3.6 14.4 - - - +
12J TYR 3.6 1.8 + - - -
13J HIS* 1.3 81.1 + - + +
15J ASP* 1.3 72.0 + - - +
17J GLU* 3.4 7.1 + - - +
18J GLU* 3.0 47.5 + - + +
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Residues in contact with ASP 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J HIS* 3.0 22.2 + - + +
14J GLN* 1.3 87.3 - - - +
16J SER* 1.3 58.0 + - - +
18J GLU* 3.4 13.6 + - - +
19J ALA* 3.0 28.2 + - - +
22J ARG* 4.8 1.4 + - - -
120J LEU* 3.6 24.7 - - + +
124J LYS* 3.7 16.1 + - - -
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Residues in contact with SER 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J TYR* 4.1 11.7 - - - -
13J HIS* 2.9 25.4 + - - +
15J ASP* 1.3 76.9 - - - +
17J GLU* 1.3 64.6 + - - +
19J ALA* 3.2 3.4 + - - +
20J ILE* 2.9 28.1 + - - +
117J LEU* 5.3 0.7 - - - -
120J LEU* 4.1 13.8 - - - +
121J ALA* 4.7 3.6 - - - -
124J LYS* 4.3 13.5 - - - +
126J ASP* 4.5 3.2 + - - -
129J LEU* 3.8 26.3 - - - +
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Residues in contact with GLU 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J ARG* 2.8 32.5 + - - +
12J TYR* 3.7 23.0 - - + -
13J HIS 3.1 3.8 + - - -
14J GLN* 3.5 13.2 - - - +
16J SER* 1.3 73.2 - - - +
18J GLU* 1.4 66.5 + - + +
20J ILE 3.3 1.2 + - - -
21J ASN* 3.1 12.5 + - - +
73J GLN* 3.0 36.6 + - - +
78J GLY* 3.5 7.8 - - - -
79J ARG* 2.8 37.4 + - - +
81J PHE* 4.9 5.0 - - - -
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Residues in contact with GLU 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J GLN* 3.0 41.1 + - + +
15J ASP* 3.7 17.2 - - - +
17J GLU* 1.4 79.8 - - + +
19J ALA* 1.3 61.6 + - - +
21J ASN* 3.1 14.3 + - - +
22J ARG* 3.1 41.1 + - - +
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Residues in contact with ALA 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J ASP 3.0 18.0 + - - +
16J SER 3.6 2.2 - - - +
18J GLU* 1.3 75.6 - - - +
20J ILE* 1.3 58.0 + - - +
22J ARG* 3.3 26.6 + - - +
23J GLN* 2.9 29.1 + - - +
117J LEU* 3.4 28.0 - - + +
120J LEU* 3.8 10.8 - - + -
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Residues in contact with ILE 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J TYR* 3.5 16.4 - - + +
16J SER 2.9 20.4 + - - +
17J GLU 3.7 4.5 - - - +
18J GLU 3.2 0.2 - - - -
19J ALA* 1.3 76.8 - - - +
21J ASN* 1.3 57.4 + - - +
23J GLN* 3.1 3.6 + - - +
24J ILE* 2.8 34.0 + - + +
69J LEU* 3.8 44.9 - - + +
72J LEU* 4.2 7.4 - - + -
73J GLN* 3.8 16.8 - - + +
117J LEU* 3.8 22.7 - - + -
129J LEU* 3.9 23.6 - - + -
132J PHE* 5.1 0.9 - - + -
133J ILE* 5.6 0.2 - - + -
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Residues in contact with ASN 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J GLU* 3.1 15.6 + - - +
18J GLU* 3.1 12.7 + - - +
20J ILE* 1.3 76.7 - - - +
22J ARG* 1.3 61.4 + - + +
24J ILE* 3.5 14.5 + - - +
25J ASN* 3.3 19.1 + - - +
73J GLN* 3.0 19.6 + - - +
79J ARG 3.0 20.2 + - - -
80J ILE* 3.4 6.2 - - - +
81J PHE* 3.2 50.2 + - + +
