Contacts of the helix formed by residues 28 - 59 (chain J) in PDB entry 2FJC
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 ASP 28 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J PRO* 1.3 82.8 - - - +
29J ALA* 1.3 63.8 + - - +
30J ARG* 3.7 18.1 + - - +
31J ALA* 2.9 41.5 + - + +
32J ILE* 3.4 11.1 + - - +
148J SER* 4.8 7.3 - - - +
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Residues in contact with ALA 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J PRO* 4.9 2.9 - - + +
28J ASP* 1.3 73.5 + - - +
30J ARG* 1.3 63.4 + - - +
32J ILE* 3.1 17.7 + - + +
33J ALA* 3.0 23.9 + - - +
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Residues in contact with ARG 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J ASP* 3.1 15.9 + - - +
29J ALA* 1.3 78.9 - - - +
31J ALA* 1.3 64.5 + - - +
33J ALA* 3.4 7.4 + - - +
34J ALA* 3.2 30.5 + - - +
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Residues in contact with ALA 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J ASP* 2.9 26.9 + - + +
30J ARG* 1.3 80.3 - - + +
32J ILE* 1.3 62.1 - - + +
34J ALA* 3.2 7.0 + - - +
35J ILE* 2.8 36.6 + - + +
144J LEU* 5.5 2.9 - - + +
148J SER* 3.5 30.1 - - - +
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Residues in contact with ILE 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J PRO* 5.2 11.2 - - + -
28J ASP 3.7 12.1 - - - +
29J ALA* 3.1 20.8 + - + +
31J ALA* 1.3 76.7 - - + +
33J ALA* 1.3 58.5 + - - +
35J ILE* 3.4 10.4 + - + +
36J CYS* 2.9 41.1 + - - -
93J LEU* 4.3 31.2 - - + +
150J ASP* 5.8 1.8 - - - +
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Residues in contact with ALA 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J ALA 3.0 12.0 + - - +
30J ARG* 3.6 11.2 - - - +
31J ALA 3.2 0.2 - - - -
32J ILE* 1.3 73.8 - - - +
34J ALA* 1.3 67.4 + - - +
36J CYS* 3.4 6.9 + - - +
37J GLU* 3.0 24.9 + - - +
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Residues in contact with ALA 34 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J ARG* 3.2 26.3 + - - +
31J ALA* 3.6 9.9 - - - +
33J ALA* 1.3 78.0 - - - +
35J ILE* 1.3 62.7 + - - +
37J GLU* 3.3 8.1 + - - +
38J GLN* 3.2 24.9 + - - +
144J LEU* 4.4 20.4 - - + -
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Residues in contact with ILE 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J ALA* 2.8 24.2 + - + +
32J ILE* 3.7 8.5 - - + +
34J ALA* 1.3 78.3 - - - +
36J CYS* 1.3 59.0 + - - +
38J GLN* 3.0 8.4 + - - +
39J LEU* 2.8 40.0 + - + +
93J LEU* 4.2 9.4 - - + -
141J THR* 4.4 4.0 - - + +
144J LEU* 4.0 21.5 - - + -
145J ALA* 3.8 15.7 - - + +
148J SER* 3.5 24.5 - - - +
150J ASP* 3.8 16.8 - - + +
153J THR* 3.9 24.5 - - + -
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Residues in contact with CYS 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J ILE* 2.9 29.5 + - - +
33J ALA* 3.7 7.4 - - - +
34J ALA 3.3 0.2 - - - -
35J ILE* 1.3 75.6 - - - +
37J GLU* 1.3 58.1 + - - +
39J LEU* 3.3 1.9 + - - -
40J ARG* 2.8 38.3 + - - +
90J LEU* 3.5 25.8 - - + +
93J LEU* 3.8 31.0 - - - -
95J ALA* 4.0 15.3 - - + -
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Residues in contact with GLU 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ALA 3.0 14.5 + - - +
34J ALA* 3.5 11.4 - - - +
35J ILE 3.2 0.2 - - - -
36J CYS* 1.3 75.7 - - - +
38J GLN* 1.3 65.0 + - + +
40J ARG* 2.8 43.0 + - - +
41J GLN* 3.3 24.4 + - - +
107J LEU* 5.0 2.6 - - - +
