Contacts of the helix formed by residues 59 - 86 (chain F) in PDB entry 1DPS
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 PHE 59 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F HIS 4.3 1.1 - - - -
54F MET* 3.2 43.2 - - + +
56F GLY 3.1 19.9 + - - +
58F ASN* 1.3 77.1 - - - +
60F ILE* 1.3 77.0 + - - +
62F VAL* 3.8 0.9 - - - +
63F HIS* 2.8 68.1 + + + +
114F VAL* 4.0 8.1 - - + -
160J TRP* 4.3 9.4 - + - -
161J PHE* 3.6 32.8 - + - -
164J CYS* 3.3 32.8 - - + +
165J ASN* 3.6 16.9 + - - +
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Residues in contact with ILE 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F PHE* 1.3 85.3 - - + +
61F ALA* 1.3 60.7 + - - +
63F HIS* 3.5 3.4 - - + +
64F GLU* 2.9 64.9 + - + +
58J ASN* 4.8 3.1 - - - +
61J ALA* 3.7 33.4 - - + +
62J VAL* 4.6 1.8 - - + +
65J MET* 4.1 16.8 - - + -
161J PHE* 3.7 41.3 - - + -
165J ASN* 3.3 24.9 + - - +
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Residues in contact with ALA 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 3.7 19.6 - - + +
61B ALA* 4.1 18.6 - - + -
58F ASN* 3.7 19.3 + - - +
59F PHE 3.4 0.4 - - - -
60F ILE* 1.3 80.8 - - - +
62F VAL* 1.3 58.2 + - - +
64F GLU* 3.5 7.3 + - - +
65F MET* 2.9 30.1 + - - +
61J ALA* 4.1 10.5 - - + -
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Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 4.7 1.3 - - + -
54F MET* 3.8 22.4 - - + -
58F ASN* 3.3 39.8 + - + +
59F PHE 3.3 2.8 + - - +
60F ILE 3.3 0.2 - - - -
61F ALA* 1.3 74.3 - - - +
63F HIS* 1.3 65.1 + - - +
65F MET* 3.3 10.6 + - + +
66F LEU* 3.0 30.4 + - + +
114F VAL* 4.5 10.8 - - + -
118F LEU* 3.9 22.0 - - + -
165F ASN* 4.1 22.2 - - + +
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Residues in contact with HIS 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F HIS* 2.6 83.7 + + - -
52F TRP* 4.6 1.8 - + - -
54F MET* 4.1 8.0 - - - -
59F PHE* 2.8 44.8 + + + +
60F ILE* 3.5 5.6 - - + +
62F VAL* 1.3 75.1 - - - +
64F GLU* 1.3 72.3 + - + +
66F LEU* 3.6 0.5 + - - +
67F ASP 3.4 5.4 + - - -
82H GLU* 4.7 6.7 + - - -
160J TRP* 3.9 22.6 - + - -
161J PHE* 4.0 24.7 - + - -
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Residues in contact with GLU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F ILE* 2.9 46.4 + - + +
61F ALA* 4.0 5.2 - - - +
63F HIS* 1.3 81.8 - - + +
65F MET* 1.3 64.4 + - - +
67F ASP* 3.2 17.0 + - - +
68F GLY* 3.3 9.2 + - - -
161J PHE* 5.1 3.5 - - + -
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Residues in contact with MET 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 3.9 25.6 - - + -
61F ALA 2.9 19.5 + - - +
62F VAL* 3.6 18.8 - - + +
64F GLU* 1.3 76.3 - - - +
66F LEU* 1.3 75.7 + - + +
68F GLY* 3.1 12.5 + - - -
69F PHE* 3.2 49.3 + - + -
118F LEU* 4.8 2.7 - - + -
161F PHE* 3.9 13.5 - - + +
162F ILE* 4.4 11.9 - - + -
165F ASN* 3.7 28.7 - - - +