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Residues in contact with ARG 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J ASP 4.8 2.4 + - - -
18J GLU* 3.1 26.1 + - - +
19J ALA* 3.6 34.0 - - - +
21J ASN* 1.3 76.0 - - + +
23J GLN* 1.3 57.9 + - - +
25J ASN* 3.2 7.8 + - - +
26J LEU* 3.0 26.0 + - - +
113J SER* 5.9 0.7 - - - -
120J LEU* 5.4 2.4 - - - +
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Residues in contact with GLN 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J ALA 2.9 16.7 + - - +
20J ILE* 3.1 6.0 + - - +
22J ARG* 1.3 74.3 - - - +
24J ILE* 1.3 66.0 + - - +
26J LEU* 3.1 10.6 + - - +
27J GLU* 2.9 52.1 + - - +
69J LEU* 3.7 21.3 - - + -
110J VAL* 3.8 11.7 + - - +
113J SER* 2.6 37.0 + - - +
114J LEU* 3.4 28.8 + - + +
117J LEU* 4.2 15.6 - - + +
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Residues in contact with ILE 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J ILE* 2.8 25.1 + - + +
21J ASN* 3.7 24.7 - - - +
22J ARG 3.3 0.2 - - - -
23J GLN* 1.3 77.2 - - - +
25J ASN* 1.4 62.9 + - - +
27J GLU* 3.3 3.5 + - - +
28J LEU* 3.0 40.2 + - + +
66J ALA* 4.1 4.4 - - + +
69J LEU* 3.6 30.7 - - + +
70J MET* 3.8 41.1 - - + +
73J GLN* 4.8 0.7 - - + -
80J ILE* 4.8 9.0 - - + -
82J LEU* 4.1 15.0 - - + -
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Residues in contact with ASN 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ASN 3.3 9.1 + - - +
22J ARG* 3.2 11.2 + - - +
24J ILE* 1.4 78.9 - - - +
26J LEU* 1.3 59.4 + - - +
28J LEU* 3.3 8.7 + - - +
29J TYR* 2.8 31.7 + - - +
83J GLN* 3.3 31.1 + - + +
84J ASP 2.8 30.0 + - - +
85J ILE* 4.3 9.0 - - - +
86J GLN* 5.4 5.5 - - - +
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Residues in contact with LEU 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J ARG 3.0 14.4 + - - +
23J GLN* 3.1 15.2 + - - +
25J ASN* 1.3 78.4 - - - +
27J GLU* 1.3 57.5 + - - +
29J TYR* 3.4 24.6 + - + +
30J ALA* 2.9 26.9 + - - +
106J LEU* 5.5 1.3 - - + -
109J ASN* 4.6 4.7 - - + +
110J VAL* 4.1 29.8 - - + +
113J SER* 3.6 33.7 - - - +
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Residues in contact with GLU 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J GLN* 2.9 42.9 + - - +
24J ILE 3.8 4.0 - - - +
26J LEU* 1.3 73.9 - - - +
28J LEU* 1.3 63.3 + - - +
30J ALA* 3.3 5.1 + - - +
31J SER* 3.0 21.8 + - - -
62J GLU* 2.7 18.1 - - - +
65J HIS* 3.3 11.5 - - + +
66J ALA* 3.8 18.6 - - + +
69J LEU* 3.6 19.3 - - + -
110J VAL* 3.5 11.1 - - - +
114J LEU* 4.3 1.2 - - - +
137J TYR* 4.2 11.5 - - - -
201J FE 2.1 33.7 - - - -
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Residues in contact with LEU 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ILE* 3.0 36.4 + - + +
25J ASN* 3.6 8.3 - - - +
27J GLU* 1.3 73.7 - - - +
29J TYR* 1.3 64.8 + - - +
31J SER* 3.3 9.0 + - - -
32J TYR* 3.1 22.2 + - - +
63J ARG* 4.0 27.8 - - - +
66J ALA* 3.6 19.7 - - + -
70J MET* 5.6 5.2 - - - -
82J LEU* 4.7 11.4 - - + -
83J GLN 5.8 1.1 - - - +
