Contacts of the helix formed by residues 50 - 78 (chain F) in PDB entry 6R93
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 50 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E MET* 5.7 7.6 - - + -
122E PRO* 4.0 30.3 - - + +
48F SER* 3.2 5.6 - - - -
49F GLY* 1.3 75.5 - - - +
51F ILE* 1.3 64.6 + - - +
52F TYR 3.3 1.7 + - - -
53F GLU* 3.8 13.6 + - - +
54F GLU* 3.8 7.1 + - - +
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Residues in contact with ILE 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E PHE* 4.3 14.4 - - + -
120E ILE* 3.7 23.3 - - + +
121E MET* 3.5 37.2 - - - +
122E PRO* 3.6 5.2 - - + -
125E ILE* 3.8 21.5 - - + -
35F ILE* 5.2 2.5 - - + -
47F ILE* 3.8 19.7 - - + -
48F SER* 3.5 18.4 - - - +
49F GLY 3.3 0.8 - - - -
50F LEU* 1.3 76.7 - - - +
52F TYR* 1.3 63.1 + - + +
54F GLU* 3.0 6.7 + - - +
55F THR* 2.8 43.0 + - - +
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Residues in contact with TYR 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LYS* 3.5 44.7 - - + +
35F ILE* 4.1 26.9 - - + +
36F ARG* 3.3 32.1 + - + -
47F ILE* 4.5 19.7 + - + +
48F SER 4.2 5.7 + - - -
49F GLY* 3.1 36.7 - - - -
50F LEU 3.3 1.0 - - - -
51F ILE* 1.3 75.0 - - + +
53F GLU* 1.3 71.0 + - - +
55F THR* 3.1 9.4 + - - -
56F ARG* 2.9 46.2 + - - +
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Residues in contact with GLU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F GLN* 5.3 3.3 + - - -
49F GLY 4.1 9.5 - - - +
50F LEU* 3.8 8.7 + - - +
51F ILE 3.4 0.4 - - - -
52F TYR* 1.3 82.3 - - - +
54F GLU* 1.3 64.3 + - - +
56F ARG* 3.1 28.2 + - - +
57F GLY* 3.1 18.5 + - - -
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Residues in contact with GLU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E PRO* 3.2 29.1 - - + +
125E ILE* 3.2 46.6 - - - +
126E GLN* 3.3 27.4 - - - +
129E ARG* 5.1 2.4 + - - -
50F LEU 3.8 8.2 + - - +
51F ILE* 3.0 8.2 + - - +
53F GLU* 1.3 77.2 - - - +
55F THR* 1.3 65.4 + - - +
57F GLY* 3.0 4.6 + - - -
58F VAL* 2.9 27.4 + - + +
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Residues in contact with THR 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E LEU* 4.1 27.1 - - + +
104E LEU* 6.3 1.8 - - + -
105E PHE* 4.1 19.7 - - + -
125E ILE* 4.2 8.1 - - + +
35F ILE* 4.3 19.5 - - + -
51F ILE* 2.8 30.1 + - - +
52F TYR* 3.4 10.1 - - - -
54F GLU* 1.3 76.5 - - - +
56F ARG* 1.3 56.6 + - - +
58F VAL* 3.0 8.2 + - + +
59F LEU* 2.8 30.8 + - + +
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Residues in contact with ARG 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ILE* 4.2 31.9 + - + +
28F GLN* 3.1 36.5 + - - +
30F ILE* 3.7 26.8 + - + +
31F THR* 4.9 0.8 - - - +
32F LYS* 4.2 17.4 - - - +
35F ILE* 4.4 11.0 - - + +
52F TYR* 2.9 34.1 + - - +
53F GLU* 3.1 45.4 + - - +
55F THR* 1.3 75.0 - - - +
57F GLY* 1.3 57.3 + - - +
59F LEU* 3.1 10.7 + - + +
60F LYS* 2.8 30.3 + - - +
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Residues in contact with GLY 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F GLU 3.1 8.7 + - - -
54F GLU 3.0 7.1 + - - -
56F ARG* 1.3 74.7 - - - +
58F VAL* 1.3 63.4 + - - +
