Contacts of the helix formed by residues 13 - 41 (chain J) in PDB entry 2FFX
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 13 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J ARG* 3.5 3.9 + - - -
11J ASN 3.9 3.6 + - - -
12J TYR* 1.3 76.8 - - - +
14J THR* 1.3 61.3 + - - +
15J ASP* 3.0 22.4 + - - +
16J VAL* 3.2 14.4 + - - +
17J GLU* 3.0 18.2 + - - +
124J ARG* 3.6 17.6 + - - -
126J ASP* 4.9 0.8 + - - -
189J SO4 2.7 43.0 + - - -
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Residues in contact with THR 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J ARG* 3.5 21.8 - - - +
12J TYR 3.7 0.6 + - - +
13J SER* 1.3 73.9 + - - +
15J ASP* 1.3 66.8 + - - +
16J VAL 3.4 0.2 - - - -
17J GLU* 3.6 8.6 - - - +
18J ALA* 3.1 27.4 + - - +
189J SO4 4.7 3.8 + - - -
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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 SER* 3.0 9.1 + - - +
14J THR* 1.3 83.6 + - - +
16J VAL* 1.3 60.2 + - - +
18J ALA* 3.4 6.1 + - - +
19J ALA* 2.9 28.4 + - - +
120J LEU* 3.7 11.9 - - + +
124J ARG* 2.6 36.5 + - - +
189J SO4 3.5 1.9 + - - -
192J CD 2.1 32.1 - - - -
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Residues in contact with VAL 16 (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 26.7 - - + -
13J SER* 3.2 24.3 + - - +
15J ASP* 1.3 73.8 - - - +
17J GLU* 1.3 56.4 + - - +
19J ALA* 3.1 1.3 + - - +
20J VAL* 2.8 47.9 + - + +
117J LEU* 4.4 1.6 - - + -
120J LEU* 4.0 24.5 - - + -
121J GLY* 4.4 8.7 - - - -
124J ARG* 4.4 5.8 - - + -
126J ASP* 4.7 6.1 - - - +
129J LEU* 3.6 33.2 - - + -
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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* 2.7 33.2 + - - -
12J TYR* 3.8 17.4 + - + -
13J SER 3.0 12.2 + - - +
14J THR* 3.6 14.3 - - - +
16J VAL* 1.3 79.0 - - - +
18J ALA* 1.3 61.4 + - - +
20J VAL 3.3 0.2 + - - -
21J ASN* 3.2 24.5 + - - +
73J GLN* 3.2 29.9 + - - +
78J GLY* 3.6 2.6 - - - -
79J ARG* 2.7 35.7 + - - +
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Residues in contact with ALA 18 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J THR 3.1 18.7 + - - +
15J ASP* 3.7 6.5 - - - +
17J GLU* 1.3 77.9 - - - +
19J ALA* 1.3 62.4 + - - +
21J ASN* 3.2 11.6 + - - +
22J SER* 3.0 21.7 + - - -
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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 2.9 17.4 + - - +
16J VAL 3.1 4.2 + - - +
18J ALA* 1.3 76.2 - - - +
20J VAL* 1.3 57.4 + - - +
22J SER* 3.3 8.9 + - - -
23J LEU* 2.9 29.3 + - - +
117J LEU* 4.0 17.5 - - + +
120J LEU* 3.7 20.2 - - + -
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Residues in contact with VAL 20 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J TYR* 3.5 14.4 - - - +
16J VAL* 2.8 29.5 + - + +
17J GLU 3.6 5.2 - - - +
19J ALA* 1.3 77.9 - - - +
21J ASN* 1.3 56.9 + - - +
23J LEU* 3.2 7.2 + - - +
24J VAL* 2.9 34.8 + - + +
69J LEU* 4.0 27.1 - - + +
70J LEU* 6.1 0.2 - - + -
72J MET* 3.9 21.5 - - + -