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Residues in contact with GLN 38 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J ALA 3.2 14.5 + - - +
35J ILE 3.0 8.4 + - - +
37J GLU* 1.3 76.4 - - + +
39J LEU* 1.3 65.8 + - - +
41J GLN* 3.0 19.0 + - - +
42J HIS* 2.9 31.4 + - - -
137J ARG* 3.5 33.7 + - - +
140J GLN* 3.6 14.8 + - - +
141J THR* 3.1 32.9 + - + +
144J LEU* 3.9 20.0 - - + -
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Residues in contact with LEU 39 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J ILE* 2.8 23.6 + - + +
36J CYS* 3.6 4.7 - - - +
38J GLN* 1.3 77.5 - - - +
40J ARG* 1.3 62.2 + - - +
42J HIS* 3.0 15.0 + - + +
43J VAL* 3.0 26.9 + - - +
86J ILE* 3.8 18.1 - - + +
89J ARG* 4.1 18.2 - - + -
90J LEU* 3.6 24.2 - - + +
93J LEU* 3.7 29.8 - - + -
141J THR* 3.7 24.7 - - + -
153J THR* 4.3 1.1 - - + -
157J ILE* 4.3 13.2 - - + -
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Residues in contact with ARG 40 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J CYS* 2.8 24.1 + - - +
37J GLU* 2.8 42.3 + - - +
39J LEU* 1.3 75.6 - - - +
41J GLN* 1.3 62.7 + - - +
43J VAL* 3.4 3.7 + - - +
44J ALA* 3.2 19.8 + - - +
90J LEU* 3.8 24.4 - - + +
95J ALA* 5.8 2.9 - - - -
96J GLN 4.7 6.4 + - - +
98J PRO* 3.7 24.6 - - + +
103J GLU* 5.4 3.0 + - - -
107J LEU* 3.3 40.8 - - + +
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Residues in contact with GLN 41 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J GLU* 3.3 11.1 + - - +
38J GLN* 3.0 23.6 + - - +
40J ARG* 1.3 78.4 - - - +
42J HIS* 1.3 62.7 + - + +
44J ALA* 3.2 8.0 + - - +
45J ASP* 2.8 40.1 + - - +
107J LEU* 3.5 29.3 - - + +
109J GLY* 4.4 3.5 + - - -
133J TYR* 3.7 14.7 + - - -
137J ARG* 4.6 21.6 + - - +
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Residues in contact with HIS 42 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J GLN* 2.9 30.9 + - - -
39J LEU* 3.0 20.8 + - + +
41J GLN* 1.3 80.5 - - + +
43J VAL* 1.3 53.1 + - - +
45J ASP* 3.2 8.4 + - - +
46J LEU* 2.8 40.3 + - - +
86J ILE* 4.0 12.3 - - + -
134J LEU* 5.4 2.0 - - - +
137J ARG* 3.6 30.0 - - + +
138J PHE* 3.3 44.1 - + + -
141J THR* 2.6 31.0 + - + -
157J ILE* 4.9 1.1 - - + -
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Residues in contact with VAL 43 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J LEU 3.0 21.0 + - - +
40J ARG 3.7 7.0 - - - +
42J HIS* 1.3 74.5 - - - +
44J ALA* 1.3 58.3 + - - +
46J LEU* 4.4 3.1 - - - +
47J GLY* 2.8 26.2 + - - -
83J PHE* 3.4 35.0 - - + +
86J ILE* 3.8 17.7 - - + -
87J ALA* 3.8 21.5 - - + +
90J LEU* 4.4 8.3 - - + -
98J PRO* 3.9 11.2 - - + +
104J TYR* 3.8 17.7 - - + +
58K TRP* 4.4 7.2 - - + -
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Residues in contact with ALA 44 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J ARG 3.2 6.9 + - - +
41J GLN 3.2 8.9 + - - +
43J VAL* 1.3 79.2 - - - +
45J ASP* 1.3 63.5 + - - +
47J GLY* 3.3 1.7 + - - -
48J VAL* 3.0 27.5 + - - +
104J TYR* 3.5 26.7 - - + +
107J LEU* 3.6 31.6 - - + -
108J SER* 3.8 11.7 - - - +
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Residues in contact with ASP 45 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J GLN* 2.8 32.1 + - - +
42J HIS* 3.8 4.5 + - - +
44J ALA* 1.3 69.9 - - - +
46J LEU* 1.3 61.6 + - - +
48J VAL* 3.2 3.5 + - - +
49J LEU* 2.8 30.0 + - - +
108J SER* 2.7 18.3 + - - -
109J GLY 2.7 28.8 + - - -
110J ILE* 3.5 10.0 + - + +
133J TYR* 3.2 30.2 + - - -
