Contacts of the helix formed by residues 48 - 77 (chain E) in PDB entry 5JKL
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 LEU 48 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PHE* 3.0 32.6 + - + +
46E VAL* 3.5 14.1 - - + +
47E ALA* 1.3 83.0 - - - +
49E LYS* 1.3 63.5 + - - +
50E ASN 3.2 2.8 + - - -
51E PHE* 3.3 25.5 + - + -
52E ALA 3.1 17.2 + - - -
167E GLU* 4.1 25.1 - - + +
168E TYR* 4.1 23.1 - - + +
171E ASP* 3.4 27.4 - - + +
172E LYS* 4.8 4.3 - - - +
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Residues in contact with LYS 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PHE 5.0 1.1 - - - +
42E ASP* 6.1 1.6 - - - +
47E ALA* 3.8 21.7 + - - +
48E LEU* 1.3 72.8 - - - +
50E ASN* 1.3 62.8 + - - +
52E ALA* 3.4 8.7 + - - +
53E LYS* 2.9 37.8 + - - +
171E ASP* 3.5 3.6 + - - +
172E LYS* 6.5 1.1 - - - +
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Residues in contact with ASN 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LYS* 1.3 80.2 - - - +
51E PHE* 1.3 60.3 + - - +
52E ALA 3.2 0.7 - - - -
53E LYS* 3.8 22.4 + - - +
54E TYR* 2.9 30.0 + - - +
171E ASP* 2.9 45.9 + - - +
172E LYS* 4.3 8.9 - - - +
175E LEU* 3.7 17.3 - - + +
176E GLY* 3.7 19.3 - - - -
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Residues in contact with PHE 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PHE* 3.6 22.2 - + + -
48E LEU* 3.3 19.9 + - + +
50E ASN* 1.3 75.8 - - - +
52E ALA* 1.3 60.6 + - - +
54E TYR* 3.3 1.4 + - - +
55E PHE* 3.1 49.7 + + - -
96E GLY* 3.4 38.4 - - - -
100E MET* 3.9 16.8 - - + -
155E LEU* 4.2 10.3 - - + -
167E GLU* 3.7 22.4 - - + -
170E PHE* 3.6 25.1 - + - -
171E ASP* 3.0 22.8 + - + -
175E LEU* 3.7 14.1 - - + +
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Residues in contact with ALA 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E SER* 2.7 48.2 + - - +
41E PHE* 3.7 6.2 - - + +
42E ASP* 4.1 15.3 - - + +
48E LEU 3.1 13.2 + - - +
49E LYS* 3.4 13.2 - - - +
50E ASN 3.2 0.2 - - - -
51E PHE* 1.3 76.0 - - - +
53E LYS* 1.3 63.4 + - + +
56E LEU* 3.0 12.2 + - - +
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Residues in contact with LYS 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LYS* 2.9 26.8 + - - +
50E ASN* 3.9 21.2 + - - +
52E ALA* 1.3 79.6 - - + +
54E TYR* 1.3 62.6 + - - +
56E LEU* 3.3 6.4 + - + +
57E HIS* 3.0 25.6 + - - +
175E LEU 6.1 0.9 - - - +
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Residues in contact with TYR 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ASN 2.9 18.1 + - - +
51E PHE* 3.3 6.7 + - - +
53E LYS* 1.3 76.9 - - - +
55E PHE* 1.3 83.3 + + - +
57E HIS* 3.3 7.6 + - + +
58E GLN* 3.0 53.6 + - + +
100E MET* 3.6 28.0 - - + -
147E GLU* 2.5 35.5 + - - +
148E LEU* 3.6 19.8 - - + +
151E HIS* 3.7 14.9 - - - -
175E LEU* 3.9 19.7 - - + +
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Residues in contact with PHE 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TYR* 3.5 53.6 - + + +
37E MET* 3.9 17.5 - - + -
38E SER* 3.7 7.6 - - - +
41E PHE* 3.5 33.9 - + - -