73J GLN* 3.8 18.4 - - + +
117J LEU* 4.3 14.6 - - + -
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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* 3.2 19.2 + - - +
18J ALA* 3.2 9.5 + - - +
20J VAL* 1.3 77.0 - - - +
22J SER* 1.3 63.8 + - - +
24J VAL* 3.3 8.9 + - - +
25J ASN* 3.1 20.6 + - - +
70J LEU* 5.1 4.3 - - - +
73J GLN* 3.1 17.5 + - - +
79J ARG 3.1 20.8 + - - -
80J ALA* 3.4 6.9 - - - +
81J LEU* 3.2 48.0 + - + +
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Residues in contact with SER 22 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ALA 3.0 13.2 + - - -
19J ALA* 3.5 11.7 - - - -
20J VAL 3.2 0.2 - - - -
21J ASN* 1.3 78.1 - - - +
23J LEU* 1.3 62.2 + - - +
25J ASN* 3.1 9.6 + - - +
26J LEU* 3.0 20.9 + - - +
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Residues in contact with LEU 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 17.2 + - - +
20J VAL* 3.6 6.1 - - - +
22J SER* 1.3 72.7 - - - +
24J VAL* 1.3 64.9 + - - +
26J LEU* 3.0 11.2 + - + +
27J TYR* 2.9 42.4 + - + -
69J LEU* 3.8 28.7 - - + -
110J LEU 4.9 0.7 - - - +
113J ALA* 3.8 32.8 - - + +
114J LEU* 3.8 20.4 - - + -
117J LEU* 3.7 29.4 - - + -
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Residues in contact with VAL 24 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J VAL* 2.9 23.0 + - + +
21J ASN* 3.5 12.1 - - - +
22J SER 3.2 0.2 - - - -
23J LEU* 1.3 77.4 - - - +
25J ASN* 1.3 58.0 + - - +
27J TYR* 3.2 2.9 + - - +
28J LEU* 2.9 43.8 + - + +
66J TYR* 4.1 14.0 - - + +
69J LEU* 3.7 31.6 - - + -
70J LEU* 3.7 32.1 - - + -
81J LEU 6.0 0.7 - - - +
82J PHE* 4.1 11.9 - - + -
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Residues in contact with ASN 25 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ASN 3.1 11.5 + - - +
22J SER* 3.1 11.7 + - - +
24J VAL* 1.3 76.6 - - - +
26J LEU* 1.3 63.7 + - - +
28J LEU* 3.3 11.4 + - - +
29J GLN* 3.0 34.3 + - - +
83J GLN* 3.5 31.6 + - + +
84J ASP 3.1 27.9 + - - +
85J ILE* 4.5 8.4 - - - +
86J LYS* 5.4 0.7 + - - +
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Residues in contact with LEU 26 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J SER 3.0 13.3 + - - +
23J LEU* 3.0 15.7 + - + +
25J ASN* 1.3 79.0 + - - +
27J TYR* 1.3 57.3 + - - +
29J GLN* 3.4 14.5 + - - +
30J ALA* 3.0 27.0 + - - +
109J LYS* 3.5 38.4 + - + +
110J LEU* 3.6 23.9 - - + +
113J ALA* 3.4 33.0 - - + -
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Residues in contact with TYR 27 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J LEU* 2.9 50.0 + - + +
24J VAL* 3.2 4.7 + - - +
26J LEU* 1.3 76.0 - - - +
28J LEU* 1.3 60.9 + - - +
30J ALA* 3.6 4.5 - - - +
31J SER* 2.9 31.0 + - - -
61J GLU 5.4 0.2 - - - -
62J LYS* 3.5 47.6 - - + +
65J GLY* 4.0 9.4 - - - -
66J TYR* 3.8 19.4 - - + -
69J LEU* 4.2 5.2 - - + -
110J LEU* 3.9 20.4 - - + +
114J LEU* 3.5 21.3 - - + +
137J PHE* 3.4 32.1 - + - -
141J GLU* 4.1 9.7 + - - -