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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
----------------------------------------------------------
47F THR* 3.2 27.5 - - + +
51F HIS* 3.9 23.8 - - + +
54F MET* 3.6 31.2 - - + -
62F VAL* 3.0 19.8 + - + +
63F HIS 4.0 0.4 - - - +
65F MET* 1.3 80.9 - - + +
67F ASP* 1.3 65.8 + - - +
69F PHE* 3.2 29.0 + - + +
70F ARG* 3.1 18.0 + - - +
118F LEU* 5.7 0.4 - - + -
121F LEU* 3.6 29.2 - - + -
125F TYR* 4.8 1.1 - - - +
162F ILE* 4.5 7.0 - - + -
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Residues in contact with ASP 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LYS* 3.0 30.7 + - - +
51F HIS* 3.8 22.3 + - + -
63F HIS 3.4 3.6 + - - +
64F GLU* 3.2 13.4 + - - +
66F LEU* 1.3 78.0 - - - +
68F GLY* 1.3 64.9 + - - +
70F ARG* 3.2 18.5 + - - +
71F THR* 3.3 17.5 + - - -
78H ASP* 4.6 0.3 - - - +
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Residues in contact with GLY 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F GLU 3.3 5.5 + - - -
65F MET 3.1 8.4 + - - -
67F ASP* 1.3 80.4 + - - +
69F PHE* 1.3 64.3 + - - +
71F THR* 3.3 10.1 + - - -
72F ALA* 3.2 19.8 + - - +
158F PHE* 5.2 0.8 - - - -
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Residues in contact with PHE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F MET* 3.5 33.4 - - + -
66F LEU* 3.2 27.0 + - + +
68F GLY* 1.3 77.9 - - - +
70F ARG* 1.3 62.9 + - - +
72F ALA* 3.1 3.5 + - - +
73F LEU* 2.9 27.4 + - - +
125F TYR* 3.5 30.1 - + - +
158F PHE* 3.3 58.2 - + + -
161F PHE* 3.9 20.2 - + + -
162F ILE* 3.8 24.9 - - + -
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Residues in contact with ARG 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F SER* 3.8 26.9 - - - +
47F THR* 4.3 7.5 - - + +
48F LYS* 3.5 41.2 - - + +
66F LEU 3.1 11.9 + - - +
67F ASP* 3.2 15.1 + - - +
69F PHE* 1.3 76.1 - - - +
71F THR* 1.3 65.5 + - - +
73F LEU* 3.3 9.2 + - - +
74F ILE* 3.0 46.0 + - - +
74H ILE* 4.0 33.8 - - - +
75H ASP* 5.2 2.4 + - - -
77H LEU* 5.7 2.8 - - - +
78H ASP* 2.9 29.7 + - - -
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Residues in contact with THR 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ASP* 3.3 14.7 + - - -
68F GLY* 3.5 12.0 - - - -
69F PHE 3.2 0.4 - - - -
70F ARG* 1.3 83.6 + - - +
72F ALA* 1.3 62.5 + - - +
74F ILE* 3.4 14.3 + - + +
75F ASP* 3.2 35.3 + - - +
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Residues in contact with ALA 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F GLY 3.2 6.8 + - - +
69F PHE 3.1 4.8 + - - +
71F THR* 1.3 79.9 - - - +
73F LEU* 1.3 63.6 + - - +
75F ASP* 3.2 7.6 + - - +
76F HIS* 3.0 30.9 + - + -
154F ASP* 4.2 11.9 - - - +
158F PHE* 3.6 32.3 - - + -
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F PHE* 3.9 19.1 - - + +
43F LEU* 4.0 20.4 - - + -
44F SER* 3.8 35.9 - - - +
47F THR* 4.0 2.5 - - - +
69F PHE 2.9 21.0 + - - +
70F ARG* 3.6 4.7 - - - +
