Contacts of the helix formed by residues 28 - 59 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ALA* 1.3 58.9 + - - +
30G ARG* 2.9 35.7 + - - +
31G ALA* 3.0 30.8 + - + +
32G ILE* 3.3 22.8 + - - +
148G SER* 5.6 3.8 - - - +
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Residues in contact with ALA 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G ASP* 1.3 72.2 + - - +
30G ARG* 1.3 57.8 + - - +
32G ILE* 4.2 12.3 - - - +
33G ALA* 3.5 19.6 + - - +
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Residues in contact with ARG 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G ASP* 2.9 13.1 + - - +
29G ALA* 1.3 78.6 - - - +
31G ALA* 1.3 59.1 + - - +
32G ILE 3.3 0.4 - - - -
33G ALA* 3.4 6.0 + - + +
34G ALA* 3.0 27.6 + - + +
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Residues in contact with ALA 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G ASP* 3.0 28.4 + - + +
30G ARG* 1.3 72.1 - - - +
32G ILE* 1.3 61.9 + - + +
34G ALA* 3.2 6.9 + - - +
35G ILE* 2.8 37.7 + - + +
144G LEU 5.6 0.2 - - - +
148G SER* 3.6 31.4 - - - -
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Residues in contact with ILE 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G ASP 3.4 22.0 - - - +
29G ALA* 4.2 9.2 - - - +
31G ALA* 1.3 77.9 - - + +
33G ALA* 1.3 59.3 + - - +
35G ILE* 3.3 9.8 + - + +
36G CYS* 2.9 42.9 + - - -
93G LEU* 4.3 30.3 - - + +
150G ASP* 6.0 1.8 - - - +
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Residues in contact with ALA 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ALA 3.5 17.4 + - - +
30G ARG* 3.4 8.2 + - + +
31G ALA 3.2 0.2 - - - -
32G ILE* 1.3 81.1 - - - +
34G ALA* 1.3 61.3 + - - +
36G CYS* 3.4 7.2 + - - +
37G GLU* 3.0 24.6 + - - +
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Residues in contact with ALA 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ARG* 3.0 15.2 + - + +
31G ALA* 3.2 10.3 + - - +
33G ALA* 1.3 75.2 - - - +
35G ILE* 1.3 63.6 + - - +
37G GLU* 3.3 8.0 + - - +
38G GLN* 3.1 24.9 + - - +
144G LEU* 4.2 19.3 - - + -
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Residues in contact with ILE 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G ALA* 2.8 23.9 + - + +
32G ILE* 3.6 8.3 - - + +
34G ALA* 1.3 76.9 - - - +
36G CYS* 1.3 56.6 + - - +
38G GLN* 3.0 6.6 + - - +
39G LEU* 2.9 46.6 + - + +
93G LEU* 4.1 9.6 - - + -
141G THR* 4.5 4.3 - - + +
144G LEU* 4.0 24.2 - - + +
145G ALA* 3.8 17.5 - - - +
148G SER* 3.5 24.9 - - - +
150G ASP* 3.8 14.8 - - + +
153G THR* 4.0 16.6 - - + -
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Residues in contact with CYS 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G ILE* 2.9 31.1 + - - +
33G ALA* 3.8 7.2 - - - +
35G ILE* 1.3 75.6 - - - +
37G GLU* 1.3 58.9 + - - +
39G LEU* 3.3 1.5 + - - -
40G ARG* 2.8 38.5 + - + +
90G LEU* 3.6 22.9 - - + +
93G LEU* 3.8 34.3 - - - -
95G ALA* 4.0 14.6 - - + -
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Residues in contact with GLU 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G ALA 3.0 14.6 + - - +
34G ALA* 3.5 11.0 - - - +
36G CYS* 1.3 77.8 - - - +
38G GLN* 1.3 66.1 + - + +
40G ARG* 3.5 27.1 + - - +
41G GLN* 3.3 19.9 + - - +
107G LEU* 4.9 9.9 - - - +
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Residues in contact with GLN 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ALA 3.1 14.7 + - - +
35G ILE 3.0 9.1 + - - +
37G GLU* 1.3 77.1 - - + +
