Contacts of the helix formed by residues 46 - 74 (chain F) in PDB entry 2J3W
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 46 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B MET 3.4 19.2 + - - -
72B ARG 3.7 14.6 - - - -
75B ASN* 3.8 12.8 + - - -
44F VAL* 2.9 21.8 - - - +
45F TYR* 1.3 80.6 - - - +
47F VAL* 1.3 66.1 + - - +
48F SER* 3.1 15.3 + - - -
49F GLU* 3.2 15.0 + - - +
50F LEU* 3.0 5.2 + - - +
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Residues in contact with VAL 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F SER* 1.3 73.8 - - - +
48F SER* 1.3 57.7 + - - +
50F LEU* 3.2 14.3 - - + +
51F GLN* 2.9 54.0 + - + +
136F THR* 6.3 1.8 - - - -
137F LEU 6.1 0.9 - - - +
138F ASN* 4.8 8.3 - - - +
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Residues in contact with SER 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 2.9 39.2 + - - +
46F SER* 3.0 5.5 + - - -
47F VAL* 1.3 81.3 - - - +
49F GLU* 1.3 62.8 + - - +
51F GLN* 3.3 12.3 + - - +
52F ALA* 3.1 19.2 + - - +
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Residues in contact with GLU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR* 4.5 17.3 - - - +
71B MET* 4.9 6.7 - - - +
75B ASN 6.5 1.3 - - - -
43F ARG 5.5 0.7 - - - +
44F VAL* 3.4 22.3 - - + +
45F TYR* 2.9 50.3 + - - +
46F SER* 3.2 9.7 + - - +
48F SER* 1.3 76.2 - - - +
50F LEU* 1.3 67.8 + - - +
52F ALA* 2.9 11.1 + - - +
53F ARG* 2.8 32.5 + - - +
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Residues in contact with LEU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F VAL* 3.9 4.0 - - + +
40F CYS* 3.7 24.0 - - + -
41F GLN* 3.6 41.7 - - + +
44F VAL* 3.4 13.4 - - + +
46F SER 3.0 12.9 + - - +
47F VAL* 3.2 23.6 - - + +
49F GLU* 1.3 78.4 - - - +
51F GLN* 1.3 61.3 + - - +
53F ARG* 3.3 3.1 + - - +
54F LEU* 3.1 34.3 + - + +
138F ASN* 3.1 33.4 - - - +
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Residues in contact with GLN 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F VAL* 2.9 42.5 + - + +
48F SER* 3.6 11.2 + - - +
50F LEU* 1.3 75.4 - - - +
52F ALA* 1.3 57.7 + - - +
54F LEU* 3.3 3.6 + - - -
55F ALA* 2.9 26.9 + - - +
137F LEU* 3.6 29.1 + - - +
138F ASN* 4.1 10.8 - - - +
141F ALA* 3.4 28.2 - - + +
162F VAL* 4.0 19.0 + - + +
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F SER 3.1 12.0 + - - +
49F GLU* 2.9 14.0 + - - +
51F GLN* 1.3 77.4 - - - +
53F ARG* 1.3 57.1 + - + +
55F ALA* 3.2 9.0 + - - +
56F ASP* 2.6 34.0 + - - +
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Residues in contact with ARG 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR* 6.0 4.2 - - - +
101A ASP* 4.2 18.4 + - - -
136A LYS* 5.6 5.5 - - - +
29D GLN* 5.2 11.2 + - - +
33D ASP* 5.7 4.8 + - - -
39F TYR* 6.4 1.1 - - - -
40F CYS* 4.1 28.9 - - + +
43F ARG* 4.4 23.6 + - - +
44F VAL* 3.9 27.6 - - - +
49F GLU* 2.8 20.7 + - - +
50F LEU 3.7 7.9 - - - +
52F ALA* 1.3 74.3 - - - +