51E PHE* 3.1 35.8 + + - +
54E TYR* 1.3 91.7 - + - +
56E LEU* 1.3 61.4 + - - +
58E GLN* 3.2 2.4 + - + -
59E SER* 2.9 24.6 + - - -
99E ALA* 4.1 18.6 - - + -
100E MET* 3.9 25.6 - - + -
103E ALA* 4.3 5.8 - - + -
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Residues in contact with LEU 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E LEU* 4.0 26.5 - - + -
38E SER* 3.5 16.2 - - - +
39E TYR* 4.1 23.8 - - + +
52E ALA 3.0 12.6 + - - +
53E LYS* 3.8 7.0 - - + +
55E PHE* 1.3 76.3 - - - +
57E HIS* 1.3 62.6 + - - +
59E SER* 3.2 7.3 + - - -
60E HIS* 3.0 52.9 + - + +
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Residues in contact with HIS 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E LYS 3.0 14.0 + - - +
54E TYR* 3.4 11.2 - + + +
56E LEU* 1.3 75.2 - - - +
58E GLN* 1.3 81.5 + - - +
60E HIS* 3.2 10.0 + - + +
61E GLU* 2.9 34.6 + - + +
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Residues in contact with GLN 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TYR* 3.8 31.3 - - + +
54E TYR* 3.0 64.0 + - + +
55E PHE* 3.6 7.6 - - - +
56E LEU 3.2 0.2 - - - -
57E HIS* 1.3 91.3 - - - +
59E SER* 1.4 57.9 + - - +
61E GLU* 3.0 28.1 + - - +
62E GLU* 2.9 35.9 + - - +
107E GLU* 5.3 2.3 - - - +
144E ALA* 6.0 2.1 - - - +
147E GLU* 4.3 4.4 + - - -
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Residues in contact with SER 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E SER* 2.7 52.7 + - - +
34E TYR* 3.6 8.0 - - - +
35E LEU* 3.7 24.7 - - - +
55E PHE 2.9 13.3 + - - -
56E LEU* 3.2 13.0 + - - -
58E GLN* 1.4 75.9 - - - +
60E HIS* 1.3 70.2 + - - +
62E GLU 3.3 1.7 + - - -
63E ARG* 3.2 10.2 + - - +
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Residues in contact with HIS 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E LEU* 6.0 0.4 - - - +
56E LEU* 3.0 43.7 + - + +
57E HIS* 3.8 10.5 - - + +
59E SER* 1.3 81.1 - - - +
61E GLU* 1.3 65.5 + - - +
63E ARG* 3.2 10.2 + - + +
64E GLU* 3.1 27.5 + - + +
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Residues in contact with GLU 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E HIS* 2.9 25.8 + - + +
58E GLN* 3.0 30.7 + - - +
59E SER 3.3 0.2 - - - -
60E HIS* 1.3 77.7 - - - +
62E GLU* 1.3 60.6 + - - +
64E GLU* 3.1 10.0 + - + +
65E HIS* 2.9 54.2 + - + +
140E GLU* 4.0 15.2 - - - +
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Residues in contact with GLU 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E GLU* 2.8 13.5 - - - +
30E ALA* 3.9 13.9 - - + +
31E SER* 3.5 29.4 - - - +
34E TYR* 3.8 18.5 - - + -
58E GLN* 2.9 21.1 + - - +
61E GLU* 1.3 75.4 - - - +
63E ARG* 1.3 65.8 + - - +
65E HIS* 3.1 14.2 + - - +
66E ALA* 3.0 22.2 + - - +
107E GLU* 3.3 24.9 - - - +
110E VAL* 6.2 0.9 - - - -
201E FE 2.1 32.7 - - - -
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Residues in contact with ARG 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E LEU* 3.9 23.9 - - - +
31E SER* 3.9 12.3 + - - +
59E SER 3.2 12.6 + - - +
60E HIS* 3.5 13.0 - - + +
62E GLU* 1.3 75.2 - - - +