134J LEU* 3.7 21.4 - - + +
137J ARG* 4.8 3.3 - - - +
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Residues in contact with LEU 46 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J HIS 2.8 31.1 + - - +
43J VAL* 3.7 4.5 - - - +
45J ASP* 1.3 72.2 - - - +
47J GLY* 1.3 58.4 + - - +
49J LEU* 3.2 2.3 + - + -
50J TYR* 2.8 31.4 + - - +
79J VAL* 3.4 32.8 - - + +
82J ALA* 4.0 7.6 - - + -
83J PHE* 3.9 31.2 - - + +
86J ILE* 3.9 21.8 - - + -
134J LEU* 3.6 29.2 - - + -
138J PHE* 3.9 13.7 - - + -
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Residues in contact with GLY 47 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J VAL 2.8 17.3 + - - -
44J ALA 3.7 1.8 - - - -
45J ASP 3.2 0.2 - - - -
46J LEU* 1.3 78.8 - - - +
48J VAL* 1.3 60.1 + - - +
50J TYR* 3.3 18.4 - - - +
51J ILE* 3.5 4.7 + - - +
83J PHE* 3.7 17.2 - - - -
104J TYR* 4.7 3.8 - - - -
51K ILE* 5.5 1.5 - - - +
101K MET* 3.2 22.3 - - - +
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Residues in contact with VAL 48 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J ALA 3.0 17.9 + - - +
45J ASP 3.6 6.7 - - - +
47J GLY* 1.3 74.2 - - - +
49J LEU* 1.3 63.7 + - - +
51J ILE* 3.3 4.9 + - - +
52J LYS* 3.0 21.1 + - + +
104J TYR* 4.3 8.1 - - + +
105J LEU* 4.6 7.9 - - + -
108J SER* 3.5 22.0 - - - +
110J ILE* 3.6 33.2 - - + +
111J ALA 4.7 2.0 - - - +
112J GLU* 4.0 22.7 - - + +
101K MET* 3.6 22.4 - - - +
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Residues in contact with LEU 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J ASP 2.8 16.6 + - - +
46J LEU* 3.6 6.3 - - - +
48J VAL* 1.3 75.0 - - - +
50J TYR* 1.3 57.8 + - - +
52J LYS* 4.0 10.5 - - + -
53J LEU* 2.7 57.6 + - + +
56J TYR* 6.0 0.7 - - + -
79J VAL* 3.9 14.4 - - + -
110J ILE* 4.1 14.6 - - + +
127J VAL* 5.5 2.7 - - + -
130J ASP* 4.2 21.5 - - + +
131J PHE* 3.6 25.4 - - + -
134J LEU* 3.5 29.2 - - + -
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Residues in contact with TYR 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J LEU 2.8 13.6 + - - +
47J GLY* 3.3 14.1 - - - +
49J LEU* 1.3 77.8 - - - +
51J ILE* 1.3 72.8 + - + +
53J LEU* 3.6 3.7 + - - +
54J HIS* 2.8 53.2 + + - -
76J TYR* 3.3 41.5 - + + -
79J VAL* 3.9 8.5 - - + +
80J THR* 3.6 23.0 - - + +
83J PHE* 6.3 1.6 - - + -
50K TYR* 3.5 36.7 + + - -
51K ILE* 6.5 0.4 - - + -
80K THR* 2.7 29.5 + - - +
83K PHE* 5.3 4.5 - + - -
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Residues in contact with ILE 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J GLY 3.5 2.8 + - - +
48J VAL 3.3 6.7 + - - +
49J LEU 3.2 0.2 - - - -
50J TYR* 1.3 89.7 - - + +
52J LYS* 1.3 66.8 + - - +
54J HIS* 3.0 18.8 + - + +
55J ASN* 3.0 10.7 + - - +
101J MET* 3.9 10.1 - - + -
112J GLU* 4.8 1.6 - - - +
47K GLY* 5.6 1.6 - - - +
51K ILE* 4.9 2.7 - - + -
83K PHE* 5.0 7.0 - - + -
99K ALA* 3.7 4.3 - - - +
100K SER* 3.6 35.2 - - - +
101K MET* 3.5 37.5 - - + +
104K TYR* 3.6 29.4 - - + +
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Residues in contact with LYS 52 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J VAL* 3.0 17.5 + - + +
49J LEU* 3.4 9.6 - - + +
51J ILE* 1.3 78.7 - - - +
53J LEU* 1.3 62.1 + - - +
55J ASN* 3.0 23.1 + - - +
56J TYR* 3.2 43.1 + - + -
110J ILE* 3.7 10.7 - - + +
111J ALA* 2.7 33.3 + - - +
112J GLU* 4.4 2.5 - - + -
113J GLU* 4.0 23.3 - - + +
126J ARG* 5.4 2.2 + - - +
130J ASP* 2.7 37.6 + - - +
99K ALA 4.9 2.5 - - - -