54F LEU* 1.3 63.1 + - - +
56F ASP* 3.1 27.4 + - + +
57F MET* 3.3 13.8 + - - +
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Residues in contact with LEU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F PHE* 4.5 12.6 - - + -
36F MET* 4.8 3.1 - - + -
37F VAL* 4.3 23.1 - - + +
40F CYS* 4.1 19.1 - - + -
50F LEU* 3.1 22.6 + - + +
51F GLN* 3.6 8.5 - - - +
53F ARG* 1.3 74.6 - - - +
55F ALA* 1.3 64.5 + - - +
57F MET* 3.3 10.1 + - - +
58F GLY 3.1 17.3 + - - -
138F ASN* 3.3 51.4 - - + +
141F ALA* 4.2 0.2 - - + -
142F PHE* 3.4 27.6 - - + +
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Residues in contact with ALA 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F GLN 2.9 13.9 + - - +
52F ALA* 3.3 13.0 - - - +
54F LEU* 1.3 78.2 - - - +
56F ASP* 1.3 61.9 + - - +
58F GLY 3.3 0.3 + - - -
59F GLN* 3.1 26.5 + - - +
141F ALA* 3.3 21.7 + - + +
144F GLY 5.2 0.4 - - - -
145F GLY* 3.2 19.0 - - - +
160F VAL 5.8 3.4 - - - +
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Residues in contact with ASP 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLN* 5.7 7.9 - - + +
52F ALA* 2.6 27.7 + - - +
53F ARG* 3.3 20.2 - - + +
55F ALA* 1.3 77.4 - - - +
57F MET* 1.3 64.6 + - + +
59F GLN* 3.3 30.0 + - - +
60F GLY* 3.8 3.3 + - - -
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Residues in contact with MET 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ALA* 3.3 43.7 - - + +
26D LEU* 3.3 27.1 - - + +
29D GLN* 3.5 30.1 - - + -
36F MET* 3.6 20.0 - - + -
39F TYR* 5.8 2.9 - - + -
40F CYS* 4.1 24.5 - - - -
53F ARG 3.3 10.9 + - - +
54F LEU* 3.3 10.5 + - - +
56F ASP* 1.3 76.1 - - + +
58F GLY* 1.3 62.3 + - - +
60F GLY* 3.2 10.4 + - - -
61F VAL* 3.3 13.7 + - - +
142F PHE* 4.0 10.8 - - + -
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Residues in contact with GLY 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F LEU 3.1 9.9 + - - -
55F ALA 3.7 3.8 - - - -
56F ASP 3.2 0.4 - - - -
57F MET* 1.3 76.7 - - - +
59F GLN* 1.3 59.1 + - - +
61F VAL* 3.1 3.6 + - - -
62F GLY 2.8 24.8 + - - -
142F PHE* 3.6 32.9 - - - -
145F GLY 3.7 6.5 - - - -
146F ILE* 3.3 12.3 - - - +
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Residues in contact with GLN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ALA* 3.1 18.4 + - - +
56F ASP* 3.6 21.6 + - - +
57F MET 3.2 0.8 - - - -
58F GLY* 1.3 75.8 - - - +
60F GLY* 1.3 56.9 + - - +
63F ALA* 2.9 27.5 + - - +
145F GLY* 3.1 23.1 - - - +
148F GLU* 3.5 32.3 + - - +
149F ALA* 3.2 18.4 + - + +
152F THR* 5.2 2.3 + - - +
153F HIS* 5.4 0.2 + - - -
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Residues in contact with GLY 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 5.4 0.2 - - - +
25D ALA* 5.7 2.7 - - - -
56F ASP 3.8 4.6 + - - -
57F MET 3.2 8.2 + - - -
58F GLY 3.1 1.0 - - - -
59F GLN* 1.3 78.9 - - - +
61F VAL* 1.3 60.1 + - - +
63F ALA* 3.5 12.2 + - - +
64F SER* 3.3 18.9 + - - -
