Contacts of the helix formed by residues 28 - 59 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ALA* 1.3 61.2 - - - +
30E ARG* 2.8 18.2 + - - +
31E ALA* 2.6 48.6 + - + +
32E ILE* 3.4 20.2 + - - +
148E SER* 5.7 2.5 - - - +
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Residues in contact with ALA 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E ASP* 1.3 71.8 - - - +
30E ARG* 1.3 63.6 + - + +
31E ALA 3.3 0.2 - - - -
32E ILE* 3.8 10.2 + - - +
33E ALA* 3.3 23.0 + - - +
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Residues in contact with ARG 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E ASP* 2.8 13.1 + - - +
29E ALA* 1.3 78.7 - - + +
31E ALA* 1.3 58.3 + - - +
33E ALA* 4.0 4.6 - - - +
34E ALA* 3.1 27.4 + - - +
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Residues in contact with ALA 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E ASP* 2.6 31.2 + - + +
30E ARG* 1.3 72.0 - - - +
32E ILE* 1.3 62.2 + - + +
34E ALA* 3.1 6.4 + - - +
35E ILE* 2.8 37.5 + - + +
144E LEU 5.6 0.2 - - - +
148E SER* 3.6 31.4 - - - -
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Residues in contact with ILE 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E ASP 3.4 16.5 + - - +
29E ALA* 4.1 9.4 - - - +
31E ALA* 1.3 77.1 - - + +
33E ALA* 1.3 57.3 + - - +
35E ILE* 3.4 10.0 + - + +
36E CYS* 2.9 42.7 + - - -
93E LEU* 4.3 28.9 - - + +
150E ASP* 6.0 1.3 - - - +
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Residues in contact with ALA 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ALA 3.3 17.0 + - - +
30E ARG* 4.0 5.8 - - - +
31E ALA 3.2 0.6 - - - -
32E ILE* 1.3 77.2 - - - +
34E ALA* 1.3 65.3 + - - +
36E CYS* 3.8 6.7 - - - +
37E GLU* 3.0 25.6 + - - +
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Residues in contact with ALA 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ARG 3.1 19.5 + - - +
31E ALA* 3.1 7.4 + - - +
33E ALA* 1.3 76.2 - - - +
35E ILE* 1.3 63.4 + - - +
37E GLU* 3.3 8.1 + - - +
38E GLN* 3.1 25.3 + - - +
144E LEU* 4.1 20.0 - - + -
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Residues in contact with ILE 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E ALA* 2.8 22.1 + - + +
32E ILE* 3.7 8.5 - - + +
34E ALA* 1.3 77.4 - - - +
36E CYS* 1.3 57.6 + - - +
38E GLN* 3.1 8.9 + - - +
39E LEU* 2.8 48.0 + - + +
93E LEU* 4.1 9.9 - - + -
141E THR* 4.5 3.8 - - + +
144E LEU* 4.0 21.1 - - + -
145E ALA* 3.7 18.8 - - + +
148E SER* 3.5 24.0 - - - +
150E ASP* 3.8 15.5 - - + +
153E THR* 4.0 16.2 - - + -
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Residues in contact with CYS 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E ILE* 2.9 31.2 + - - +
33E ALA* 3.8 7.2 - - - +
35E ILE* 1.3 76.9 - - - +
37E GLU* 1.3 58.5 + - - +
39E LEU* 3.3 1.2 + - - -
40E ARG* 2.8 39.4 + - + +
90E LEU* 3.6 22.2 - - + +
93E LEU* 3.8 34.3 - - - -
95E ALA* 4.1 15.5 - - + -
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Residues in contact with GLU 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ALA 3.0 13.9 + - - +
34E ALA* 3.5 11.0 - - - +
36E CYS* 1.3 77.5 - - - +
38E GLN* 1.3 64.1 + - + +
40E ARG* 3.5 26.9 + - - +
41E GLN* 3.2 20.6 + - - +
107E LEU* 4.9 9.9 - - - +
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Residues in contact with GLN 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ALA 3.1 15.8 + - - +
35E ILE* 3.1 9.4 + - - +