60F LYS* 3.0 10.6 + - - +
61F VAL* 2.9 29.2 + - - +
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Residues in contact with VAL 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E TYR* 3.6 33.2 + - + +
101E LEU* 4.8 4.5 - - + -
104E LEU* 3.9 13.9 - - + -
125E ILE* 4.5 10.1 - - + -
129E ARG* 3.6 42.9 + - - +
134E GLU* 5.2 0.3 - - - +
54F GLU* 2.9 24.4 + - + +
55F THR* 3.4 10.8 - - + +
57F GLY* 1.3 73.3 - - - +
59F LEU* 1.3 65.7 + - - +
61F VAL* 3.1 6.1 + - - +
62F PHE* 3.1 20.7 + - - +
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Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ILE* 5.5 3.8 - - + -
68E PHE* 5.5 3.1 - - + -
71E LEU* 4.8 8.7 - - + -
97E CYS* 3.6 40.2 - - + -
100E TYR* 5.3 2.2 - - + -
101E LEU* 4.6 25.4 - - + -
27F ILE* 5.8 2.7 - - + -
30F ILE* 4.2 36.3 - - + -
55F THR* 2.8 14.4 + - + +
56F ARG* 3.5 11.9 - - + +
58F VAL* 1.3 77.6 - - - +
60F LYS* 1.3 64.5 + - - +
62F PHE* 3.1 10.5 + - + +
63F LEU* 2.8 30.7 + - + +
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Residues in contact with LYS 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E LEU* 3.7 13.5 - - - +
74E GLU* 5.6 3.6 + - - +
75E ILE* 3.3 36.8 - - + +
27F ILE* 3.8 25.9 - - + +
56F ARG 2.8 13.1 + - - +
57F GLY* 3.0 11.9 + - - +
59F LEU* 1.3 76.6 - - - +
61F VAL* 1.3 53.5 + - + +
63F LEU* 3.1 7.9 + - - +
64F GLU* 2.7 46.8 + - - +
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Residues in contact with VAL 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E ARG* 4.6 3.8 - - - +
134E GLU* 4.0 16.8 - - - +
136E ALA* 4.3 23.8 - - + -
57F GLY 2.9 19.2 + - - +
58F VAL* 3.1 8.0 + - - +
60F LYS* 1.3 75.5 - - + +
62F PHE* 1.3 67.8 + - - +
64F GLU* 3.1 9.1 + - - +
65F ASN* 3.0 36.0 + - - +
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Residues in contact with PHE 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E LEU* 6.1 1.6 - - + -
96E ALA* 4.4 19.5 - - + -
97E CYS* 4.2 24.9 - - - -
100E TYR* 4.1 50.9 - + + +
134E GLU* 5.0 7.4 + - - +
58F VAL 3.1 11.3 + - - +
59F LEU* 3.1 9.7 + - + +
61F VAL* 1.3 79.2 - - - +
63F LEU* 1.3 66.9 + - + +
65F ASN* 3.1 14.0 + - + +
66F VAL* 3.1 39.5 + - + +
91F LEU* 4.2 14.1 - - + -
94F GLN* 5.6 9.2 - - + -
96F ARG* 4.6 16.8 - - + -
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Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E PHE* 4.3 16.2 - - + -
71E LEU* 3.7 34.8 - - + -
72E VAL* 4.4 11.9 - - + -
75E ILE* 4.3 12.1 - - + -
93E LEU* 4.2 19.7 - - + -
97E CYS* 4.0 25.8 - - - -
59F LEU* 2.8 20.2 + - + +
60F LYS* 3.6 4.0 - - - +
62F PHE* 1.3 78.7 - - + +
64F GLU* 1.3 64.2 + - - +
66F VAL* 3.0 4.3 + - + +
67F ILE* 2.9 46.9 + - + +
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Residues in contact with GLU 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E ILE* 4.2 21.6 - - + +
79E PHE* 3.8 24.6 - - + -
60F LYS* 2.7 32.6 + - + +
61F VAL* 3.5 9.1 - - - +
63F LEU* 1.3 72.2 - - - +
65F ASN* 1.3 66.5 + - - +
68F ARG* 3.0 34.9 + - - +
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Residues in contact with ASN 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E GLU* 5.6 4.0 + - - -
