Contacts of the helix formed by residues 67 - 89 (chain F) in PDB entry 4HRE
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 67 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F PHE* 4.0 3.1 - - - -
24F TYR* 6.0 0.2 - - - -
65F LYS* 3.4 11.7 + - - +
66F VAL* 1.3 76.3 - - - +
68F PHE* 1.3 56.8 + - - -
69F GLN* 3.0 5.4 - - - -
70F SER* 2.9 15.7 + - - -
71F PHE* 2.7 32.6 + - - +
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Residues in contact with PHE 68 (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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79E THR* 4.3 24.2 - - + -
80E ILE* 4.5 15.0 - - + -
83E ASN* 3.8 39.3 - - + +
11F MET* 4.0 1.6 - - + -
12F MET* 3.7 39.5 - - + -
15F PHE* 3.3 53.2 - + + -
67F GLY* 1.3 70.8 - - - -
69F GLN* 1.3 57.8 + - - +
71F PHE* 4.0 15.5 - + - -
72F PHE* 2.9 44.6 + + - +
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Residues in contact with GLN 69 (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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80E ILE* 4.0 24.1 - - + +
59F ASP* 2.9 39.9 + - + +
67F GLY* 4.6 2.7 - - - -
68F PHE* 1.3 79.1 - - - +
70F SER* 1.3 58.0 + - - +
72F PHE* 3.6 2.4 + - - +
73F SER* 2.9 21.5 + - - -
1G PHE* 3.5 25.0 - - - -
-2H PRO 4.1 5.2 - - - +
-1H THR* 3.2 27.7 + - - +
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Residues in contact with SER 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F LEU* 4.0 10.5 - - - +
59F ASP* 3.3 34.9 + - - +
60F GLN* 3.3 15.8 + - - +
66F VAL* 3.5 14.1 - - - +
67F GLY* 2.9 24.4 + - - -
69F GLN* 1.3 76.5 - - - +
71F PHE* 1.3 61.0 + - - +
73F SER* 3.1 3.1 - - - -
74F LEU* 2.9 26.5 + - - +
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Residues in contact with PHE 71 (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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4E MET* 4.3 21.3 - - + -
11F MET* 3.8 31.4 - - + -
14F THR* 4.3 3.8 - - - -
15F PHE* 3.6 45.1 - + + -
25F LEU* 4.7 3.1 - - + -
30F LEU* 6.4 0.2 - - + -
33F LEU* 4.0 28.7 - - + -
66F VAL* 3.6 9.8 - - + +
67F GLY 2.7 19.9 + - - +
68F PHE* 3.9 21.3 - + - +
70F SER* 1.3 69.3 - - - +
72F PHE* 1.3 68.4 - - - +
74F LEU* 3.4 14.1 + - + +
75F ILE* 3.2 34.0 + - + +
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Residues in contact with PHE 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E PHE* 3.4 31.0 - + - -
75E ILE* 3.7 27.6 - - + -
76E ALA* 3.5 28.0 - - + -
79E THR* 3.9 20.2 - - + -
80E ILE* 4.7 11.0 - - + -
11F MET* 3.4 31.4 - - + -
68F PHE* 2.9 33.7 + + + +
69F GLN* 3.7 5.6 - - - +
71F PHE* 1.3 76.8 - - - +
73F SER* 1.3 61.0 + - - +
75F ILE* 3.4 6.0 + - + +
76F ALA* 2.9 32.7 + - + +
-1H THR* 5.1 5.4 - - - +
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Residues in contact with SER 73 (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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58F LEU* 4.3 1.2 - - - -
59F ASP* 3.7 9.0 + - - -
69F GLN 2.9 17.0 + - - -
70F SER* 3.1 18.4 + - - -
72F PHE* 1.3 77.7 - - - +
74F LEU* 1.3 61.3 + - - +
76F ALA* 3.3 10.2 - - - +
77F GLY 3.8 1.4 + - - -
-1H THR* 3.4 18.6 - - - -
0H PHE 2.9 21.5 + - - -
1H PHE* 3.1 29.0 - - - +
2H PRO* 4.3 4.0 - - - +
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Residues in contact with LEU 74 (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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30F LEU* 4.6 13.7 - - + -
33F LEU* 6.0 2.2 - - + -
34F MET* 3.6 33.7 - - + -
38F PHE* 5.6 0.7 - - + -
54F ILE* 4.7 19.7 - - + -
58F LEU* 4.0 24.0 - - + +
