Contacts of the helix formed by residues 56 - 86 (chain F) in PDB entry 5HHM
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 56 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F GLN 4.1 1.4 + - - -
55F GLU* 1.3 76.3 + - - +
57F PRO* 1.4 73.8 - - - +
58F GLU* 3.3 3.6 - - - -
59F TYR* 3.3 12.9 + - - +
60F TRP* 3.0 17.9 - - - -
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Residues in contact with PRO 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ARG* 4.3 1.1 + - - +
56F GLY* 1.4 81.4 - - - +
58F GLU* 1.3 53.2 + - + +
60F TRP* 3.1 11.1 + - + +
61F ASP* 2.7 48.3 + - - +
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Residues in contact with GLU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F GLY* 3.3 0.9 - - - -
57F PRO* 1.3 81.6 - - + +
59F TYR* 1.4 52.0 + - - +
61F ASP* 3.7 9.1 + - + +
62F GLY* 2.8 30.1 + - - -
65F ARG* 4.5 10.1 + - - +
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Residues in contact with TYR 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F TYR* 4.8 0.7 + - - -
33F PHE* 4.2 6.4 - - - -
34F VAL* 4.8 2.6 - - + +
52F ILE* 3.5 16.5 - - + +
55F GLU* 3.6 37.9 - - + +
56F GLY* 3.3 13.2 + - - +
57F PRO 3.2 0.2 - - - -
58F GLU* 1.4 77.0 - - - +
60F TRP* 1.3 84.8 + + - +
62F GLY* 3.3 1.8 + - - -
63F GLU* 2.9 70.6 + - + +
167F TRP* 3.7 28.9 - + - -
171F TYR* 2.8 28.1 + + - -
1H GLY 4.3 0.7 + - - -
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Residues in contact with TRP 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F VAL* 3.7 24.2 - - + -
44F ARG* 3.1 24.5 + - - +
45F MET* 3.3 36.1 - - + -
46F GLU 3.8 0.4 - - - -
47F PRO* 3.5 43.7 - - + -
52F ILE* 3.3 27.3 + - + -
53F GLU* 4.7 4.5 + - - +
55F GLU* 3.2 22.4 + - - +
56F GLY 3.0 24.2 - - - -
57F PRO* 3.1 9.1 + - + +
59F TYR* 1.3 91.0 - + - +
61F ASP* 1.3 60.1 + - - +
63F GLU* 4.3 1.9 - - + +
64F THR* 2.7 33.6 + - - -
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Residues in contact with ASP 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ARG* 3.2 16.9 + - - +
57F PRO* 2.7 34.7 + - - +
58F GLU* 3.8 8.8 + - + +
60F TRP* 1.3 74.0 - - - +
62F GLY* 1.3 60.5 + - - +
64F THR* 3.7 3.4 + - - +
65F ARG* 3.2 50.8 + - - +
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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 GLU 2.8 16.6 + - - -
59F TYR* 3.3 2.2 + - - -
61F ASP* 1.3 73.2 - - - +
63F GLU* 1.3 64.6 + - - +
65F ARG* 3.3 17.0 + - - +
66F LYS* 3.1 35.0 + - - +
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Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F TYR* 4.4 1.7 + - - -
34F VAL* 6.0 0.4 - - + -
45F MET* 3.6 36.2 - - + +
59F TYR* 2.9 55.5 + - + +
60F TRP* 4.3 3.6 - - + +
62F GLY* 1.3 69.8 - - - +
64F THR* 1.3 56.7 + - - +
66F LYS* 3.1 28.8 + - - +
67F VAL* 2.9 32.6 + - - +
167F TRP* 4.8 2.6 - - - -
1H GLY* 3.5 13.7 - - - -
2H ILE* 3.2 28.9 + - - +
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Residues in contact with THR 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F GLN 3.8 22.7 - - - +
44F ARG* 3.6 19.5 - - + +
45F MET* 2.9 21.3 + - - +
60F TRP 2.7 22.6 + - - -
61F ASP* 3.8 7.0 - - - +
62F GLY 3.2 0.6 - - - -
63F GLU* 1.3 76.7 - - - +
65F ARG* 1.3 61.2 + - + +