39G LEU* 1.3 66.0 + - - +
41G GLN* 3.0 11.1 + - - +
42G HIS* 2.9 31.2 + - - -
137G ARG* 3.5 35.8 + - - +
140G GLN* 3.7 15.3 + - - +
141G THR* 3.0 32.9 + - + +
144G LEU* 3.9 18.6 - - + -
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Residues in contact with LEU 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G ILE* 2.9 24.9 + - + +
36G CYS 3.6 4.3 - - - +
38G GLN* 1.3 77.6 - - - +
40G ARG* 1.3 62.7 - - - +
42G HIS* 3.0 15.5 + - + +
43G VAL* 2.9 26.9 + - - +
86G ILE* 3.8 16.8 - - + +
89G ARG* 4.2 17.9 - - + -
90G LEU* 3.7 24.5 - - + +
93G LEU* 3.8 28.3 - - + -
141G THR* 3.7 24.9 - - + -
153G THR* 4.3 1.8 - - + -
157G ILE* 4.2 13.0 - - + -
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Residues in contact with ARG 40 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F LYS* 5.2 3.0 - - - +
36G CYS* 2.8 28.2 + - - +
37G GLU* 3.6 32.0 + - - +
39G LEU* 1.3 76.1 - - - +
41G GLN* 1.3 62.3 + - - +
43G VAL* 3.5 0.9 + - - -
44G ALA* 3.2 19.4 + - - +
90G LEU* 3.7 20.9 - - + -
96G GLN 3.3 21.9 + - - +
97G ALA 4.3 0.2 - - - -
98G PRO* 3.4 34.8 - - + +
103G GLU* 4.2 9.5 + - - +
107G LEU* 3.3 34.2 - - + +
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Residues in contact with GLN 41 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G GLU 3.3 9.6 + - - +
38G GLN* 3.0 14.9 + - - +
40G ARG* 1.3 78.8 - - - +
42G HIS* 1.3 64.6 + - - +
44G ALA* 3.1 7.0 + - - +
45G ASP* 2.8 42.8 + - - +
107G LEU* 4.0 25.1 + - + +
109G GLY* 5.4 1.6 - - - +
133G TYR* 4.1 7.0 + - - -
137G ARG* 2.7 49.3 + - - +
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Residues in contact with HIS 42 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G GLN* 2.9 29.8 + - - -
39G LEU* 3.0 20.8 + - + +
41G GLN* 1.3 82.6 + - - +
43G VAL* 1.3 57.1 + - - +
45G ASP* 3.2 7.1 + - - +
46G LEU* 2.8 37.3 + - - +
86G ILE* 4.0 12.8 - - + -
134G LEU* 5.4 2.0 - - - +
137G ARG* 3.6 26.5 - - + +
138G PHE* 3.3 45.4 - + + -
141G THR* 2.7 30.6 + - + -
157G ILE* 4.9 1.1 - - + -
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Residues in contact with VAL 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F TRP* 4.5 6.1 - - + -
39G LEU 2.9 19.6 + - - +
40G ARG 3.7 6.7 - - - +
41G GLN 3.3 0.2 - - - -
42G HIS* 1.3 75.5 - - - +
44G ALA* 1.3 59.6 + - - +
46G LEU* 3.3 3.5 + - - -
47G GLY* 2.8 25.6 + - - -
83G PHE* 3.4 34.3 - - + +
86G ILE* 3.8 18.2 - - + -
87G ALA* 3.8 22.2 - - + +
90G LEU* 4.6 8.3 - - + -
98G PRO* 3.8 12.8 - - + +
104G TYR* 3.7 18.4 - - + +
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Residues in contact with ALA 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ARG 3.2 7.1 + - - +
41G GLN 3.1 8.6 + - - +
43G VAL* 1.3 80.3 - - - +
45G ASP* 1.3 62.0 + - - +
47G GLY* 3.3 1.4 + - - -
48G VAL* 3.0 28.1 + - - +
104G TYR* 3.5 32.9 - - + +
107G LEU* 3.6 31.6 - - + -
108G SER* 3.8 6.5 - - - +
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Residues in contact with ASP 45 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G GLN* 2.8 34.3 + - - +
42G HIS* 3.8 4.4 + - - +
44G ALA* 1.3 69.1 - - - +
46G LEU* 1.3 61.6 + - - +
48G VAL* 3.2 2.9 + - - +
49G LEU* 2.8 31.1 + - - +
108G SER* 2.7 19.3 + - - -
109G GLY 2.7 29.8 + - - -
110G ILE* 3.6 9.5 + - + +
133G TYR* 3.2 30.7 + - - -
134G LEU* 3.7 20.7 - - + +
137G ARG* 4.7 1.0 - - - +
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Residues in contact with LEU 46 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G HIS 2.8 26.9 + - - +