70F SER 2.9 13.2 + - - +
71F PHE* 3.4 18.8 - - + +
72F PHE 3.2 0.2 - - - -
73F SER* 1.3 72.3 - - - +
75F ILE* 1.3 88.5 + - + +
76F ALA 2.9 2.5 + - - -
77F GLY* 3.0 13.3 + - - -
78F LEU* 3.6 18.4 + - + +
2H PRO* 4.8 5.8 - - + +
4H PHE* 4.7 9.6 - - + -
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Residues in contact with ILE 75 (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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4E MET* 4.2 23.3 - - + -
8E MET* 3.9 21.8 - - + -
11E MET* 5.6 0.9 - - - -
72E PHE* 4.5 8.1 - - + -
11F MET* 4.5 17.7 - - + -
38F PHE* 4.4 18.4 - - + -
71F PHE* 3.2 25.6 + - + +
72F PHE 3.9 6.3 - - - +
74F LEU* 1.3 95.8 - - + +
76F ALA* 1.3 60.6 + - - +
78F LEU* 3.0 9.3 + - + -
79F THR* 2.5 47.1 + - + +
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Residues in contact with ALA 76 (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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72E PHE* 3.9 25.5 - - + -
72F PHE* 2.9 15.9 + - + +
73F SER* 3.3 16.2 - - - +
74F LEU 2.9 0.2 + - - -
75F ILE* 1.3 76.0 - - - +
77F GLY* 1.3 58.3 + - - +
79F THR* 3.4 0.9 + - - -
80F ILE* 2.9 41.0 + - + +
-1H THR* 5.7 5.6 - - + +
1H PHE* 3.9 14.1 - - + -
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Residues in contact with GLY 77 (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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74F LEU 3.0 8.4 + - - -
76F ALA* 1.3 79.0 - - - +
78F LEU* 1.3 55.3 + - - +
80F ILE* 3.8 3.4 - - - +
81F ALA* 2.9 31.5 + - - +
1H PHE* 3.8 5.5 - - - -
2H PRO 3.2 25.9 + - - -
3H ARG* 4.0 8.1 - - - +
4H PHE* 4.1 11.3 + - - -
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Residues in contact with LEU 78 (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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8C LEU* 3.5 29.2 - - + -
11C LEU* 5.4 2.9 - - + -
8E MET* 3.8 12.1 - - + -
34F MET* 5.0 4.9 - - + -
38F PHE* 4.5 24.5 - - + -
41F PHE* 4.7 14.8 - - + -
74F LEU* 3.7 33.4 - - + +
75F ILE* 3.0 11.0 + - + +
77F GLY* 1.3 73.9 - - - +
79F THR* 1.3 59.2 + - - +
81F ALA* 3.1 4.4 + - - +
82F CYS* 2.9 38.3 + - - -
4H PHE* 3.4 34.7 - - + -
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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
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8E MET* 3.3 47.6 - - + +
11E MET* 4.1 4.9 - - + -
12E MET* 3.5 28.6 - - + +
68E PHE* 4.1 3.7 - - + -
72E PHE* 3.5 28.3 - - + -
75F ILE* 2.5 44.0 + - - +
76F ALA 4.0 0.2 - - - -
78F LEU* 1.3 72.1 - - - +
80F ILE* 1.3 62.6 + - - +
82F CYS* 4.7 1.8 - - - -
83F ASN* 3.5 5.9 + - - +
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Residues in contact with ILE 80 (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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77C ARG* 5.9 2.7 - - - -
68E PHE* 4.5 24.4 - - + -
69E GLN* 4.4 28.3 - - + +
72E PHE* 5.1 7.2 - - + -
76F ALA* 2.9 33.5 + - + +
77F GLY* 3.8 3.4 - - - +
79F THR* 1.3 76.5 - - - +
81F ALA* 1.3 61.1 + - - +
83F ASN* 3.1 6.4 + - - +
84F ASP* 2.7 44.9 + - - +
-1G THR* 5.8 0.2 - - + -
1H PHE* 3.4 35.0 - - + -
3H ARG* 5.2 8.3 - - + -
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Residues in contact with ALA 81 (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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11C LEU* 3.9 20.6 - - + -
73C PHE* 5.6 1.9 - - - -
77F GLY 2.9 20.8 + - - +
78F LEU 3.5 3.4 - - - +
80F ILE* 1.3 76.8 - - - +
82F CYS* 1.3 63.3 + - - +
84F ASP* 3.2 13.6 - - - +
85F TYR* 2.9 23.4 + - - +