67F VAL* 3.3 22.2 - - + +
68F LYS* 3.3 26.6 + - + +
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Residues in contact with ARG 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F GLU* 4.5 11.5 + - - +
61F ASP* 3.2 47.9 + - - +
62F GLY* 3.6 14.6 - - - +
64F THR* 1.3 75.5 - - + +
66F LYS* 1.4 63.7 - - + +
68F LYS* 3.6 10.2 + - + +
69F ALA* 3.3 21.5 + - - +
56J ASP* 4.3 6.5 - - - +
57J PHE 6.1 0.9 - - - +
58J GLN* 5.8 12.6 - - + +
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Residues in contact with LYS 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F GLY* 3.1 22.6 + - - +
63F GLU* 3.1 29.9 + - - +
65F ARG* 1.4 76.9 - - + +
67F VAL* 1.3 54.4 + - - +
69F ALA* 3.3 8.7 - - - +
70F HIS* 2.8 37.6 + - - -
167F TRP* 5.0 7.7 - - - +
1H GLY* 4.2 3.2 - - - -
2H ILE* 2.8 41.7 + - + +
3H LEU 3.6 18.1 - - - +
4H GLY* 3.8 17.4 - - - +
6H VAL* 4.6 0.2 - - - +
96I GLN* 4.3 14.2 + - - +
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Residues in contact with VAL 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F PHE* 4.7 2.7 - - + -
22F PHE* 3.7 12.2 - - + -
24F ALA* 3.6 31.4 - - + -
36F PHE* 3.5 34.5 - - + -
45F MET* 4.2 10.5 - - + -
63F GLU 2.9 16.6 + - - +
64F THR* 3.3 20.4 - - - +
66F LYS* 1.3 74.6 - - - +
68F LYS* 1.3 56.5 + - - +
70F HIS* 3.3 3.8 + - - +
71F SER* 2.9 29.3 + - - -
2H ILE* 3.5 15.2 - - + +
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Residues in contact with LYS 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F PHE* 4.0 14.1 - - + -
43F GLN* 3.4 46.4 + - - +
64F THR* 3.3 30.4 + - + +
65F ARG* 3.8 9.0 - - + +
66F LYS 3.4 0.2 - - - -
67F VAL* 1.3 73.3 - - - +
69F ALA* 1.3 57.0 + - - +
71F SER* 3.7 9.2 - - - -
72F GLN* 3.3 32.1 + - - +
56J ASP* 4.1 11.2 - - - +
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Residues in contact with ALA 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F ARG 3.3 13.3 + - - +
66F LYS* 3.3 13.9 + - - +
67F VAL 3.2 0.2 - - - -
68F LYS* 1.3 76.2 - - - +
70F HIS* 1.4 57.7 + - - +
72F GLN* 3.5 2.9 + - - +
73F THR* 2.9 31.5 + - - -
6H VAL* 3.9 21.1 - - + -
52J GLN* 5.1 7.4 - - - +
53J ILE* 3.8 3.2 - - + +
56J ASP* 3.7 25.4 - - - +
58J GLN* 5.5 0.4 - - - +
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Residues in contact with HIS 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F PHE* 3.6 24.6 - + + -
22F PHE* 4.0 11.4 - - + -
66F LYS 2.8 26.5 + - - -
67F VAL* 3.4 10.8 - - - +
69F ALA* 1.4 73.4 - - - +
71F SER* 1.3 56.1 + - - +
73F THR* 3.0 6.9 + - - -
74F HIS* 2.9 38.5 + + + -
97F ARG* 3.3 28.5 + - - -
99F TYR* 3.0 21.9 + - - -
2H ILE* 3.9 7.4 - - + +
3H LEU* 3.4 30.3 - - + +
5H LEU 5.0 0.2 + - - -
6H VAL* 3.5 18.9 - - + +
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Residues in contact with SER 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F SER* 5.1 1.6 + - - -
22F PHE* 3.6 40.5 - - - +
36F PHE* 4.7 6.2 - - - -
38F SER* 5.7 1.6 - - - -
67F VAL 2.9 17.1 + - - -
68F LYS* 3.7 11.4 - - - -
70F HIS* 1.3 75.8 - - - +
72F GLN* 1.3 60.0 + - - +
74F HIS* 3.4 3.1 + - - +
75F ARG* 3.1 27.4 + - - +
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Residues in contact with GLN 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F LYS 3.3 18.2 + - - +