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Residues in contact with LEU 53 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J LEU* 2.7 39.3 + - + +
50J TYR 3.8 4.7 - - - +
52J LYS* 1.3 68.7 - - - +
54J HIS* 1.3 61.1 + - - +
56J TYR* 3.4 6.4 + - + +
57J HIS* 2.8 29.1 + - - +
72J LEU* 4.1 14.5 - - + +
75J TYR* 3.8 16.4 - - + -
76J TYR* 3.6 39.9 - - + +
79J VAL* 3.7 22.7 - - + -
127J VAL* 3.8 31.9 - - + -
131J PHE* 4.8 3.1 - - + -
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Residues in contact with HIS 54 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J TYR* 2.8 58.1 + + - -
51J ILE* 3.0 12.3 + - + +
53J LEU* 1.3 75.9 - - - +
55J ASN* 1.3 60.2 + - - +
57J HIS* 3.1 7.0 + - - +
58J TRP* 2.8 62.3 + + + -
76J TYR* 3.4 37.7 + + - -
80K THR* 4.7 1.4 + - - -
83K PHE* 3.5 28.2 - + + -
84K ASP* 3.7 14.9 + - - +
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Residues in contact with ASN 55 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J ILE 3.0 8.1 + - - +
52J LYS* 3.0 14.1 + - - +
54J HIS* 1.3 77.4 - - - +
56J TYR* 1.3 58.7 + - - +
58J TRP* 4.2 0.7 - - - -
59J HIS* 2.8 54.7 + - - +
113J GLU* 3.1 43.9 + - + +
115J GLU 3.4 14.7 + - - +
116J LYS* 5.0 4.2 - - - +
118J ILE* 5.6 0.7 - - - +
99K ALA* 3.1 38.2 + - + +
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Residues in contact with TYR 56 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J LEU* 6.0 0.7 - - + -
52J LYS* 3.2 48.6 + - + -
53J LEU* 3.8 7.6 - - + +
55J ASN* 1.3 77.2 - - - +
57J HIS* 1.3 64.4 + - - +
59J HIS 4.5 0.4 - - - +
60J ILE* 3.0 34.6 + - - +
72J LEU* 4.0 11.9 - - + -
113J GLU* 2.6 43.3 + - + -
118J ILE* 3.8 22.9 - - + -
123J ALA* 3.8 25.6 - - + -
126J ARG* 3.4 19.3 - - + +
127J VAL* 3.6 32.1 - - + -
130J ASP* 5.3 0.7 - - - -
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Residues in contact with HIS 57 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J LEU 2.8 18.9 + - - +
54J HIS* 3.2 8.5 - - - +
56J TYR* 1.3 78.4 - - - +
58J TRP* 1.3 83.5 + + - +
60J ILE* 4.2 5.9 - - - +
65J PHE* 4.2 1.2 - - - -
69J HIS* 2.7 80.7 + + - -
72J LEU* 3.9 14.7 - - + +
73J GLU* 3.9 22.4 + - + -
76J TYR* 3.7 15.0 + + + -
84K ASP* 3.8 3.6 - - - -
611K FE 2.1 31.4 - - - -
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Residues in contact with TRP 58 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TRP* 4.1 10.2 + - - -
51J ILE 5.4 0.2 - - - -
54J HIS* 2.8 47.9 + + + +
55J ASN* 3.8 1.6 - - - +
57J HIS* 1.3 89.0 - + - +
59J HIS* 1.3 72.3 + + - +
60J ILE 3.7 3.7 + - - +
65J PHE* 4.8 1.3 - - - -
69J HIS* 5.0 0.4 - + - -
43K VAL* 4.5 0.9 - - + -
83K PHE* 3.5 32.3 - + - -
84K ASP* 3.0 21.3 + - - -
87K ALA* 3.4 27.7 - - + +
88K GLU* 4.0 10.7 - - + +
91K LEU* 3.4 39.4 - - + +
97K ALA* 3.8 14.1 - - + -
98K PRO 3.5 21.5 - - - -
99K ALA* 3.7 16.6 - - + -
104K TYR* 3.6 4.5 - - - -
----------------------------------------------------------
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Residues in contact with HIS 59 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LYS* 5.6 0.3 + - - -
55J ASN* 2.8 41.8 + - - +
58J TRP* 1.3 85.9 - + + +
60J ILE* 1.3 66.1 + - - +
61J TYR* 4.1 1.9 - - - +
116J LYS* 3.2 27.8 - - + +
117J GLU* 3.1 25.8 - - - +
118J ILE* 3.0 22.9 + - + +
91K LEU* 3.8 15.7 - - + +
96K GLN* 3.8 11.4 - - + -
97K ALA 3.3 36.2 + - - -
99K ALA* 4.1 8.7 - - + -
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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