3H ARG* 5.7 1.1 - - + -
4H PHE* 3.5 29.2 - - + +
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Residues in contact with CYS 82 (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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4C VAL* 4.7 7.0 - - + -
7C ILE* 3.6 27.4 - - + +
8C LEU* 4.3 30.1 - - - -
11C LEU* 4.6 9.4 - - - +
8E MET* 4.5 9.2 - - - -
12E MET* 3.4 22.2 - - + -
78F LEU 2.9 31.4 + - - +
81F ALA* 1.3 71.5 - - - +
83F ASN* 1.3 58.3 + - - +
85F TYR* 3.1 3.9 + - - +
86F PHE* 2.9 28.9 + - - +
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Residues in contact with ASN 83 (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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12E MET* 3.4 33.1 - - + +
15E PHE* 5.1 0.2 - - - -
16E HIS* 3.0 38.1 + - - -
68E PHE* 3.1 33.8 - - + +
79F THR 3.5 10.9 + - - +
80F ILE* 3.1 11.3 + - - +
82F CYS* 1.3 77.0 - - - +
84F ASP* 1.3 67.9 + - - +
86F PHE* 3.6 5.9 - - - -
87F VAL* 3.0 31.1 + - - +
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Residues in contact with ASP 84 (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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73C PHE* 4.5 20.0 - - + -
77C ARG* 3.6 30.4 - - + +
68E PHE* 6.1 0.5 - - - +
80F ILE* 2.7 37.8 + - - +
81F ALA* 3.2 14.1 - - - +
83F ASN* 1.3 73.3 - - - +
85F TYR* 1.3 58.9 + - - +
87F VAL* 3.8 3.7 - - - +
88F VAL* 2.9 40.4 + - + +
4H PHE 5.3 0.9 - - - +
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Residues in contact with TYR 85 (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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7C ILE* 3.5 29.4 - - + -
10C LYS* 3.8 29.5 + - + +
11C LEU* 6.4 0.7 - - + -
73C PHE* 5.4 9.4 - + + -
81F ALA 2.9 10.3 + - - +
82F CYS 3.1 8.3 + - - +
84F ASP* 1.3 80.6 - - - +
86F PHE* 1.3 59.5 + - - +
88F VAL* 3.0 7.2 + - + +
89F HIS* 2.4 68.9 + - + +
90F MET* 3.8 14.0 - - + +
6H PHE* 3.0 40.7 - + - +
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Residues in contact with PHE 86 (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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3C THR* 5.5 4.7 - - - -
7C ILE* 3.9 13.7 - - + -
9E GLU* 5.4 2.9 - - - -
12E MET* 3.5 32.1 - - + -
13E PHE* 5.2 12.6 - - + -
16E HIS* 4.8 11.2 - + + -
82F CYS 2.9 10.9 + - - +
83F ASN* 3.6 15.0 - - - -
85F TYR* 1.3 77.1 - - - +
87F VAL* 1.3 72.9 + - + +
89F HIS 3.5 2.5 - - - -
90F MET* 2.3 71.1 + - + +
91F LYS* 5.1 17.5 - - + -
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Residues in contact with VAL 87 (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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16E HIS* 3.4 36.3 - - + +
83F ASN* 3.0 22.3 + - - +
84F ASP* 3.8 5.4 - - - +
86F PHE* 1.3 84.8 - - + +
88F VAL* 1.3 73.9 + - + +
90F MET 4.6 4.9 - - - +
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Residues in contact with VAL 88 (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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73C PHE* 5.8 9.9 - - + -
76C GLN* 4.0 29.6 - - - +
82C GLU* 6.1 0.9 - - - +
84F ASP* 2.9 30.2 + - + +
85F TYR* 3.4 3.8 - - + +
87F VAL* 1.3 84.6 - - + +
89F HIS* 1.3 69.2 + - + +
90F MET 3.9 2.1 + - - +
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Residues in contact with HIS 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F TYR* 2.4 51.0 + + + +
86F PHE* 3.4 1.8 - - - -
88F VAL* 1.3 75.5 + - + +
90F MET* 1.3 86.9 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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