Contacts of the helix formed by residues 25 - 52 (chain F) in PDB entry 5YWB
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 GLY 25 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ASN* 1.3 74.8 - - - +
26F CYS* 1.3 63.8 + - - +
28F VAL* 3.1 9.7 + - - +
29F ASP* 2.9 22.1 + - - +
106F LEU* 5.1 4.7 - - - -
153F LYS* 4.6 2.4 + - - -
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Residues in contact with CYS 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E TRP* 5.6 0.9 - - - -
95E PHE* 4.2 18.6 - - + -
24F ASN 3.4 0.4 - - - -
25F GLY* 1.3 75.0 - - - +
27F PHE* 1.3 57.3 + - - +
29F ASP* 3.3 8.9 + - - +
30F ALA* 2.9 29.6 + - - +
103F HIS* 5.7 4.0 - - - -
105F HIS* 5.1 13.6 - - + +
106F LEU* 3.6 25.3 - - - +
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Residues in contact with PHE 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E LEU* 4.1 17.4 - - + +
95E PHE* 3.4 36.2 - + + -
96E ALA* 3.6 31.4 - - + -
24F ASN* 3.1 30.4 + - + +
26F CYS* 1.3 78.3 - - - +
28F VAL* 1.3 67.6 + - + +
30F ALA* 3.3 4.7 + - - +
31F LEU* 2.9 46.2 + - + +
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Residues in contact with VAL 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ASN* 3.2 18.8 - - + +
25F GLY* 3.1 7.7 + - - +
27F PHE* 1.3 81.7 - - + +
29F ASP* 1.3 65.5 + - - +
31F LEU* 3.3 10.1 + - + +
32F ASN* 2.9 31.7 + - - +
149F THR 4.8 0.2 - - - +
152F ILE* 3.6 28.9 - - + +
153F LYS* 3.5 35.4 - - + +
156F LYS* 5.0 13.7 - - + -
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Residues in contact with ASP 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F GLY 2.9 12.9 + - - +
26F CYS* 3.3 12.1 + - - +
28F VAL* 1.3 77.0 - - - +
30F ALA* 1.3 57.3 + - - +
32F ASN* 3.1 5.0 + - - +
33F VAL* 2.9 31.8 + - - +
105F HIS* 3.2 26.7 - - + +
106F LEU* 4.8 7.6 - - + +
109F PRO* 3.7 10.9 - - + +
153F LYS* 3.5 14.0 - - - +
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Residues in contact with ALA 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E MET* 5.4 1.7 - - + +
91E TRP* 3.6 35.0 - - + -
92E LEU* 4.7 10.3 - - + -
95E PHE* 5.6 2.0 - - + -
26F CYS 2.9 16.6 + - - +
27F PHE* 3.7 7.0 - - - +
29F ASP* 1.3 75.4 - - - +
31F LEU* 1.3 63.5 + - - +
33F VAL* 2.9 21.0 + - - +
34F VAL* 3.0 19.2 + - + +
105F HIS* 6.2 1.5 - - + +
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E LEU* 4.9 19.0 - - + +
27F PHE* 2.9 38.1 + - + +
28F VAL* 3.3 9.6 + - + +
30F ALA* 1.3 76.1 - - - +
32F ASN* 1.3 60.4 + - - +
34F VAL* 3.7 8.6 + - + +
35F PRO* 3.2 17.5 - - + +
149F THR* 3.4 21.8 - - + +
152F ILE* 4.9 21.5 - - + -
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Residues in contact with ASN 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F VAL* 2.9 20.2 + - - +
29F ASP 3.5 8.1 - - - +
31F LEU* 1.3 76.8 - - - +
33F VAL* 1.3 64.7 + - - +
34F VAL 3.1 0.4 - - - -
35F PRO* 3.1 12.1 - - - +
36F HIS* 3.1 23.9 + - - +
109F PRO* 4.4 11.1 - - + +
149F THR* 3.4 35.0 + - - +
150F LYS* 3.4 42.0 - - - +
153F LYS* 3.4 23.3 - - - +
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Residues in contact with VAL 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E MET* 4.2 21.8 - - + -
29F ASP 2.9 18.3 + - - +
30F ALA* 2.9 11.9 + - - +
32F ASN* 1.3 76.4 - - - +
34F VAL* 1.3 65.8 + - - +
35F PRO 3.5 0.3 - - - -
36F HIS* 3.5 11.9 + - - +
37F VAL* 3.3 20.9 + - + +
105F HIS 5.5 1.1 - - - +
108F MET* 4.1 13.2 - - + -
109F PRO* 3.8 30.7 - - + -
112F MET* 4.1 15.7 - - + -
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Residues in contact with VAL 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E MET* 4.2 25.1 - - + -
89E VAL* 6.1 4.3 - - + -
92E LEU* 4.0 30.3 - - + -
30F ALA* 3.0 16.5 + - + +