37E GLU* 1.3 75.6 - - - +
39E LEU* 1.3 66.5 + - - +
41E GLN* 3.0 9.8 + - - +
42E HIS* 2.9 31.2 + - - -
137E ARG* 2.8 46.4 + - - +
140E GLN* 3.7 11.3 + - - +
141E THR* 3.0 32.5 + - + +
144E LEU* 4.1 17.7 - - + -
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Residues in contact with LEU 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ILE* 2.8 24.6 + - + +
36E CYS 3.6 4.9 - - - +
38E GLN* 1.3 75.7 - - - +
40E ARG* 1.3 62.0 + - - +
42E HIS* 3.1 16.0 + - + +
43E VAL* 3.0 27.2 + - - +
86E ILE* 3.8 16.7 - - + +
89E ARG* 4.1 17.5 - - + -
90E LEU* 3.7 23.8 - - + +
93E LEU* 3.8 29.4 - - + -
141E THR* 3.8 24.7 - - + -
153E THR* 4.3 1.3 - - + -
157E ILE* 4.3 13.0 - - + -
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Residues in contact with ARG 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E CYS* 2.8 28.8 + - - +
37E GLU* 3.6 32.1 + - - +
39E LEU* 1.3 77.0 - - - +
41E GLN* 1.3 62.4 + - - +
43E VAL* 3.4 4.0 + - - +
44E ALA* 3.2 19.4 + - - +
90E LEU* 3.6 21.8 - - + -
95E ALA* 5.8 2.7 - - - -
96E GLN 3.3 21.2 + - - -
97E ALA 4.5 0.2 - - - -
98E PRO* 3.7 29.2 - - + +
103E GLU* 4.5 8.3 + - - -
107E LEU* 3.7 30.5 - - + +
116H LYS* 6.3 0.4 - - - +
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Residues in contact with GLN 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E GLU 3.2 9.2 + - - +
38E GLN* 3.0 13.3 + - - +
40E ARG* 1.3 78.0 - - - +
42E HIS* 1.3 64.5 + - + +
44E ALA* 3.1 7.4 + - - +
45E ASP* 2.8 42.1 + - - +
107E LEU* 3.2 31.4 + - + +
109E GLY* 4.4 4.4 - - - +
133E TYR* 4.1 14.1 + - - -
137E ARG* 2.8 35.6 + - - +
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Residues in contact with HIS 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E GLN* 2.9 29.8 + - - -
39E LEU* 3.1 21.7 + - + +
41E GLN* 1.3 81.3 - - + +
43E VAL* 1.3 53.8 + - - +
45E ASP* 3.2 7.5 + - - +
46E LEU* 2.7 41.6 + - - +
86E ILE* 4.0 12.3 - - + -
134E LEU* 5.3 1.8 - - - +
137E ARG* 3.6 31.5 - - + +
138E PHE* 3.3 43.3 - + + -
141E THR* 2.6 30.4 + - - -
157E ILE* 4.9 1.1 - - + -
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Residues in contact with VAL 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E LEU 3.0 20.0 + - - +
40E ARG 3.7 7.0 - - - +
42E HIS* 1.3 75.5 - - - +
44E ALA* 1.3 58.4 + - - +
46E LEU* 4.4 2.9 - - - -
47E GLY* 2.8 26.2 + - - -
83E PHE* 3.4 34.1 - - + +
86E ILE* 3.8 9.6 - - + -
87E ALA* 3.8 30.3 - - + +
90E LEU* 4.6 7.4 - - + -
98E PRO* 3.9 12.3 - - + +
104E TYR* 3.8 18.8 - - + +
58H TRP* 4.5 6.3 - - + -
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Residues in contact with ALA 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E ARG 3.2 7.5 + - - +
41E GLN 3.1 8.4 + - - +
43E VAL* 1.3 79.1 - - - +
45E ASP* 1.3 61.7 + - - +
47E GLY* 3.3 1.7 + - - -
48E VAL* 3.0 27.9 + - - +
104E TYR* 3.5 28.4 - - + +
107E LEU* 3.6 31.0 - - + -
108E SER* 3.8 11.7 - - - +
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Residues in contact with ASP 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E GLN* 2.8 32.7 + - - +
42E HIS* 3.8 4.7 + - - +
44E ALA* 1.3 69.1 - - - +
46E LEU* 1.3 61.8 + - - +
48E VAL* 3.2 2.8 + - - +
49E LEU* 2.8 29.5 + - - +
108E SER* 2.8 12.9 + - - -
109E GLY 2.7 29.0 + - - -
110E ILE* 3.6 9.4 + - + +
133E TYR* 3.2 30.0 + - - -
134E LEU* 3.7 21.3 - - + +
137E ARG* 4.9 2.3 - - - +