72F ALA* 1.3 77.2 - - - +
74F ILE* 1.3 56.7 + - - +
76F HIS* 3.3 4.4 + - + +
77F LEU* 3.0 33.3 + - - +
125F TYR* 3.7 21.3 - - - +
155F LEU* 3.8 30.3 - - + -
158F PHE* 4.7 10.3 - - + -
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Residues in contact with ILE 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F SER* 4.0 21.3 - - - +
70F ARG* 3.0 31.3 + - - +
71F THR* 3.5 18.2 - - + +
73F LEU* 1.3 74.7 - - - +
75F ASP* 1.3 66.5 + - - +
77F LEU* 3.7 12.9 - - + +
78F ASP* 3.1 30.4 + - - +
70H ARG* 4.0 30.7 - - - +
74H ILE* 3.8 28.9 - - + -
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Residues in contact with ASP 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F THR* 3.2 27.3 + - - +
72F ALA* 3.2 9.6 + - - +
74F ILE* 1.3 81.5 - - - +
76F HIS* 1.3 67.3 + - + +
78F ASP* 3.5 9.8 + - - +
79F THR* 3.1 26.5 + - - -
70H ARG* 5.1 2.3 + - - -
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Residues in contact with HIS 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F PHE* 3.9 18.4 - + + -
72F ALA* 3.0 30.1 + - + +
73F LEU* 3.3 6.5 + - + +
75F ASP* 1.3 77.9 - - + +
77F LEU* 1.3 62.6 + - - +
79F THR* 3.2 10.4 + - - -
80F MET* 3.0 27.1 + - + +
147F ILE* 4.9 4.1 + - - +
150F ALA* 3.5 31.8 + - + +
151F ALA* 3.6 22.3 + - + +
154F ASP* 2.7 36.3 + - + +
155F LEU* 5.3 1.8 - - + -
158F PHE* 5.7 0.2 - + - -
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Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F VAL* 4.1 13.0 - - + +
40F PHE* 3.7 23.7 - - + +
41F ILE* 3.6 48.9 - - + +
44F SER* 4.6 0.2 - - - +
73F LEU 3.0 19.7 + - - +
74F ILE* 3.7 23.8 - - + +
76F HIS* 1.3 75.9 - - - +
78F ASP* 1.3 63.4 + - - +
80F MET* 3.3 11.2 + - - +
81F ALA* 2.9 29.6 + - - +
52H TRP* 3.8 24.0 - - + -
70H ARG* 5.9 2.2 - - - +
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Residues in contact with ASP 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ILE 3.1 20.7 + - - +
75F ASP* 3.7 9.0 - - - +
77F LEU* 1.3 80.9 - - - +
79F THR* 1.3 57.1 + - - +
81F ALA* 3.3 1.2 + - - +
82F GLU* 2.9 45.1 + - - +
48H LYS* 2.7 34.3 + - - +
52H TRP* 3.3 29.9 + - - +
67H ASP* 4.4 0.7 - - - +
70H ARG* 3.0 16.7 + - - -
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Residues in contact with THR 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F ASP 3.1 12.7 + - - -
76F HIS* 3.2 12.4 + - - -
78F ASP* 1.3 78.1 - - - +
80F MET* 1.3 62.0 + - - +
82F GLU* 3.5 10.3 + - - +
83F ARG* 3.1 22.0 + - - +
147F ILE* 3.7 22.9 - - + -
153K ARG* 3.5 27.8 - - - +
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Residues in contact with MET 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LEU* 3.8 24.2 - - + +
36F GLN* 3.6 32.1 - - + -
37F VAL* 4.1 10.5 - - + -
40F PHE* 3.7 25.4 - - + -
76F HIS 3.0 18.5 + - - +
77F LEU* 3.5 12.6 - - - +
78F ASP 3.2 0.2 - - - -
79F THR* 1.3 74.4 - - - +
81F ALA* 1.3 63.9 + - - +
83F ARG* 3.3 4.5 + - - +