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Residues in contact with VAL 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LEU* 4.3 13.7 - - + -
21D LEU* 3.9 46.3 - - + +
22D THR* 4.4 1.1 - - - +
25D ALA* 4.2 4.7 - - + -
57F MET 3.3 17.5 - - - +
58F GLY 3.1 2.0 + - - +
60F GLY* 1.3 72.1 - - - +
62F GLY* 1.3 64.6 + - - +
64F SER* 3.4 1.0 + - - -
65F LEU* 2.9 35.6 + - + +
142F PHE* 4.0 17.0 - - + -
146F ILE* 3.4 33.7 - - + -
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Residues in contact with GLY 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F GLY 2.8 15.9 + - - -
59F GLN 3.8 1.8 - - - -
61F VAL* 1.3 79.7 - - - +
63F ALA* 1.3 60.8 + - - +
65F LEU* 3.3 2.0 + - - +
66F LEU* 3.1 21.3 + - - +
146F ILE* 3.7 31.4 - - - -
149F ALA* 4.0 5.2 - - - -
150F ILE* 3.5 12.1 + - - +
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Residues in contact with ALA 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C PRO* 6.2 2.2 - - + -
59F GLN 2.9 18.2 + - - +
60F GLY* 3.7 8.7 - - - +
61F VAL 3.3 0.4 - - - -
62F GLY* 1.3 75.9 - - - +
64F SER* 1.3 61.1 + - - +
66F LEU* 3.8 9.5 - - - +
67F ASP* 3.8 13.5 - - - +
149F ALA* 3.8 1.4 - - - +
153F HIS* 3.8 37.4 + - + +
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Residues in contact with SER 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ILE* 5.3 1.6 - - - +
110C ALA* 3.9 15.3 + - - -
111C MET* 3.8 32.2 + - - +
21D LEU* 3.9 21.6 - - - +
60F GLY 3.3 11.8 + - - -
61F VAL 3.4 3.0 + - - -
62F GLY 3.2 0.4 - - - -
63F ALA* 1.3 76.1 - - - +
65F LEU* 1.3 68.5 + - - +
66F LEU 3.1 1.0 + - - -
67F ASP* 3.5 13.6 + - - +
68F VAL* 3.7 10.5 + - - +
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Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLU* 4.9 11.7 - - + +
18D LEU* 4.9 8.1 - - + +
21D LEU* 3.7 22.2 - - + -
61F VAL* 2.9 24.7 + - + +
62F GLY* 3.7 4.9 - - - +
64F SER* 1.3 77.1 - - - +
66F LEU* 1.3 63.5 + - - +
68F VAL* 3.3 17.7 + - + +
69F LEU* 2.9 46.9 + - + +
93F VAL* 5.3 0.4 - - + -
96F ALA* 5.3 2.9 - - + -
97F LEU* 3.8 28.9 - - + -
146F ILE* 4.3 14.6 - - + -
150F ILE* 4.7 5.6 - - + -
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Residues in contact with LEU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ALA* 3.6 23.1 - - + +
79C GLY* 3.5 21.8 - - - +
62F GLY 3.1 12.2 + - - +
63F ALA 3.8 12.6 - - - +
64F SER 3.1 0.2 + - - -
65F LEU* 1.3 75.0 - - - +
67F ASP* 1.3 65.3 + - - +
69F LEU* 3.9 3.0 - - - +
70F VAL* 3.0 32.0 + - + +
88F PHE* 4.7 3.4 - - + -
150F ILE* 3.7 35.3 - - + +
153F HIS* 3.4 33.7 - - + -
154F SER* 3.9 11.4 - - - +
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Residues in contact with ASP 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C THR* 4.1 1.9 + - - -
78C ALA* 4.1 4.5 - - - -
79C GLY* 3.5 23.4 + - - -
103C TYR* 2.7 37.8 + - - +
106C TYR* 5.0 9.9 - - - -
107C ILE* 3.8 24.5 - - + -
110C ALA* 6.2 0.2 - - - +