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Residues in contact with LEU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E HIS 2.7 27.0 + - - +
43E VAL* 3.7 3.8 - - - +
45E ASP* 1.3 70.3 - - - +
47E GLY* 1.3 58.3 + - - +
49E LEU* 3.2 1.6 + - + -
50E TYR* 2.8 28.1 + - - +
79E VAL* 3.4 37.1 - - + +
82E ALA* 4.0 7.4 - - + -
83E PHE* 3.9 30.3 - - + +
86E ILE* 3.9 16.2 - - + -
134E LEU* 3.6 33.2 - - + -
138E PHE* 3.9 21.3 - - + -
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Residues in contact with GLY 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E VAL 2.8 18.2 + - - -
44E ALA 3.7 1.3 - - - -
45E ASP 3.3 0.2 - - - -
46E LEU* 1.3 78.0 - - - +
48E VAL* 1.3 60.3 + - - +
50E TYR* 3.3 18.6 - - - +
51E ILE* 3.5 5.0 + - - +
83E PHE* 3.7 18.5 - - - -
104E TYR* 4.7 3.8 - - - -
51H ILE* 5.5 1.5 - - - +
101H MET* 3.2 22.0 - - - +
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Residues in contact with VAL 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E ALA 3.0 18.5 + - - +
45E ASP 3.6 6.5 - - - +
47E GLY* 1.3 73.7 - - - +
49E LEU* 1.3 63.2 + - - +
51E ILE* 3.3 5.0 + - - +
52E LYS* 3.0 20.1 + - + +
104E TYR* 4.3 6.5 - - + +
105E LEU* 4.7 7.2 - - + -
108E SER* 3.4 23.6 - - - +
110E ILE* 3.6 32.1 - - + +
111E ALA 4.7 2.2 - - - +
112E GLU* 4.0 23.2 - - + +
101H MET* 3.6 24.0 - - + +
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Residues in contact with LEU 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E ASP 2.8 17.8 + - - +
46E LEU* 3.6 6.3 - - - +
48E VAL* 1.3 75.7 - - - +
50E TYR* 1.3 57.3 + - - +
52E LYS* 3.0 11.6 + - + -
53E LEU* 2.7 55.4 + - + +
56E TYR* 6.1 0.4 - - + -
79E VAL* 3.9 13.7 - - + -
110E ILE* 4.2 13.4 - - + +
127E VAL* 5.6 2.7 - - + -
130E ASP* 4.2 22.2 - - + +
131E PHE* 3.7 25.6 - - + -
134E LEU* 3.5 28.7 - - + -
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Residues in contact with TYR 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E LEU 2.8 13.4 + - - +
47E GLY* 3.3 14.6 - - - +
49E LEU* 1.3 77.7 - - - +
51E ILE* 1.3 74.6 + - + +
53E LEU* 3.6 3.2 + - - +
54E HIS* 2.8 51.8 + + - -
76E TYR* 3.3 41.9 - + + +
79E VAL* 4.0 7.8 - - + +
80E THR* 3.6 23.2 - - + +
83E PHE* 6.2 0.9 - - + -
50H TYR* 3.4 37.6 + + - -
51H ILE* 6.6 0.4 - - + -
80H THR* 2.6 30.7 + - - +
83H PHE* 5.3 4.5 - + - -
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Residues in contact with ILE 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLY 3.5 3.5 + - - +
48E VAL 3.3 7.2 + - - +
49E LEU 3.2 0.4 - - - -
50E TYR* 1.3 90.7 - - + +
52E LYS* 1.3 66.2 + - - +
54E HIS* 3.1 9.3 + - + +
55E ASN* 3.1 19.2 + - - +
101E MET* 3.8 11.2 - - + -
112E GLU* 4.9 1.6 - - - +
47H GLY* 5.5 1.6 - - - +
50H TYR* 6.5 0.4 - - + -
51H ILE* 5.0 3.4 - - + -
83H PHE* 5.0 8.1 - - + -
99H ALA* 3.7 4.4 - - - +
100H SER* 3.6 33.2 - - - +
101H MET* 3.6 32.3 - - + +
104H TYR* 3.5 31.2 - - + +
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Residues in contact with LYS 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E VAL* 3.0 19.0 + - + +
49E LEU* 3.4 11.2 - - + +
51E ILE* 1.3 77.7 - - - +
53E LEU* 1.3 62.6 - - - +
55E ASN* 3.0 23.5 + - - +
56E TYR* 3.2 38.1 + - + -
110E ILE* 3.8 9.6 - - + +
111E ALA* 2.7 33.4 + - - +
112E GLU* 4.5 2.0 - - - -
113E GLU* 4.0 25.8 - - + +
126E ARG* 5.3 3.0 + - - +
130E ASP* 2.7 36.6 + - - +
99H ALA 4.9 2.7 - - - -