61F VAL* 3.0 33.2 + - - +
62F PHE* 3.6 8.1 - - + +
64F GLU* 1.3 76.5 - - - +
66F VAL* 1.3 66.7 + - + +
68F ARG* 3.1 30.2 + - - +
69F ASP* 3.1 28.9 + - - +
94F GLN* 4.9 24.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E LEU* 3.7 28.3 - - + -
62F PHE* 3.4 44.4 - - + +
63F LEU* 3.0 6.4 + - - +
65F ASN* 1.3 76.2 - - + +
67F ILE* 1.3 59.4 + - - +
69F ASP* 3.0 7.0 + - - +
70F ALA* 2.8 26.1 + - + +
87F VAL* 4.6 5.2 - - + -
90F ALA* 3.7 18.4 - - + +
91F LEU* 4.1 21.5 - - + -
94F GLN* 5.2 10.5 - - + -
----------------------------------------------------------
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Residues in contact with ILE 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E VAL* 4.0 35.0 - - + +
75E ILE* 4.2 15.5 - - + -
76E ALA* 4.1 23.1 - - + +
79E PHE* 4.6 5.8 - - + -
85E PHE* 4.6 7.4 - - + -
93E LEU* 4.6 13.5 - - + -
63F LEU* 2.9 41.0 + - + +
64F GLU 4.3 1.3 - - - +
66F VAL* 1.3 74.0 - - - +
68F ARG* 1.3 54.2 + - - +
70F ALA* 3.0 8.5 + - + +
71F VAL* 2.7 49.5 + - + +
----------------------------------------------------------
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Residues in contact with ARG 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E PHE* 3.7 37.9 - - + -
64F GLU* 3.0 34.9 + - - +
65F ASN* 3.1 40.9 + - - +
67F ILE* 1.3 74.9 - - - +
69F ASP* 1.3 74.0 + - - +
71F VAL* 3.1 3.3 + - - +
72F THR* 2.9 30.0 + - - +
93F ARG* 5.9 1.2 - - - +
100H ARG 5.8 3.4 - - - -
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Residues in contact with ASP 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F ASN* 3.1 14.0 + - - +
66F VAL* 3.0 4.9 + - - +
68F ARG* 1.3 88.2 + - - +
70F ALA* 1.3 64.0 + - - +
72F THR* 3.0 4.4 + - - -
73F TYR* 3.0 29.9 + - + -
90F ALA* 3.5 27.3 - - + +
93F ARG* 2.6 44.9 + - - +
94F GLN* 5.2 3.7 + - - +
101H LEU* 3.6 20.8 - - + +
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Residues in contact with ALA 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E PHE* 5.9 1.6 - - + -
93E LEU* 6.5 0.2 - - + -
66F VAL* 2.8 13.8 + - + +
67F ILE* 3.4 14.1 - - + +
69F ASP* 1.3 75.0 - - - +
71F VAL* 1.3 63.1 + - + +
73F TYR* 3.0 7.6 + - - +
74F THR* 2.9 25.2 + - - -
82F VAL* 4.6 8.7 - - + -
86F ASP* 3.6 21.4 - - + +
87F VAL* 4.3 26.0 - - + +
90F ALA* 3.8 1.4 - - + +
----------------------------------------------------------
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Residues in contact with VAL 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E ALA* 4.8 1.3 - - + -
79E PHE* 4.8 12.6 - - + -
80E LYS* 4.2 30.3 - - + -
83E LEU* 3.7 24.7 - - + -
85E PHE* 5.3 1.1 - - + -
67F ILE* 2.7 37.9 + - + +
68F ARG* 3.7 5.2 - - - +
70F ALA* 1.3 72.4 - - + +
72F THR* 1.3 57.0 + - - +
74F THR* 3.0 11.6 + - - +
75F GLU* 2.8 33.1 + - - +
82F VAL* 4.9 7.6 - - + -
----------------------------------------------------------
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Residues in contact with THR 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F ARG* 2.9 20.9 + - - +
69F ASP* 3.0 9.6 + - - -
71F VAL* 1.3 76.4 - - - +
73F TYR* 1.3 63.0 + - - +
75F GLU* 3.1 7.8 + - - +
76F HIS* 3.0 22.0 + - - +