63F ALA 3.8 14.6 - - - +
64F SER* 3.5 4.7 + - - +
65F LEU 3.5 0.2 - - - -
66F LEU* 1.3 76.9 - - - +
68F VAL* 1.3 63.9 + - - +
70F VAL 3.4 0.2 + - - -
71F MET* 2.9 30.3 + - - +
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Residues in contact with VAL 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ILE* 4.6 5.7 - - + +
111C MET* 4.0 24.5 - - + -
17D GLU* 3.8 19.3 - - - +
64F SER 3.7 7.3 + - - +
65F LEU* 3.3 23.8 + - + +
67F ASP* 1.3 79.2 - - - +
69F LEU* 1.3 71.0 + - + +
71F MET* 3.5 4.7 + - - +
72F ARG* 3.2 56.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F LEU* 2.9 44.7 + - + +
66F LEU 3.9 2.2 - - - +
68F VAL* 1.3 75.4 - - + +
70F VAL* 1.3 63.8 + - - +
72F ARG* 3.8 22.4 - - - +
73F GLU* 3.0 52.5 + - - +
74F LYS* 4.4 0.3 - - - +
88F PHE* 4.2 13.0 - - + -
92F ASN* 4.4 3.4 - - + +
93F VAL* 4.1 28.5 - - + +
96F ALA* 3.8 29.2 - - + -
150F ILE* 5.2 1.3 - - + -
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Residues in contact with VAL 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C MET* 3.8 8.7 - - + -
78C ALA* 4.0 6.1 - - + -
66F LEU* 3.0 34.2 + - + +
67F ASP 3.9 2.7 - - - +
69F LEU* 1.3 78.2 - - - +
71F MET* 1.3 66.0 + - + +
74F LYS* 2.3 53.9 + - + +
77F LYS 3.4 28.3 - - - +
88F PHE* 3.6 25.4 - - + -
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Residues in contact with MET 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C MET* 3.3 20.6 - - + +
103C TYR* 3.1 47.6 - - + +
104C ASP* 5.4 6.7 - - - +
107C ILE* 4.8 8.1 - - + -
67F ASP 2.9 21.4 + - - +
68F VAL* 4.2 4.0 - - - +
70F VAL* 1.3 81.8 - - + +
72F ARG* 1.3 58.3 + - - +
74F LYS 3.2 11.2 - - - +
75F ASN* 3.5 19.3 + - - +
76F GLY* 3.8 22.7 - - - -
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Residues in contact with ARG 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D SER* 5.7 2.2 + - - -
17D GLU* 2.8 41.6 + - - -
68F VAL* 3.2 33.7 + - - +
69F LEU* 3.8 21.2 - - - +
71F MET* 1.3 79.2 - - - +
73F GLU* 1.3 76.0 + - + +
74F LYS 3.3 4.7 + - - -
----------------------------------------------------------
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Residues in contact with GLU 73 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F LEU* 3.0 38.3 + - - +
72F ARG* 1.3 89.3 + - + +
74F LYS* 1.3 68.8 + - + +
88F PHE* 6.2 0.2 - - + -
92F ASN* 3.5 41.8 - - - +
95F LYS* 4.6 15.0 + - - +
96F ALA* 4.9 2.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 74 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F LEU 4.4 0.9 - - - +
70F VAL* 2.3 52.8 - - + +
71F MET 3.2 13.7 - - - +
72F ARG 3.3 2.2 + - - -
73F GLU* 1.3 82.5 - - + +
75F ASN* 1.3 60.7 + - - +
77F LYS* 4.4 30.7 - - + +
79F GLU* 3.6 21.8 + - + +
88F PHE* 3.8 30.3 - - + +
92F ASN* 3.9 21.2 + - - +
----------------------------------------------------------
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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