69F ALA* 3.8 4.7 - - - +
70F HIS 3.3 0.2 - - - -
71F SER* 1.3 81.0 - - - +
73F THR* 1.3 61.3 + - - +
75F ARG* 3.5 39.7 + - - +
76F VAL* 3.3 31.5 + - - +
53J ILE* 4.1 9.4 - - + -
54J VAL 3.8 12.3 + - - +
55J ASN* 3.6 48.4 - - - +
56J ASP* 4.6 1.8 - - + +
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Residues in contact with THR 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F ALA 2.9 16.7 + - - -
70F HIS* 3.0 12.0 + - - -
72F GLN* 1.3 75.9 - - - +
74F HIS* 1.3 66.5 + - + +
76F VAL* 3.6 5.9 + - - +
77F ASP* 3.0 37.0 + - - +
97F ARG* 5.8 1.8 - - - +
116F TYR* 5.3 0.2 - - - +
6H VAL* 3.3 20.5 - - + +
7H PHE* 3.1 38.9 + - - +
8H THR* 4.1 4.1 - - + +
53J ILE* 3.7 16.2 - - - +
----------------------------------------------------------
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Residues in contact with HIS 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F PHE* 4.1 16.9 - + + +
11F SER* 4.0 22.8 - - - +
22F PHE* 3.4 23.0 - + + -
70F HIS* 2.9 24.8 + - + +
71F SER 3.8 2.2 - - - +
73F THR* 1.3 82.4 - - + +
75F ARG* 1.4 57.0 + - - +
77F ASP* 3.3 23.8 - - + +
78F LEU* 2.9 31.9 + - - +
95F VAL* 4.5 9.8 - - + +
97F ARG* 3.6 44.8 + - + +
116F TYR* 3.8 12.3 + + - -
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Residues in contact with ARG 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F SER* 4.7 0.9 + - - -
19F GLU* 2.8 29.6 + - - -
20F PRO* 3.9 28.5 - - + +
71F SER 3.1 14.4 + - - +
72F GLN* 3.5 43.7 + - - +
74F HIS* 1.4 70.1 - - - +
76F VAL* 1.3 65.3 + - + +
78F LEU* 3.4 20.9 + - - +
79F GLY* 3.4 9.2 + - - -
55J ASN* 4.2 13.1 - - - +
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Residues in contact with VAL 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F GLN* 3.3 17.4 + - - +
73F THR 3.6 7.6 - - - +
75F ARG* 1.3 77.2 - - + +
77F ASP* 1.4 55.7 + - - +
79F GLY* 3.2 4.1 + - - +
80F THR* 2.9 39.0 + - - +
8H THR* 3.9 20.0 - - + -
32J ASP* 5.4 2.7 - - - +
53J ILE* 3.8 18.4 - - + -
54J VAL* 3.9 22.0 - - + -
55J ASN* 5.9 0.2 - - - +
73J LYS* 6.0 2.9 - - - +
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Residues in contact with ASP 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F THR* 3.0 30.2 + - - +
74F HIS* 3.3 31.9 - - + +
75F ARG 3.2 0.6 - - - -
76F VAL* 1.4 72.8 - - - +
78F LEU* 1.4 54.6 + - - +
80F THR* 3.1 3.8 + - - -
81F LEU* 2.7 44.0 + - + +
95F VAL* 4.8 4.9 - - + -
116F TYR* 4.3 5.7 + - - -
8H THR* 3.5 9.8 - - - -
9H LEU* 2.9 51.5 + - + +
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Residues in contact with LEU 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F SER* 3.4 27.4 - - - +
13F SER* 3.9 19.1 - - - +
20F PRO* 3.7 29.8 - - + -
74F HIS 2.9 15.5 + - - +
75F ARG* 3.6 9.0 - - - +
76F VAL 3.4 0.4 - - - -
77F ASP* 1.4 73.5 - - - +
79F GLY* 1.3 61.3 + - - +
81F LEU* 3.6 3.1 + - - +
82F ARG* 3.1 34.9 + - - +
93F HIS* 3.4 34.3 - - + +
95F VAL* 3.6 24.7 - - + +
118F TYR* 4.5 4.3 + - + -
----------------------------------------------------------
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Residues in contact with GLY 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F ARG 3.4 5.9 + - - -
76F VAL* 3.2 7.2 + - - -
78F LEU* 1.3 77.1 - - - +