84F ALA* 3.1 22.2 + - - +
132F VAL* 4.8 0.4 - - + -
147F ILE* 3.8 19.3 - - + -
148F LEU* 4.3 13.9 - - + -
151F ALA* 3.5 31.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F VAL* 4.0 10.7 - - + +
77F LEU 2.9 14.9 + - - +
78F ASP 3.3 0.6 + - - +
80F MET* 1.3 75.8 - - - +
82F GLU* 1.3 61.8 + - - +
84F ALA* 3.2 7.8 + - - +
85F VAL* 3.1 26.3 + - - +
91F ALA* 3.8 14.5 - - + +
52H TRP* 3.3 45.8 - - + +
----------------------------------------------------------
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Residues in contact with GLU 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ASP* 2.9 30.2 + - - +
79F THR* 3.8 9.1 - - - +
81F ALA* 1.3 75.7 - - - +
83F ARG* 1.3 60.8 + - - +
85F VAL* 3.2 10.2 - - - +
86F GLN* 3.0 41.1 + - - +
48H LYS* 5.6 0.5 + - - -
51H HIS* 4.6 12.8 + - - -
52H TRP* 4.4 12.3 - - + -
63H HIS* 4.6 6.3 + - - +
157K LYS* 4.2 22.2 + - - +
160K TRP* 3.8 22.5 - - + -
161K PHE* 6.0 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ARG 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ASN* 4.7 1.6 - - - +
33F LEU* 3.7 10.5 - - + -
79F THR 3.1 7.9 + - - +
80F MET* 3.6 8.5 - - - +
81F ALA 3.3 0.4 - - - -
82F GLU* 1.3 74.9 - - - +
84F ALA* 1.3 63.6 + - - +
86F GLN* 3.2 20.7 + - - +
87F LEU* 3.1 44.3 + - + +
141F ASP* 3.0 36.9 + - - -
143F ASP* 3.4 22.5 + - - +
144F THR* 3.5 16.7 + - - +
147F ILE* 3.7 30.3 - - + -
133K ARG* 4.1 5.1 - - - +
153K ARG* 5.0 4.1 - - - +
156K ASP* 2.7 45.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F VAL* 3.4 27.4 - - + +
33F LEU* 3.7 23.0 - - + +
34F ASN* 4.7 10.5 - - - +
80F MET 3.1 13.3 + - - +
81F ALA* 3.2 12.5 + - - +
83F ARG* 1.3 76.1 - - - +
85F VAL* 1.3 59.5 + - + +
87F LEU* 3.4 6.5 + - - -
89F GLY* 3.0 22.2 + - - -
91F ALA* 4.8 6.5 - - + +
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Residues in contact with VAL 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F LEU* 6.4 0.2 - - + -
81F ALA 3.1 13.2 + - - +
82F GLU* 3.2 17.3 - - - +
84F ALA* 1.3 71.8 - - - +
86F GLN* 1.3 64.8 + - - +
87F LEU 3.2 0.7 - - - -
88F GLY* 3.0 14.0 + - - -
89F GLY 3.6 14.5 - - - +
91F ALA* 3.8 14.6 - - + +
52H TRP* 3.7 15.5 - - + +
53H ASN* 3.4 26.2 - - - +
55H ARG* 4.1 16.3 + - - +
160K TRP* 3.4 36.6 - - + +
----------------------------------------------------------
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Residues in contact with GLN 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F THR* 4.0 18.7 + - - +
19F ASN* 4.2 10.9 + - - +
82F GLU* 3.0 36.8 + - - +
83F ARG* 3.5 39.6 + - - +
85F VAL* 1.3 75.7 - - - +
87F LEU* 1.3 59.2 + - - +
88F GLY 3.2 3.0 + - - -
153K ARG 4.7 2.6 + - - +
156K ASP* 3.9 10.6 - - + +
157K LYS* 3.7 23.8 + - - +
160K TRP* 3.6 51.2 - - + +
----------------------------------------------------------
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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