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Residues in contact with LEU 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LEU* 2.7 34.8 + - + +
50E TYR 3.8 5.2 - - - +
51E ILE 3.2 0.2 - - - -
52E LYS* 1.3 74.3 - - - +
54E HIS* 1.3 58.7 + - - +
56E TYR* 3.4 5.5 + - + +
57E HIS* 2.8 28.9 + - - +
72E LEU* 4.1 14.6 - - + +
75E TYR* 3.9 16.6 - - + -
76E TYR* 3.7 36.8 - - + +
79E VAL* 3.7 25.6 - - + -
127E VAL* 3.8 32.3 - - + -
131E PHE* 4.8 3.4 - - + -
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Residues in contact with HIS 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E TYR* 2.8 57.0 + + - -
51E ILE* 3.1 12.0 + - - +
53E LEU* 1.3 75.4 - - - +
55E ASN* 1.3 58.2 + - - +
57E HIS* 3.1 7.3 + + - +
58E TRP* 2.7 66.8 + + + -
76E TYR* 3.3 41.1 + + - -
80H THR* 4.7 1.2 + - - -
83H PHE* 3.6 27.5 - + + -
84H ASP* 3.8 12.0 + - - +
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Residues in contact with ASN 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ILE 3.1 8.3 + - - +
52E LYS* 3.0 16.5 + - - +
54E HIS* 1.3 77.9 - - - +
56E TYR* 1.3 55.7 + - - +
58E TRP* 3.7 1.3 - - - -
59E HIS* 2.8 60.4 + - - +
113E GLU* 3.1 43.7 + - + +
115E GLU 3.5 14.2 + - - +
116E LYS* 4.5 4.8 - - - +
118E ILE* 5.6 1.0 - - - +
99H ALA* 3.0 37.8 + - + +
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Residues in contact with TYR 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LEU* 6.1 0.4 - - + -
52E LYS* 3.2 46.4 + - + -
53E LEU* 3.9 7.6 - - + +
55E ASN* 1.3 75.3 - - - +
57E HIS* 1.3 68.3 + - - +
59E HIS 4.4 0.2 - - - +
60E ILE* 3.0 34.8 + - - +
72E LEU* 3.9 15.5 - - + -
113E GLU* 2.7 43.3 + - + -
118E ILE* 3.8 24.0 - - + -
123E ALA* 3.8 22.9 - - + -
126E ARG* 3.3 19.9 - - + +
127E VAL* 3.5 33.0 - - + -
130E ASP* 5.4 0.2 - - - -
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Residues in contact with HIS 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E LEU 2.8 20.5 + - - +
54E HIS* 3.1 10.5 - + - +
56E TYR* 1.3 78.0 - - - +
58E TRP* 1.3 81.1 + + - +
60E ILE* 4.3 1.2 - - - +
65E PHE* 4.3 5.4 - - - -
69E HIS* 2.7 78.8 + + - -
72E LEU* 3.8 14.1 - - + +
73E GLU* 3.9 23.0 + - + -
76E TYR* 3.7 14.3 + + + -
84H ASP* 3.8 3.6 - - - -
608H FE 2.1 31.2 - - - -
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Residues in contact with TRP 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E HIS* 2.7 49.0 + + + +
55E ASN* 3.8 2.2 - - - +
57E HIS* 1.3 91.5 - + - +
59E HIS* 1.3 69.0 + + - +
60E ILE 3.7 4.0 - - - +
65E PHE* 4.8 0.7 - - - -
69E HIS* 5.0 0.4 - + - -
43H VAL* 4.5 0.9 - - + -
83H PHE* 3.5 33.2 - + - -
84H ASP* 3.1 21.4 + - - -
87H ALA* 3.3 28.6 - - + +
88H GLU* 3.8 13.6 - - + +
91H LEU* 3.4 36.4 - - + +
97H ALA* 3.8 14.1 - - + -
98H PRO 3.6 22.0 - - - -
99H ALA* 3.8 15.5 - - + -
104H TYR* 3.7 3.8 - - - -
169K TRP* 3.9 10.9 + - - -
----------------------------------------------------------
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Residues in contact with HIS 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ASN* 2.8 41.0 + - - +
58E TRP* 1.3 86.7 - + + +
60E ILE* 1.3 64.3 + - - +
61E TYR* 4.1 2.9 - - - +
116E LYS* 3.4 14.6 - - + +
117E GLU* 3.2 25.6 - - - +
118E ILE* 3.1 23.4 + - + +
91H LEU* 3.8 15.8 - - + +
96H GLN* 3.8 16.4 - - + -
97H ALA* 3.2 42.8 + - - -
99H ALA* 4.1 8.3 - - + -
176K LYS* 5.5 0.5 + - - -
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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