31F LEU* 3.8 9.6 - - + +
33F VAL* 1.3 76.9 - - - +
35F PRO* 1.3 73.9 - - + +
37F VAL* 3.0 20.5 + - + +
38F PHE* 3.0 14.4 + - + +
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Residues in contact with PRO 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 3.2 15.0 - - + +
32F ASN 3.1 23.6 - - - +
34F VAL* 1.3 83.1 - - + +
36F HIS* 1.3 65.9 + - + +
38F PHE* 3.1 11.0 + - + +
39F LEU 3.0 18.9 + - - -
142F TYR* 3.5 23.2 - - + -
145F LEU* 4.2 30.5 - - + +
146F ALA* 4.6 5.6 - - + +
149F THR* 4.1 17.7 - - + +
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Residues in contact with HIS 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F ASN* 3.1 35.9 + - - +
33F VAL* 3.8 3.6 - - - +
34F VAL 3.3 0.4 - - - -
35F PRO* 1.3 76.4 - - + +
37F VAL* 1.3 56.6 + - - +
39F LEU* 3.3 2.1 + - - +
40F LEU* 2.9 35.5 + - - +
109F PRO* 3.9 8.0 + - + +
112F MET* 3.6 32.8 - - + +
113F ALA* 3.4 38.6 - - + +
116F ALA* 3.6 3.4 - - + +
142F TYR* 2.8 36.8 + + - -
146F ALA* 5.0 5.6 - - + -
150F LYS* 5.6 5.2 + - - -
179F TYR* 3.5 11.0 - + - -
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Residues in contact with VAL 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E LEU* 4.9 6.3 - - + -
88E MET* 4.4 29.8 - - + -
33F VAL* 3.3 12.4 + - + +
34F VAL* 3.0 14.4 + - + +
36F HIS* 1.3 77.1 - - - +
38F PHE* 1.3 67.1 + - - +
40F LEU* 3.4 4.6 + - - -
41F PHE* 2.9 63.2 + - + -
112F MET* 3.9 21.3 - - + -
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Residues in contact with PHE 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E LEU* 4.5 25.4 - - + -
34F VAL* 3.0 15.0 + - + +
35F PRO* 3.1 13.7 + - + +
37F VAL* 1.3 79.2 - - + +
39F LEU* 1.3 64.6 + - + +
41F PHE* 3.2 6.3 + - - +
42F ILE* 3.0 58.1 + - + +
138F ALA 5.7 2.9 - - - -
141F ILE* 5.2 14.6 - - + -
142F TYR* 5.4 8.7 - + + -
145F LEU* 5.3 14.4 - - + -
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Residues in contact with LEU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F PRO 3.0 15.6 + - - +
36F HIS* 3.9 3.1 - - - +
38F PHE* 1.3 78.7 - - + +
40F LEU* 1.3 60.5 + - - +
41F PHE 3.0 1.6 - - - -
42F ILE* 3.3 7.0 + - + +
43F THR* 2.9 28.9 + - - -
116F ALA* 3.9 21.8 - - + +
119F THR* 3.9 11.9 - - + -
120F SER* 4.7 1.1 - - - +
123F TYR* 4.5 15.0 - - + -
138F ALA* 4.3 13.9 - - + +
139F LEU* 4.3 18.6 - - + -
142F TYR* 3.5 52.0 - - + -
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Residues in contact with LEU 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F HIS 2.9 17.6 + - - +
37F VAL* 3.9 4.3 - - - +
39F LEU* 1.3 75.8 - - - +
41F PHE* 1.3 65.8 + - + +
43F THR* 3.1 8.0 - - + +
44F PHE* 2.9 40.1 - - + -
112F MET* 3.7 28.5 - - + +
115F MET* 3.3 56.8 - - + +
116F ALA* 4.0 4.3 - - - +
119F THR* 3.6 20.2 - - + +
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Residues in contact with PHE 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E CYS* 3.6 45.6 - - + +
84E LEU* 3.7 29.6 - - + -
85E LEU* 3.4 43.1 - - + -
88E MET* 5.8 0.2 - - + -
37F VAL* 2.9 48.1 + - + +
38F PHE 3.7 3.8 - - - +
40F LEU* 1.3 89.5 - - + +
42F ILE* 1.3 65.8 + - - +
43F THR 3.2 0.2 - - - -
44F PHE* 3.6 8.1 + + - +
45F PRO* 3.3 17.7 - - - +
112F MET* 6.5 0.2 - - + -
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Residues in contact with ILE 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E LEU* 5.7 3.4 - - + -
38F PHE* 3.0 50.9 + - + +
39F LEU* 3.3 8.7 + - + +
41F PHE* 1.3 75.7 - - + +
43F THR* 1.3 64.4 + - - +
44F PHE 3.3 0.7 + - - -
45F PRO* 3.4 11.7 - - - +
46F ILE* 4.2 12.6 + - + +
123F TYR* 3.4 18.4 + - + +
138F ALA* 5.3 11.4 - - + -
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Residues in contact with THR 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F LEU 2.9 14.3 + - - +