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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 VAL* 2.9 35.4 + - + +
25J ASN* 3.3 13.9 + - - +
27J TYR* 1.3 77.3 - - - +
29J GLN* 1.3 57.5 + - - +
31J SER* 3.5 2.6 + - - -
32J TYR* 3.1 27.0 + - - +
66J TYR* 3.4 42.6 - - + +
82J PHE* 4.3 18.2 - - + -
83J GLN 5.6 1.8 - - - +
85J ILE* 3.9 38.1 - - + +
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Residues in contact with GLN 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J ASN* 3.0 29.8 + - - +
26J LEU* 3.6 17.1 - - - +
27J TYR 3.2 0.2 - - - -
28J LEU* 1.3 76.6 - - - +
30J ALA* 1.3 59.2 + - - +
32J TYR* 3.3 4.4 + - - +
33J THR* 3.0 35.2 + - - +
85J ILE* 3.9 13.6 - - + +
86J LYS* 3.6 51.4 + - - +
87J LYS 4.9 3.0 - - - +
88J PRO* 6.1 0.2 - - + -
106J LEU* 6.4 0.7 - - + -
109J LYS* 4.3 17.2 + - - +
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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 3.0 17.3 + - - +
27J TYR* 3.2 6.5 + - - +
29J GLN* 1.3 74.8 - - - +
31J SER* 1.3 66.2 + - - +
33J THR* 3.1 4.2 + - - -
34J TYR* 3.0 28.8 + - - -
62J LYS* 4.1 7.2 - - + -
106J LEU* 4.1 25.7 - - + +
110J LEU* 3.9 27.8 - - + -
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Residues in contact with SER 31 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J TYR 2.9 17.1 + - - -
28J LEU 3.7 4.5 - - - -
30J ALA* 1.3 77.0 - - - +
32J TYR* 1.3 57.3 + - - +
34J TYR 3.3 1.2 + - - -
35J LEU* 3.0 27.4 + - - +
59J ALA* 2.9 34.9 + - - +
62J LYS* 3.8 13.0 - - - +
63J ARG* 4.2 6.4 + - - +
66J TYR* 4.2 15.0 + - - -
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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 14.6 + - - +
29J GLN 3.3 10.8 - - - +
31J SER* 1.3 75.6 - - - +
33J THR* 1.3 64.6 + - - +
35J LEU* 3.2 24.0 + - + +
36J SER* 3.1 18.1 + - - -
85J ILE* 3.9 18.6 - - + -
86J LYS 3.6 18.2 - - - -
87J LYS* 3.7 22.9 - - + +
88J PRO* 3.7 20.8 - - + +
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Residues in contact with THR 33 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J GLN* 3.0 18.1 + - - +
30J ALA* 3.5 8.0 - - - -
32J TYR* 1.3 77.7 - - - +
34J TYR* 1.3 56.2 + - - +
36J SER* 3.3 4.2 + - - -
37J LEU* 2.9 38.5 + - + +
88J PRO* 3.9 24.0 - - - +
89J ALA 4.8 1.3 + - - +
93J TRP* 3.7 25.6 - - + -
102J ALA* 6.3 1.6 - - + -
106J LEU* 3.9 22.8 - - + +
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Residues in contact with TYR 34 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J ALA 3.0 19.7 + - - -
31J SER 3.8 1.6 - - - +
33J THR* 1.3 74.1 - - - +
35J LEU* 1.3 61.2 + - - +
37J LEU* 3.7 10.8 - - + +
38J GLY* 2.8 27.0 + - - -
55J PHE* 3.4 49.0 - + - +
56J ARG 4.4 0.2 + - - -
58J LEU* 3.7 26.0 - - + -
59J ALA* 3.6 14.7 - - + +
62J LYS* 3.9 23.6 - - + -
103J ALA* 3.5 25.8 + - + -
106J LEU* 3.8 18.2 - - + +
107J GLU* 2.5 34.5 + - - +
148J MET* 3.5 6.1 - - - +
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Residues in contact with LEU 35 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J SER 3.0 14.2 + - - +