97H THR* 3.5 29.6 - - + +
100H ARG* 4.7 22.2 - - + +
101H LEU* 3.8 22.6 - - + +
----------------------------------------------------------
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Residues in contact with TYR 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F ASP* 3.0 26.5 + - - -
70F ALA 3.0 3.6 + - - +
72F THR* 1.3 76.0 - - - +
74F THR* 1.3 64.1 + - - +
76F HIS* 3.5 6.1 + - + +
77F ALA* 3.3 19.9 + - - +
79F ARG* 4.8 0.5 + - - -
86F ASP* 3.3 38.0 - - + +
89F TYR* 3.9 32.2 + + + +
90F ALA* 4.0 12.8 - - - -
93F ARG* 4.8 6.9 - - - +
77H GLU* 2.7 22.6 + - - -
81H LEU* 3.7 34.3 - - + -
84H TYR* 4.9 9.3 - + - -
85H ASN* 5.3 5.6 + - - +
97H THR* 5.4 0.2 - - - -
101H LEU* 3.5 22.8 - - + +
----------------------------------------------------------
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Residues in contact with THR 74 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E LYS* 6.0 2.2 - - + -
83E LEU* 4.5 19.1 - - + -
70F ALA 2.9 16.6 + - - -
71F VAL* 3.0 16.1 + - - -
73F TYR* 1.3 76.6 - - - +
75F GLU* 1.3 63.3 + - - +
77F ALA* 3.2 11.6 + - - +
78F LYS 3.3 8.1 + - - -
79F ARG* 3.1 42.4 + - + +
81F THR 4.3 17.0 - - - +
82F VAL* 3.8 14.8 - - + +
86F ASP* 3.0 11.7 + - - -
----------------------------------------------------------
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Residues in contact with GLU 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E LYS* 3.8 33.6 + - + +
71F VAL* 2.8 23.0 + - + +
72F THR* 3.1 7.2 + - + +
74F THR* 1.3 74.4 - - - +
76F HIS* 1.3 63.1 + - - +
78F LYS* 3.1 17.5 + - - +
79F ARG 5.1 2.0 - - - -
93H ARG* 4.6 3.3 + - - -
100H ARG* 4.0 22.4 + - - +
----------------------------------------------------------
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Residues in contact with HIS 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F THR 3.0 15.2 + - - +
73F TYR* 3.8 5.8 - - + +
74F THR 3.3 0.2 - - - -
75F GLU* 1.3 77.6 - - - +
77F ALA* 1.3 61.9 + - - +
78F LYS* 3.4 3.8 + - - +
81H LEU* 4.1 17.6 - - + +
82H ALA* 5.7 0.2 - - - -
85H ASN* 3.8 22.8 + - - -
87H ARG* 3.3 30.6 + - - -
93H ARG* 3.9 33.1 + - + +
94H GLU* 3.1 33.2 + - + +
97H THR* 3.3 35.7 - - + +
----------------------------------------------------------
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Residues in contact with ALA 77 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F TYR 3.3 8.8 + - - +
74F THR 3.2 6.5 + - - +
76F HIS* 1.3 77.8 + - - +
78F LYS* 1.3 74.7 + - - +
79F ARG* 3.7 35.3 - - + +
85H ASN* 3.2 28.5 - - - +
----------------------------------------------------------
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Residues in contact with LYS 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F THR 3.3 0.4 + - - -
75F GLU* 3.1 13.8 + - - +
76F HIS 4.3 4.9 + - - -
77F ALA* 1.3 83.1 + - - +
79F ARG* 1.3 59.9 + - - +
80F LYS* 5.4 2.2 - - - +
87H ARG* 4.6 7.1 - - - +
93H ARG* 3.7 40.0 - - - +
101I A 4.2 6.1 + - - -
40J G 3.9 19.8 + - - +
----------------------------------------------------------
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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