80F THR* 1.3 65.4 + - - +
82F ARG* 3.4 18.7 + - - +
83F GLY* 3.3 15.8 + - - -
----------------------------------------------------------
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Residues in contact with THR 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F VAL* 2.9 25.5 + - - +
77F ASP* 3.6 10.6 + - - -
79F GLY* 1.3 74.2 - - - +
81F LEU* 1.3 58.0 + - - +
83F GLY* 3.2 5.4 + - - -
84F TYR* 3.0 62.3 + - + +
146F LYS* 5.6 0.7 - - - +
8H THR* 5.6 0.9 - - - -
9H LEU* 3.9 17.8 + - + +
----------------------------------------------------------
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Residues in contact with LEU 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F ASP 2.7 24.1 + - - +
78F LEU 4.1 1.8 - - - +
80F THR* 1.3 69.9 - - - +
82F ARG* 1.3 65.8 + - - +
84F TYR* 4.2 6.1 - - + -
85F TYR* 3.1 45.4 + - + +
87F GLN* 3.9 0.2 - - - +
95F VAL* 3.9 16.6 - - + -
118F TYR* 3.7 39.0 - - + -
123F TYR* 3.4 43.1 - - + +
9H LEU* 3.8 28.0 - - + -
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Residues in contact with ARG 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F SER* 4.3 21.3 - - - -
14F ARG 5.8 1.4 + - - -
78F LEU* 3.1 26.4 + - - +
79F GLY* 3.5 16.5 - - - +
81F LEU* 1.3 74.1 - - - +
83F GLY* 1.3 52.6 + - - +
85F TYR* 3.3 1.0 + - - -
86F ASN 2.8 29.1 + - - -
87F GLN* 3.0 38.1 + - + +
88F SER 3.8 24.3 + - - +
89F GLU* 3.6 33.0 - - - +
91F GLY 5.4 1.6 - - - -
93F HIS* 4.5 12.1 - - - +
118F TYR* 4.1 2.3 + - - +
----------------------------------------------------------
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Residues in contact with GLY 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F GLY 3.3 5.6 + - - -
80F THR 3.2 8.0 + - - -
82F ARG* 1.3 76.1 - - - +
84F TYR* 1.3 63.9 + - - +
86F ASN* 3.0 26.1 + - - +
----------------------------------------------------------
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Residues in contact with TYR 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F THR* 3.0 39.1 + - + +
81F LEU* 3.8 16.4 - - + +
83F GLY* 1.3 76.3 - - - +
85F TYR* 1.3 61.8 - - + +
86F ASN* 3.8 6.2 + - - +
123F TYR* 3.3 27.1 - - - -
139F ALA* 3.8 30.9 - - + +
142F THR* 3.5 33.6 + - + +
143F THR* 3.8 5.4 - - - -
146F LYS* 4.9 4.2 + - - +
9H LEU* 3.2 20.0 + - + -
----------------------------------------------------------
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Residues in contact with TYR 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F LEU* 3.1 47.3 + - + +
83F GLY 3.2 0.8 - - - -
84F TYR* 1.3 79.0 - - + +
86F ASN* 1.3 70.7 + - - +
87F GLN* 3.3 25.0 + - + +
118F TYR* 3.7 23.5 - + - +
123F TYR* 3.5 16.1 - - - -
137F ASP* 3.1 30.4 + - - -
139F ALA* 3.7 18.6 - - + -
----------------------------------------------------------
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Residues in contact with ASN 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F ARG 2.8 7.8 + - - -
83F GLY* 3.0 18.4 + - - +
84F TYR 4.2 5.7 - - - +
85F TYR* 1.3 81.0 - - - +
87F GLN* 1.3 60.9 + - - +
----------------------------------------------------------
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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