43G VAL* 3.7 4.3 - - - +
45G ASP* 1.3 73.0 - - - +
47G GLY* 1.3 57.7 + - - +
49G LEU* 3.2 1.7 + - + -
50G TYR* 2.8 27.6 + - - +
79G VAL* 3.4 36.2 - - + +
82G ALA* 4.0 7.0 - - + -
83G PHE* 3.9 29.2 - - + +
86G ILE* 3.9 28.3 - - + -
134G LEU* 3.7 33.2 - - + -
138G PHE* 3.9 12.3 - - + -
160G ILE* 6.2 0.2 - - + -
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Residues in contact with GLY 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F ILE* 5.5 1.5 - - - +
101F MET* 3.2 22.4 - - - +
43G VAL 2.8 17.1 + - - -
44G ALA 3.7 2.2 - - - -
45G ASP 3.2 0.2 - - - -
46G LEU* 1.3 78.6 - - - +
48G VAL* 1.3 59.7 + - - +
50G TYR* 3.3 18.0 - - - +
51G ILE* 3.5 5.7 + - - +
83G PHE* 3.7 17.4 - - - -
104G TYR* 4.6 4.0 - - - -
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Residues in contact with VAL 48 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F MET* 3.8 24.0 - - - -
44G ALA 3.0 20.4 + - - +
45G ASP 3.6 3.6 - - - +
47G GLY* 1.3 73.4 - - - +
49G LEU* 1.3 66.7 + - - +
51G ILE* 3.4 4.3 + - - +
52G LYS* 3.0 20.4 + - + +
104G TYR* 4.3 7.2 - - + +
105G LEU* 4.6 8.1 - - + -
108G SER* 3.5 22.0 - - - +
110G ILE* 3.5 33.9 - - + +
111G ALA 4.7 1.8 - - - +
112G GLU* 4.0 21.4 - - + +
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Residues in contact with LEU 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ASP 2.8 17.2 + - - +
46G LEU* 3.6 6.5 - - + +
48G VAL* 1.3 74.5 - - - +
50G TYR* 1.3 58.1 + - - +
52G LYS* 3.1 11.3 + - + -
53G LEU* 2.8 55.2 + - + +
56G TYR* 6.1 0.7 - - + -
79G VAL* 3.8 15.9 - - + -
110G ILE* 4.2 14.8 - - + -
127G VAL* 5.6 2.9 - - + -
130G ASP* 4.2 22.0 - - + +
131G PHE* 3.7 24.9 - - + -
134G LEU* 3.5 28.0 - - + -
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Residues in contact with TYR 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F TYR* 3.5 37.6 + + - -
51F ILE* 6.6 0.2 - - + -
80F THR* 2.7 29.8 + - - +
83F PHE* 5.2 4.9 - + - -
46G LEU 2.8 14.0 + - - +
47G GLY* 3.3 13.9 - - - +
49G LEU* 1.3 78.8 - - - +
51G ILE* 1.3 73.8 + - + +
53G LEU* 3.5 4.0 + - - +
54G HIS* 2.8 52.8 + + - -
76G TYR* 3.3 42.3 - + + -
77G VAL* 5.3 0.2 - - - -
79G VAL* 4.0 7.4 - - + +
80G THR* 3.6 21.4 - - + +
83G PHE* 6.3 1.3 - - + -
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Residues in contact with ILE 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F GLY* 5.6 1.6 - - - -
50F TYR* 6.6 0.2 - - + -
51F ILE* 4.9 2.5 - - + -
83F PHE* 5.0 6.7 - - + -
99F ALA* 3.7 5.0 - - - +
100F SER* 3.6 33.0 - - - +
101F MET* 3.5 38.1 - - + +
104F TYR* 3.6 27.1 - - + +
47G GLY 3.5 3.7 + - - +
48G VAL 3.4 6.7 + - - +
50G TYR* 1.3 88.9 - - + +
52G LYS* 1.3 67.3 + - - +
54G HIS* 3.0 17.9 + - + +
55G ASN* 3.0 11.1 + - - +
101G MET* 3.8 13.5 - - + -
112G GLU* 4.8 1.8 - - - +
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Residues in contact with LYS 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F ALA 5.0 2.2 - - - -
48G VAL* 3.0 17.1 + - + +
49G LEU* 3.5 9.4 - - + +
51G ILE* 1.3 77.9 - - - +
53G LEU* 1.3 63.1 + - - +
55G ASN* 3.0 23.4 - - - +
56G TYR* 3.2 37.8 + - + -
110G ILE* 3.8 10.6 - - + +
111G ALA* 2.7 33.9 + - - +
112G GLU* 4.4 2.5 - - - -
113G GLU* 4.0 26.0 - - + +
126G ARG* 5.3 3.1 + - - +
130G ASP* 2.7 37.6 + - - +
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Residues in contact with LEU 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G LEU* 2.8 36.5 + - + +
