Contacts of the helix formed by residues 66 - 94 (chain w) in PDB entry 6FF7
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 66 (chain w).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64w GLY* 3.3 6.4 - - - +
65w LEU* 1.3 78.1 - - - +
67w GLU* 1.3 57.0 + - - -
68w PHE* 3.1 3.8 - - - -
69w ARG* 2.6 26.5 + - - +
70w ILE* 2.9 12.2 + - - +
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Residues in contact with GLU 67 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66w GLY* 1.3 70.5 - - - -
68w PHE* 1.3 64.5 + - - +
70w ILE* 3.1 8.0 + - - +
71w ARG* 2.8 27.0 + - - +
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Residues in contact with PHE 68 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66w GLY 3.0 1.2 + - - -
67w GLU* 1.3 80.6 - - - +
69w ARG* 1.3 61.7 + - - +
71w ARG* 3.4 7.8 - - - +
72w ASP* 3.2 18.2 + - - +
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Residues in contact with ARG 69 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65w LEU* 3.3 31.0 - - + +
66w GLY* 2.6 16.4 + - - +
68w PHE* 1.3 72.0 - - - +
70w ILE* 1.3 65.5 + - - +
72w ASP* 2.9 17.3 + - - +
73w LEU* 3.0 14.1 + - - +
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Residues in contact with ILE 70 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60w ILE* 5.5 14.1 - - + +
63w ALA* 6.3 2.9 - - - -
65w LEU* 4.9 3.1 - - + +
66w GLY 2.9 11.3 + - - +
67w GLU* 3.7 11.2 - - - +
69w ARG* 1.3 75.3 - - - +
71w ARG* 1.3 57.3 + - - +
73w LEU* 3.2 6.8 + - - +
74w ASN* 2.9 32.8 + - - +
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Residues in contact with ARG 71 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67w GLU 2.8 16.6 + - - +
68w PHE* 3.4 9.2 - - - +
70w ILE* 1.3 77.4 - - - +
72w ASP* 1.3 63.1 + - - +
74w ASN* 3.4 5.3 + - - +
75w ASP* 3.0 23.0 + - - +
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Residues in contact with ASP 72 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68w PHE 3.2 8.1 + - - +
69w ARG* 2.9 11.7 + - - +
71w ARG* 1.3 78.9 - - - +
73w LEU* 1.3 66.4 + - - +
75w ASP* 3.3 8.7 + - - +
76w GLU* 3.3 15.9 + - - +
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Residues in contact with LEU 73 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56w LYS* 4.6 25.7 - - + +
59w GLN* 5.2 8.7 - - + -
60w ILE* 5.1 8.5 - - + +
69w ARG 3.0 11.2 + - - +
70w ILE* 3.6 10.5 - - - +
72w ASP* 1.3 76.0 - - - +
74w ASN* 1.3 55.6 + - - +
76w GLU* 2.7 30.6 + - - +
77w ILE* 2.9 10.9 + - - +
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Residues in contact with ASN 74 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60w ILE* 6.0 4.2 - - + +
70w ILE 2.9 17.6 + - - +
71w ARG* 3.9 4.9 - - - +
73w LEU* 1.3 76.1 - - - +
75w ASP* 1.3 65.4 + - - +
77w ILE* 3.1 17.0 + - - +
78w ASN* 3.4 10.7 + - - +
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Residues in contact with ASP 75 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71w ARG 3.0 14.2 + - - +
72w ASP* 3.4 12.6 - - - +
73w LEU 3.0 0.2 - - - -
74w ASN* 1.3 79.3 - - - +
76w GLU* 1.3 60.6 + - - +
78w ASN* 3.5 6.2 + - - +
79w LYS* 3.5 15.1 + - - +
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Residues in contact with GLU 76 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56w LYS* 5.7 5.2 - - + -
72w ASP 3.3 7.0 + - - +
73w LEU* 2.7 16.7 + - - +
75w ASP* 1.3 73.1 - - - +
77w ILE* 1.4 65.4 + - - +
79w LYS* 2.8 11.5 + - + +
80w LEU* 2.8 23.6 + - - +
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Residues in contact with ILE 77 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53w ILE* 5.4 10.7 - - + +
56w LYS* 5.2 12.7 - - + +
57w VAL* 6.2 1.8 - - - +
73w LEU 2.9 10.4 + - - +
74w ASN* 3.1 13.4 + - - +
76w GLU* 1.4 75.9 - - - +
78w ASN* 1.3 63.3 + - - +
80w LEU* 3.1 9.6 + - - +
81w LEU* 2.9 21.7 + - - +
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Residues in contact with ASN 78 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74w ASN 3.4 7.2 + - - +
75w ASP* 4.0 7.4 - - - +
76w GLU 3.2 0.4 - - - -
77w ILE* 1.3 78.4 - - - +
79w LYS* 1.3 65.0 + - - +
81w LEU* 3.0 9.3 + - - +
82w ARG* 2.8 24.8 + - - +
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Residues in contact with LYS 79 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75w ASP 3.5 9.5 + - - +
76w GLU* 2.8 13.0 + - - +
78w ASN* 1.3 78.8 - - - +
80w LEU* 1.3 61.4 + - - +
82w ARG* 3.5 7.2 + - - +
83w GLU* 3.5 17.3 + - - +
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Residues in contact with LEU 80 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49w ILE* 4.5 17.2 - - + +
52w GLU* 5.3 5.8 - - + -
53w ILE* 4.6 21.5 - - + +
76w GLU 2.8 10.7 + - - +
77w ILE* 3.1 12.1 + - - +
79w LYS* 1.3 77.7 - - - +
81w LEU* 1.4 61.7 + - - +
83w GLU* 3.2 16.4 + - - +