64E GLU* 1.3 68.7 + - - +
66E ALA* 3.2 5.2 + - - +
67E GLU* 3.0 56.6 + - - +
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Residues in contact with GLU 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E HIS* 3.1 15.3 + - + +
61E GLU* 3.1 11.5 + - + +
63E ARG* 1.3 80.6 - - - +
65E HIS* 1.3 58.9 + - + +
67E GLU* 2.9 30.7 + - - +
68E LYS* 3.0 30.7 + - - +
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Residues in contact with HIS 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E GLU* 3.3 19.5 - - - +
61E GLU* 2.9 55.1 + - + +
62E GLU* 3.1 15.3 + - - +
64E GLU* 1.3 80.0 - - + +
66E ALA* 1.3 61.4 + - - +
68E LYS* 4.8 1.6 - - - -
69E LEU* 3.3 10.9 + - - +
136E HIS 5.6 3.4 - - - -
137E TYR* 2.7 40.0 + + + -
140E GLU* 5.0 15.0 - - + +
141E GLN* 4.6 8.7 - - - -
201E FE 2.1 28.9 - - - -
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Residues in contact with ALA 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ILE* 4.1 8.1 - - + +
27E GLU* 3.7 22.1 - - + +
28E LEU* 3.6 34.1 - - + +
62E GLU 3.0 7.8 + - - +
63E ARG* 3.2 8.9 + - - +
65E HIS* 1.3 74.3 - - - +
67E GLU* 1.3 59.1 + - + +
69E LEU* 3.3 7.9 + - - +
70E MET* 3.0 34.1 + - - +
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Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ARG* 3.0 54.0 + - - +
64E GLU* 2.9 35.6 + - - +
66E ALA* 1.3 70.4 - - + +
68E LYS* 1.3 60.3 - - - +
70E MET* 3.2 17.6 + - - +
71E LYS* 3.0 28.1 + - - +
----------------------------------------------------------
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Residues in contact with LYS 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLU 3.0 15.6 + - - +
65E HIS* 4.5 1.7 - - - -
66E ALA 3.3 0.4 - - - -
67E GLU* 1.3 77.9 - - - +
69E LEU* 1.3 57.5 + - - +
71E LYS* 3.4 13.7 + - + +
72E LEU* 3.0 26.2 + - - +
132E PHE* 3.9 13.1 - - + -
136E HIS* 3.3 49.2 + - + +
137E TYR* 3.4 19.7 - - + +
----------------------------------------------------------
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Residues in contact with LEU 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ILE* 3.8 30.8 - - + +
23E GLN* 3.6 37.7 - - + -
24E ILE* 3.5 17.9 - - + +
27E GLU* 3.7 16.6 - - + -
65E HIS 3.3 12.2 + - - +
66E ALA 3.3 4.1 + - - +
68E LYS* 1.3 76.2 - - - +
70E MET* 1.3 59.3 + - - +
72E LEU* 3.3 6.0 + - + +
73E GLN* 3.0 28.2 + - - +
114E LEU* 5.8 1.1 - - + -
117E LEU* 5.3 1.8 - - + -
132E PHE* 3.7 23.3 - - + -
133E ILE* 6.3 0.4 - - + -
137E TYR* 3.4 18.4 - - + +
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Residues in contact with MET 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ILE* 3.7 30.3 - - + -
28E LEU* 5.5 5.6 - - - -
66E ALA* 3.0 19.3 + - - +
67E GLU* 3.2 18.4 + - - +
69E LEU* 1.3 75.7 - - - +
71E LYS* 1.3 62.9 + - - +
73E GLN* 3.3 3.9 + - - +
74E ASN* 3.2 21.0 + - - -
80E ILE* 3.6 43.8 - - + +
82E LEU* 4.5 14.4 - - + -
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Residues in contact with LYS 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E GLU 3.0 13.6 + - - +