85J ILE* 3.8 36.0 - - + +
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Residues in contact with TYR 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J ASN* 2.8 21.4 + - - +
26J LEU* 3.5 24.7 - - + +
28J LEU* 1.3 74.6 - - - +
30J ALA* 1.3 59.1 + - - +
32J TYR* 3.0 4.7 + - - +
33J VAL* 2.9 52.7 + - + +
85J ILE* 3.8 12.0 - - + +
86J GLN* 3.3 42.4 - - + +
87J LYS 3.9 10.5 - - - -
89J ASP* 4.1 27.9 + - - -
106J LEU* 4.1 15.9 - - + -
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Residues in contact with ALA 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J LEU 2.9 17.6 + - - +
27J GLU* 3.3 6.2 + - - +
29J TYR* 1.3 74.7 - - - +
31J SER* 1.3 62.8 + - - +
33J VAL* 3.3 2.6 + - - +
34J TYR* 3.1 28.2 + - + -
62J GLU* 3.9 24.2 - - + +
106J LEU* 4.0 33.2 - - + -
107J GLU* 5.1 0.4 - - - +
110J VAL* 4.4 10.3 - - + -
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Residues in contact with SER 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J GLU 3.0 9.1 + - - -
28J LEU* 3.4 15.5 - - - -
30J ALA* 1.3 78.6 - - - +
32J TYR* 1.3 55.1 + - - +
35J LEU* 3.0 14.2 + - - +
59J SER* 2.7 51.9 + - - +
62J GLU* 3.6 17.6 - - - +
63J ARG* 3.8 16.1 + - - +
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Residues in contact with TYR 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J LEU 3.1 11.0 + - - +
29J TYR* 3.0 9.6 + - - +
31J SER* 1.3 72.6 - - - +
33J VAL* 1.3 65.9 + - - +
35J LEU* 3.2 27.2 + - + +
36J SER* 3.0 25.1 + - - -
85J ILE* 4.0 22.2 - - + -
86J GLN 3.5 18.8 - - - +
87J LYS* 3.9 21.6 - - + +
88J PRO* 3.8 11.6 - - + +
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Residues in contact with VAL 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J TYR* 2.9 49.8 + - + +
30J ALA 3.3 6.3 + - - +
32J TYR* 1.3 77.4 - - - +
34J TYR* 1.3 57.6 + - - +
36J SER* 3.2 4.5 + - - -
37J MET* 2.9 52.8 + - + +
88J PRO* 3.7 20.2 - - + -
89J ASP 5.4 0.2 - - - +
93J TRP* 4.0 13.7 - - + -
102J GLU 6.3 0.2 - - - -
106J LEU* 4.0 22.4 - - + -
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Residues in contact with TYR 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J ALA 3.1 22.1 + - - +
33J VAL* 1.3 79.1 - - - +
35J LEU* 1.3 55.3 - - - +
37J MET* 3.3 8.6 + - - +
38J SER* 2.9 29.6 + - - -
55J PHE* 3.5 49.0 - + - +
58J GLN* 3.7 28.7 + - + +
59J SER* 3.7 9.6 - - - +
62J GLU* 3.8 20.6 - - + -
103J ALA* 3.9 17.2 + - + +
106J LEU* 4.1 15.3 - - + -
107J GLU* 2.6 41.6 + - - +
144J ALA* 5.9 0.2 - - - +
148J LEU* 3.9 11.6 - - + +
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Residues in contact with LEU 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J SER 3.0 15.3 + - - +
32J TYR* 3.2 31.6 + - + +
34J TYR* 1.3 71.9 - - - +
36J SER* 1.3 65.7 + - - +
38J SER* 3.3 3.6 + - - -
39J TYR* 3.2 57.6 + - + +
56J LEU* 3.8 15.9 - - + -
59J SER* 3.7 11.6 + - - +
60J HIS* 6.0 0.4 - - - +
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Residues in contact with SER 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J TYR* 3.0 14.5 + - - -