84w LYS* 3.4 9.7 + - - +
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Residues in contact with LEU 81 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53w ILE* 5.8 1.5 - - - +
77w ILE 2.9 12.8 + - - +
78w ASN* 3.6 9.6 - - - +
80w LEU* 1.4 73.0 - - - +
82w ARG* 1.3 68.6 + - - +
84w LYS* 2.8 21.5 + - + +
85w GLY* 3.1 9.2 + - - -
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Residues in contact with ARG 82 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78w ASN 2.8 16.1 + - - +
79w LYS* 3.9 7.6 - - - +
80w LEU 3.3 0.2 - - - -
81w LEU* 1.3 76.4 - - - +
83w GLU* 1.3 64.1 + - - +
85w GLY* 3.1 11.9 + - - +
86w HIS* 3.4 9.5 + - - +
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Residues in contact with GLU 83 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49w ILE* 5.2 8.1 - - + -
79w LYS 3.5 8.6 + - - +
80w LEU* 3.2 12.4 + - - +
81w LEU 3.1 0.6 - - - -
82w ARG* 1.3 79.4 - - - +
84w LYS* 1.3 61.9 + - - +
86w HIS* 3.0 10.3 + - - +
87w TRP* 2.9 22.4 + - - +
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Residues in contact with LYS 84 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46w ARG* 5.5 7.0 - - + +
49w ILE* 5.2 11.2 - - + +
80w LEU 3.4 6.2 + - - +
81w LEU* 2.8 15.1 + - - +
83w GLU* 1.3 76.5 - - - +
85w GLY* 1.3 60.1 + - - +
87w TRP* 3.0 6.4 + - - +
88w GLU* 2.7 40.1 + - + +
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Residues in contact with GLY 85 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81w LEU 3.1 10.8 + - - -
82w ARG* 3.1 6.1 + - - -
84w LYS* 1.3 77.4 - - - +
86w HIS* 1.3 59.1 + - - +
88w GLU* 5.2 1.8 - - - -
89w VAL* 3.2 24.0 + - - +
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Residues in contact with HIS 86 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82w ARG 3.4 7.6 + - - +
83w GLU* 3.0 12.5 + - - +
84w LYS 3.0 0.6 - - - -
85w GLY* 1.3 76.2 - - - +
87w TRP* 1.3 55.5 + - - +
89w VAL* 3.7 1.1 - - - +
90w ARG* 2.6 37.8 + - - +
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Residues in contact with TRP 87 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179o GLU* 6.2 0.2 - - - -
42w ALA* 4.4 11.0 - - + +
45w TRP* 4.9 6.7 - - + +
46w ARG* 4.1 28.7 - - + +
83w GLU 2.9 15.1 + - - +
84w LYS* 3.9 3.8 - - - +
86w HIS* 1.3 72.6 - - - +
88w GLU* 1.3 67.7 + - - +
89w VAL 3.0 1.3 - - - -
90w ARG* 2.8 17.6 + - - +
91w ILE* 2.9 14.0 + - - +
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Residues in contact with GLU 88 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177o THR 5.4 0.8 - - - +
46w ARG* 4.5 13.2 - - + +
84w LYS* 2.7 23.8 + - + +
85w GLY* 5.0 1.8 - - - +
87w TRP* 1.3 75.1 - - - +
89w VAL* 1.3 60.0 + - - +
91w ILE* 3.7 14.4 + - - +
92w LYS* 3.9 5.4 + - - +
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Residues in contact with VAL 89 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85w GLY 3.2 20.9 + - - +
86w HIS* 3.9 1.8 - - - +
87w TRP 3.0 0.4 - - - -
88w GLU* 1.3 77.3 - - - +
90w ARG* 1.3 64.4 + - - +
91w ILE 3.0 2.2 - - - -
92w LYS* 2.9 18.7 + - - +
93w GLU* 3.1 11.5 + - - +
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Residues in contact with ARG 90 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42w ALA* 5.1 8.7 - - + -
86w HIS 2.6 25.4 + - - +
87w TRP* 2.8 7.9 + - - +
89w VAL* 1.3 73.1 - - - +
91w ILE* 1.3 62.7 + - - +
93w GLU* 3.2 10.6 + - - +
94w LEU* 3.1 22.0 + - - +
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Residues in contact with ILE 91 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177o THR 3.6 23.8 - - - +
178o HIS* 4.2 15.4 - - + +
179o GLU* 5.2 0.9 - - - +
39w LEU* 5.5 2.7 - - - +
42w ALA* 4.4 16.3 - - + +
87w TRP 2.9 9.9 + - - +
88w GLU* 3.7 12.1 - - - +
89w VAL 3.0 0.2 - - - -
90w ARG* 1.3 78.9 - - - +
92w LYS* 1.3 61.1 + - - +
94w LEU* 3.3 21.0 + - - +
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Residues in contact with LYS 92 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88w GLU 3.9 5.0 + - - +
89w VAL* 2.9 13.0 + - - +
91w ILE* 1.3 77.5 - - - +
93w GLU* 1.3 64.5 + - - +
94w LEU 3.2 5.5 + - - -
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Residues in contact with GLU 93 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89w VAL 3.1 8.4 + - - +
90w ARG* 3.2 12.8 + - - +
92w LYS* 1.3 79.5 - - - +
94w LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 94 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39w LEU* 4.1 30.3 - - + +
42w ALA* 6.2 0.7 - - + -
90w ARG 3.1 12.7 + - - +
91w ILE* 3.4 18.6 - - - +
92w LYS 3.1 5.5 - - - -
93w GLU* 1.3 82.1 - - - +
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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) + - + + + + + -
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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