68E LYS* 3.6 16.8 - - + +
70E MET* 1.3 77.6 - - - +
72E LEU* 1.3 57.0 + - - +
74E ASN* 3.3 7.1 + - - +
75E GLN* 2.8 60.7 + - + +
143F LYS* 6.5 0.2 - - - -
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Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E TYR* 4.0 18.8 - - + +
20E ILE* 4.2 12.6 - - + -
68E LYS 3.0 17.4 + - - +
69E LEU* 3.5 4.7 - - - +
71E LYS* 1.3 74.8 - - - +
73E GLN* 1.3 67.6 + - - +
75E GLN* 3.1 15.6 + - - +
76E ARG* 2.9 32.7 + - + +
128E HIS* 3.7 30.1 - - + +
129E LEU* 4.2 17.7 - - + -
132E PHE* 3.7 39.7 - - + -
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Residues in contact with GLN 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E TYR* 2.5 39.2 + - - -
17E GLU* 3.0 28.8 + - - +
20E ILE* 3.7 12.0 - - + +
21E ASN* 3.0 24.0 + - - +
24E ILE* 4.7 0.7 - - + -
69E LEU 3.0 12.9 + - - +
70E MET* 3.5 9.4 - - - +
72E LEU* 1.3 80.9 - - - +
74E ASN* 1.3 61.5 + - - +
76E ARG* 3.3 1.6 + - - +
77E GLY 3.3 2.3 + - - -
78E GLY* 3.0 45.1 + - - +
79E ARG 3.9 1.1 - - - +
80E ILE* 3.7 24.5 - - + -
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Residues in contact with ASN 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E VAL* 4.2 1.9 - - - +
70E MET 3.2 11.5 + - - +
71E LYS* 3.8 7.3 - - - +
73E GLN* 1.3 73.8 - - - +
75E GLN* 1.3 66.4 + - - +
77E GLY* 3.1 12.3 + - - -
78E GLY 3.8 6.3 - - - +
79E ARG* 3.8 19.9 + - - +
80E ILE* 4.0 24.9 + - - +
146F LYS* 3.5 27.1 - - - +
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Residues in contact with GLN 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E VAL* 3.7 13.0 - - - +
71E LYS* 2.8 47.8 + - + +
72E LEU* 3.4 30.9 + - - +
74E ASN* 1.3 75.6 - - - +
76E ARG* 1.3 61.6 + - + +
77E GLY 3.6 0.3 + - - -
132E PHE* 5.4 2.9 - - - -
139F ASN* 4.4 8.9 + - - +
142F VAL* 3.8 26.9 - - + +
143F LYS* 3.9 28.5 - - - +
145F ILE* 5.7 0.7 - - - +
146F LYS* 4.1 28.6 - - + +
----------------------------------------------------------
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Residues in contact with ARG 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E VAL* 3.9 3.9 - - - +
9E ARG* 3.4 26.2 - - - +
10E GLN 3.1 20.7 + - - +
11E ASN* 3.1 30.9 + - - +
12E TYR* 3.7 39.7 - - + +
72E LEU* 2.9 31.4 + - + +
73E GLN 4.1 0.2 - - - +
74E ASN 3.2 0.2 - - - -
75E GLN* 1.3 75.6 - - - +
77E GLY* 1.3 61.0 + - - +
78E GLY 3.3 0.8 + - - -
126E ASP* 2.9 30.7 + - - -
128E HIS* 3.1 38.5 + - - +
129E LEU* 3.7 6.9 - - - +
142F VAL* 3.8 19.7 - - - +
----------------------------------------------------------
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Residues in contact with GLY 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E SER* 3.5 25.3 + - - -
8E VAL* 3.5 18.8 - - - +
9E ARG* 3.8 15.6 + - - +
74E ASN 3.1 13.3 + - - -
75E GLN 3.3 0.8 - - - -
76E ARG* 1.3 77.9 - - - +
78E GLY* 1.3 63.3 + - - +
79E ARG* 4.0 10.4 + - - +
----------------------------------------------------------
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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