33J VAL 3.4 8.7 - - - -
35J LEU* 1.3 77.5 - - - +
37J MET* 1.3 63.0 + - - +
39J TYR* 3.4 2.5 + - - +
40J TYR* 3.1 21.7 + - - +
88J PRO* 3.8 16.8 - - - +
90J GLU 3.9 8.3 + - - -
91J ASP* 4.7 4.7 + - - +
93J TRP* 2.9 20.2 + - - -
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Residues in contact with MET 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J VAL* 2.9 29.9 + - + +
34J TYR* 3.7 17.5 - - - +
36J SER* 1.3 75.8 - - - +
38J SER* 1.3 65.7 + - - +
40J TYR* 3.2 8.8 + - - +
41J PHE* 3.0 25.1 + - + -
55J PHE* 3.9 33.2 - - + -
93J TRP* 3.6 50.9 - - + +
99J ALA* 3.6 28.0 - - + +
102J GLU* 3.8 10.3 - - + -
103J ALA* 4.0 8.1 - - + +
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Residues in contact with SER 38 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR 2.9 17.2 + - - -
35J LEU* 3.5 8.3 - - - -
36J SER 3.2 0.2 - - - -
37J MET* 1.3 77.5 - - - +
39J TYR* 1.3 68.2 + - - +
41J PHE 3.2 14.2 + - - -
42J ASP* 3.4 2.0 + - - +
52J ALA* 2.7 48.2 + - - +
55J PHE* 3.8 8.0 - - - +
56J LEU* 3.5 24.6 - - - +
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Residues in contact with TYR 39 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J LEU* 3.2 42.4 + - + +
36J SER* 4.4 2.5 - - - +
38J SER* 1.3 78.4 - - - +
40J TYR* 1.3 64.9 + - - +
41J PHE 3.4 0.2 - - - -
42J ASP* 3.4 37.6 + - + +
43J ARG* 3.5 13.7 + - - +
56J LEU* 4.1 24.9 - - + +
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Residues in contact with TYR 40 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H LYS* 5.9 0.3 + - - -
36J SER 3.1 13.1 + - - +
37J MET 3.4 7.9 - - - +
39J TYR* 1.3 77.0 - - - +
41J PHE* 1.3 84.6 + + - +
42J ASP 3.1 0.2 - - - -
43J ARG* 3.1 51.5 + - - +
46J VAL* 3.5 38.7 - - + +
91J ASP 4.4 4.9 - - - +
92J ASP* 3.5 28.3 + - - -
93J TRP* 3.6 25.8 - + + -
94J GLU* 3.2 38.2 + - - -
95J SER* 4.3 3.5 - - - -
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Residues in contact with PHE 41 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J MET* 3.0 24.9 + - + -
38J SER 3.2 6.8 + - - +
40J TYR* 1.3 95.9 - + - +
42J ASP* 1.3 55.8 + - - +
43J ARG 3.3 0.2 - - - -
46J VAL* 3.5 19.1 - - + -
47J ALA* 3.3 8.2 + - - -
48J LEU* 2.9 53.3 + - + +
49J LYS* 4.5 1.2 + - - +
51J PHE* 3.6 15.5 - + + -
52J ALA* 3.7 10.7 - - - +
55J PHE* 3.5 31.4 - + - -
93J TRP* 5.0 0.2 - - + -
95J SER* 3.5 20.6 - - - -
96J GLY* 3.6 24.7 - - - -
99J ALA* 3.6 13.5 - - + -
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Residues in contact with ASP 42 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H LYS* 2.9 39.5 + - - +
38J SER 3.4 10.7 + - - +
39J TYR* 3.7 37.2 - - + +
40J TYR 3.1 0.6 - - - -
41J PHE* 1.3 75.3 - - - +
43J ARG* 1.3 58.9 + - - +
47J ALA* 5.2 1.1 - - - +
49J LYS* 5.9 6.1 - - - +
52J ALA* 4.5 9.5 - - + +
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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