50G TYR 3.7 4.9 - - - +
51G ILE 3.2 0.2 - - - -
52G LYS* 1.3 76.3 - - - +
54G HIS* 1.3 56.9 + - - +
56G TYR* 3.4 5.9 + - + +
57G HIS* 2.8 30.1 + - - +
72G LEU* 4.1 15.8 - - + +
75G TYR* 3.9 16.6 - - + -
76G TYR* 3.7 30.1 - - + +
79G VAL* 3.6 31.9 - - + -
127G VAL* 3.9 31.2 - - + -
131G PHE* 4.9 2.9 - - + -
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Residues in contact with HIS 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F THR* 4.7 1.4 + - - -
83F PHE* 3.5 27.5 - + + -
84F ASP* 3.6 22.3 + - - +
50G TYR* 2.8 58.5 + + - -
51G ILE* 3.0 13.1 + - + +
53G LEU* 1.3 74.6 - - - +
55G ASN* 1.3 57.5 + - - +
57G HIS* 3.1 6.9 + + - +
58G TRP* 2.7 58.9 + + + -
76G TYR* 3.3 36.5 + + - -
----------------------------------------------------------
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Residues in contact with ASN 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F ALA* 3.0 45.4 + - + +
51G ILE 3.0 6.7 + - - +
52G LYS* 3.0 16.1 + - - +
54G HIS* 1.3 77.9 - - - +
56G TYR* 1.3 60.4 + - - +
58G TRP* 3.2 0.6 + - - -
59G HIS* 2.8 55.4 + - - +
113G GLU* 3.1 35.0 + - + +
115G GLU 3.3 15.8 + - - +
116G LYS* 4.8 4.2 - - - +
118G ILE* 5.4 0.9 - - - +
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Residues in contact with TYR 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G LEU* 6.1 0.4 - - + -
52G LYS* 3.2 46.4 + - + -
53G LEU* 3.8 8.1 - - + +
55G ASN* 1.3 74.9 - - - +
57G HIS* 1.3 65.9 + - - +
59G HIS 4.4 0.4 - - - +
60G ILE* 3.0 34.5 + - - +
72G LEU* 3.9 14.8 - - + -
113G GLU* 2.7 42.8 + - + -
118G ILE* 3.8 22.4 - - + -
123G ALA* 3.8 23.8 - - + -
126G ARG* 3.4 19.8 - - + +
127G VAL* 3.5 33.2 - - + -
130G ASP* 5.4 0.7 - - - -
----------------------------------------------------------
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Residues in contact with HIS 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F ASP* 3.8 9.0 - - - -
606F FE 2.4 30.1 - - - -
53G LEU 2.8 19.1 + - - +
54G HIS* 3.2 8.7 - + - +
56G TYR* 1.3 78.1 - - - +
58G TRP* 1.3 64.4 + + - +
60G ILE* 4.2 0.7 - - - +
65G PHE* 4.2 6.2 - - - -
69G HIS* 2.6 85.0 + + - -
72G LEU* 3.8 14.5 - - + +
73G GLU* 3.7 22.9 + - + -
76G TYR* 3.6 19.6 + + + -
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Residues in contact with TRP 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F VAL* 4.4 0.9 - - + -
83F PHE* 3.5 34.1 - + - -
84F ASP* 3.0 19.9 + - - -
87F ALA* 3.3 27.5 - - + +
88F GLU* 3.9 12.6 - - + +
91F LEU* 3.4 39.0 - - + +
97F ALA* 3.8 14.8 - - + -
98F PRO 3.5 21.3 - - - -
99F ALA* 3.8 15.0 - - + -
104F TYR* 3.7 4.3 - - - -
54G HIS* 2.7 48.2 + + + +
55G ASN 3.8 1.8 - - - +
57G HIS* 1.3 89.3 - + - +
59G HIS* 1.3 71.8 + + - +
60G ILE 3.7 4.0 + - - +
65G PHE* 4.8 1.0 - - - -
69G HIS* 5.0 0.4 - + - -
169J TRP* 4.0 9.9 + - - -
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Residues in contact with HIS 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F LEU* 3.8 15.7 - - + +
96F GLN* 3.9 11.2 - - + -
97F ALA 3.1 42.7 + - - -
99F ALA* 4.1 8.5 - - + -
55G ASN* 2.8 42.0 + - - +
56G TYR 3.9 0.2 - - - -
58G TRP* 1.3 84.7 - + + +
60G ILE* 1.3 65.8 + - - +
61G TYR* 4.1 2.3 - - - +
116G LYS* 3.3 20.8 - - + +
117G GLU* 3.2 25.2 - - - +
118G ILE* 3.1 23.4 + - + +
176J LYS* 5.4 0.9 + - - -
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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