32J TYR* 3.2 33.0 + - + +
34J TYR* 1.3 75.6 - - - +
36J SER* 1.3 64.0 + - - +
38J GLY* 3.3 1.6 + - - -
39J PHE* 3.1 56.0 + - + +
56J ARG* 5.7 4.5 - - + +
59J ALA* 4.0 10.0 - - + +
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Residues in contact with SER 36 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J TYR* 3.1 14.5 + - - -
33J THR 3.5 8.3 - - - -
35J LEU* 1.3 76.7 - - - +
37J LEU* 1.3 64.8 + - - +
39J PHE* 3.5 2.6 + - - +
40J TYR* 3.0 24.1 + - - +
88J PRO* 3.8 17.1 - - - +
90J GLU 4.1 6.1 + - - -
91J ASP* 4.7 4.7 + - - -
93J TRP* 3.1 19.5 + - - -
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Residues in contact with LEU 37 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J THR* 2.9 32.0 + - + +
34J TYR* 3.7 28.5 - - + +
36J SER* 1.3 75.4 - - - +
38J GLY* 1.3 65.3 + - - +
40J TYR* 3.3 1.0 + - - +
41J PHE* 3.2 31.7 + - + -
55J PHE* 3.7 25.1 - - + -
93J TRP* 3.4 44.0 - - + +
99J ALA* 3.7 32.3 - - + +
102J ALA* 5.5 1.1 - - + -
103J ALA* 4.9 4.9 - - + +
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Residues in contact with GLY 38 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR 2.8 17.5 + - - -
35J LEU 3.7 2.0 - - - -
36J SER 3.2 0.2 - - - -
37J LEU* 1.3 79.4 - - - +
39J PHE* 1.3 61.3 + - - +
41J PHE 3.5 2.4 + - - -
42J ASP 3.5 1.0 + - - -
52J SER* 2.7 37.3 + - - -
55J PHE* 3.7 5.1 - - - +
56J ARG* 3.7 23.1 - - - -
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Residues in contact with PHE 39 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J LEU* 3.1 45.1 + - + +
36J SER* 4.4 2.9 - - - +
38J GLY* 1.3 74.4 - - - +
40J TYR* 1.3 66.5 + - - +
41J PHE 3.2 0.2 - - - -
42J ASP* 3.0 37.9 + - + +
43J ARG* 3.3 9.9 + - - +
56J ARG* 3.7 43.5 - - - -
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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
----------------------------------------------------------
36J SER 3.0 19.2 + - - +
37J LEU 3.3 4.0 + - - +
39J PHE* 1.3 76.0 - - - +
41J PHE* 1.3 82.6 + + - +
43J ARG* 3.1 63.6 + - - +
46J VAL* 3.5 28.7 - - + +
91J ASP 4.4 4.3 - - - +
92J GLU* 3.8 15.8 + - + +
93J TRP* 3.5 39.3 - + + -
94J GLY* 2.8 37.0 + - - -
----------------------------------------------------------
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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 LEU* 3.2 25.5 + - + +
38J GLY 3.5 0.2 + - - -
39J PHE 3.2 0.4 - - - -
40J TYR* 1.3 99.7 - + - +
42J ASP* 1.3 57.5 + - - +
43J ARG 3.3 0.7 - - - -
46J VAL* 3.4 25.1 - - + -
47J ALA* 3.6 2.9 + - - -
48J LEU* 3.1 48.1 + - + +
49J GLU* 5.0 0.3 - - - -
51J VAL* 3.5 30.7 - - + -
52J SER* 3.8 27.0 - - - +
55J PHE* 3.9 6.5 - + - -
94J GLY 4.4 1.3 - - - -
95J LYS* 4.1 4.5 - - - -
96J THR* 4.0 16.4 - - - -
99J ALA* 3.5 33.7 - - + -
167J GLU* 4.6 0.4 - - - -
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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