40F LEU* 3.1 24.9 - - + +
42F ILE* 1.3 78.6 - - - +
44F PHE* 1.3 67.4 + - + +
46F ILE* 3.6 2.2 + - - +
47F LEU* 2.8 35.2 + - + +
119F THR* 3.2 31.7 + - + +
122F VAL* 5.1 4.0 - - - +
123F TYR* 3.3 34.0 - - - -
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Residues in contact with PHE 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E MET* 4.1 24.5 - - + -
81E CYS* 5.8 2.5 - - + -
40F LEU* 2.9 36.8 - - + +
41F PHE* 3.6 8.4 + + - +
43F THR* 1.3 85.8 - - + +
45F PRO* 1.3 68.3 - - + +
47F LEU* 4.4 6.1 - - + -
48F PHE* 2.9 73.5 + + - -
115F MET* 6.3 3.6 - - + -
119F THR* 5.6 0.7 - - - -
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Residues in contact with PRO 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ILE* 4.2 11.2 - - + +
77E MET* 5.2 3.1 - - + -
78E SER* 4.4 19.5 - - - +
81E CYS* 5.3 8.5 - - + -
41F PHE 3.3 17.5 - - - +
42F ILE* 3.4 10.8 - - - +
44F PHE* 1.3 91.2 - - + +
46F ILE* 1.3 60.7 + - + +
48F PHE* 3.1 4.9 + - + +
49F ILE* 2.9 40.0 + - + +
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Residues in contact with ILE 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ILE* 4.3 11.0 - - + +
43F THR 3.6 5.5 + - - +
44F PHE 3.4 0.2 - - - -
45F PRO* 1.3 79.3 - - + +
47F LEU* 1.3 59.0 + - - +
49F ILE* 3.3 10.3 + - + +
50F GLY* 2.9 26.5 + - - -
123F TYR* 3.3 29.6 - - + +
126F ASN* 4.4 12.9 + - + +
135F LEU* 3.7 35.4 - - + -
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Residues in contact with LEU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F THR* 2.8 29.0 + - + +
44F PHE* 4.0 7.4 - - + +
46F ILE* 1.3 76.6 - - - +
48F PHE* 1.3 60.9 + - + +
50F GLY 3.8 0.5 - - - -
51F TRP* 2.9 30.1 + - - +
122F VAL* 4.6 17.5 - - + -
126F ASN* 4.2 12.7 + - - +
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Residues in contact with PHE 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E LEU* 4.8 3.5 - - - +
73E LEU* 4.8 23.8 - - + -
74E ILE* 4.4 19.7 - - + -
77E MET* 3.4 40.2 - - + -
44F PHE* 2.9 56.1 + + - +
45F PRO* 3.7 3.1 - - + +
47F LEU* 1.3 80.8 - - + +
49F ILE* 1.3 60.4 + - - +
51F TRP* 4.2 20.1 - + + +
52F GLY* 3.0 24.9 + - - -
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Residues in contact with ILE 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E VAL* 4.6 34.8 - - + +
62E THR* 5.1 16.5 - - + +
63E LEU* 4.9 14.1 - - + +
66E LEU* 4.9 11.8 - - + +
74E ILE* 3.6 20.6 - - + -
45F PRO* 2.9 25.2 + - + +
46F ILE* 3.8 8.5 - - + +
48F PHE* 1.3 76.4 - - - +
50F GLY* 1.3 62.9 + - - +
52F GLY* 3.4 15.8 + - - -
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Residues in contact with GLY 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F ILE 2.9 16.1 + - - -
47F LEU* 3.8 2.0 - - - -
49F ILE* 1.3 78.4 - - - +
51F TRP* 1.3 60.0 + - - +
52F GLY 4.8 1.4 - - - -
126F ASN* 5.2 9.9 - - - -
----------------------------------------------------------
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Residues in contact with TRP 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E HIS* 4.0 33.4 - + - -
73E LEU* 5.3 9.6 - - + -
47F LEU 2.9 19.2 + - - +
48F PHE* 4.2 20.0 - + + +
49F ILE 3.2 0.2 - - - -
50F GLY* 1.3 74.4 - - - +
52F GLY* 1.3 70.0 + - - +
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Residues in contact with GLY 52 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E LEU* 3.9 33.2 - - - +
67E LYS* 5.8 0.5 + - - -
70E HIS* 4.6 16.3 + - - -
48F PHE 3.0 17.5 + - - -
49F ILE 3.4 9.9 + - - -
50F GLY 4.8 1.6 - - - -
51F TRP* 1.3 92.3 - - - +
----------------------------------------------------------
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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