Contacts of the helix formed by residues 68 - 78 (chain F) in PDB entry 4OA5
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 68 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ALA* 5.0 0.2 - - - -
65F THR* 3.1 25.8 + - - +
66F CYS 3.4 1.0 + - - -
67F VAL* 1.3 79.9 - - - +
69F PHE* 1.3 58.8 + - - +
70F SER 3.5 1.6 - - - -
71F ALA* 3.4 8.0 + - - +
72F ILE* 2.8 43.0 + - - +
97F ALA* 4.3 4.9 - - - -
101F ILE* 5.3 4.0 - - - -
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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
----------------------------------------------------------
19F VAL* 5.0 0.9 - - + -
24F ALA* 3.3 35.7 - - + -
25F LEU* 5.0 0.4 - - - -
27F ALA* 4.6 7.3 - - + +
28F HIS* 3.6 25.8 - + + +
39F GLN* 3.6 23.7 + - + +
40F LEU* 3.2 38.4 - - + -
41F GLY 3.6 20.9 - - - -
42F THR* 4.1 17.3 - - + -
45F GLY* 4.9 0.4 - - - -
65F THR 4.3 2.4 + - - -
66F CYS* 6.0 0.2 - - - +
67F VAL* 3.5 2.8 + - - +
68F GLY* 1.3 78.6 - - - +
70F SER* 1.3 68.7 + - - +
72F ILE* 3.7 2.6 - - - +
73F CYS* 3.1 48.9 + - - -
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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
----------------------------------------------------------
40F LEU* 4.1 22.0 - - - -
48F LEU* 4.7 1.7 - - - +
62F GLU* 2.5 29.2 + - - -
64F GLY 4.5 5.5 + - - -
65F THR 4.6 3.8 + - - -
69F PHE* 1.3 83.8 - - - +
71F ALA* 1.3 57.6 + - - +
73F CYS* 3.3 6.9 + - - +
74F MET* 3.0 33.1 + - - +
134F PHE* 4.0 19.2 - - - -
136F ASP* 5.0 3.3 + - - -
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Residues in contact with ALA 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F GLU* 3.5 18.1 + - - +
68F GLY* 3.4 14.2 + - - +
69F PHE 3.2 0.4 - - - -
70F SER* 1.3 79.6 + - - +
72F ILE* 1.3 58.9 + - - +
74F MET* 3.4 10.7 + - - -
75F ALA* 2.9 27.0 + - - +
84F ILE* 3.3 15.1 - - + +
86F THR* 4.5 6.3 - - + -
101F ILE* 5.6 0.4 - - + -
110F ILE* 3.7 28.2 - - + +
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Residues in contact with ILE 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ALA* 4.0 17.7 - - + -
27F ALA* 3.7 27.1 - - + -
68F GLY 2.8 27.5 + - - +
69F PHE* 3.7 4.0 - - - +
71F ALA* 1.3 68.8 - - - +
73F CYS* 1.3 67.2 + - - +
75F ALA* 3.3 1.9 + - - +
76F HIS* 3.2 45.3 + - + -
100F ASN* 4.1 16.8 - - + +
101F ILE* 4.4 7.4 - - + +
104F CYS* 3.9 21.3 - - - -
106F LEU* 3.9 16.9 - - + +
110F ILE* 4.1 12.8 - - + -
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Residues in contact with CYS 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F VAL* 3.9 23.6 - - - -
24F ALA* 4.3 2.7 - - - -
45F GLY* 4.1 22.7 - - - +
48F LEU* 5.9 0.4 - - + -
49F GLN* 2.9 32.8 + - - +
69F PHE* 3.1 54.1 + - - -
70F SER* 3.6 8.5 - - - +
71F ALA 3.3 0.2 - - - -
72F ILE* 1.3 76.9 - - - +
74F MET* 1.3 64.8 + - + +
76F HIS* 3.4 7.3 + - - -
77F ALA 3.7 0.5 + - - -
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Residues in contact with MET 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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48F LEU* 3.9 28.9 - - + -
49F GLN* 4.8 2.0 - - - -
52F ILE* 3.5 28.7 - - + +
60F ILE* 4.1 24.9 - - + -
62F GLU* 3.3 35.9 - - + +
70F SER 3.0 18.7 + - - +
71F ALA* 4.0 5.4 - - - -
72F ILE 3.3 0.2 - - - -
73F CYS* 1.3 76.1 - - + +
75F ALA* 1.3 58.1 + - - +
77F ALA* 3.0 21.7 + - - +
78F LEU* 3.3 12.5 + - - +
84F ILE* 3.7 14.4 - - + -
132F MET* 4.1 12.3 - - - -
134F PHE* 4.0 9.2 - - + -
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Residues in contact with ALA 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F ALA 2.9 18.8 + - - +
72F ILE 3.3 4.7 + - - +
74F MET* 1.3 76.7 - - - +
76F HIS* 1.3 59.0 + - - +
78F LEU* 3.0 18.7 + - - +
84F ILE* 3.5 12.5 - - + +
106F LEU* 4.1 14.8 - - + -
109F LYS* 2.9 32.0 + - + -
110F ILE* 3.8 22.7 - - + -
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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
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19F VAL* 5.9 0.2 - - - +
21F THR* 3.8 34.3 + - + +
23F GLY* 5.8 1.1 - - - -
24F ALA* 5.1 1.8 - - - +
49F GLN* 3.9 12.5 + - - +
53F ARG* 4.5 6.4 + - - -
72F ILE* 3.2 32.6 + - + +
73F CYS* 3.7 10.6 - - - +
74F MET 3.2 0.4 - - - -
75F ALA* 1.3 77.9 - - - +
77F ALA* 1.3 57.4 + - - +
78F LEU 4.4 3.6 - - - +
104F CYS* 5.1 8.3 + - - +
106F LEU* 3.8 25.0 - - + +
109F LYS* 5.2 0.4 - - - +
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Residues in contact with ALA 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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201A LEU* 5.4 0.4 - - + -
49F GLN* 3.7 46.4 - - + +
52F ILE* 3.8 13.9 - - + +
53F ARG* 3.4 33.4 + - + +
73F CYS 3.7 1.2 + - - -
74F MET 3.0 11.5 + - - +
76F HIS* 1.3 76.4 - - - +
78F LEU* 1.3 64.0 + - - +
79F PRO* 3.8 2.4 - - - +
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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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52F ILE* 3.8 13.9 - - + -
53F ARG* 5.8 0.2 + - - -
57F ILE 3.4 23.3 - - - +
58F HIS 3.6 13.5 - - - +
60F ILE* 3.9 13.9 - - + -
74F MET 3.3 9.2 + - - +
75F ALA* 3.0 18.3 + - + +
76F HIS 4.4 3.3 - - - +
77F ALA* 1.3 81.1 - - - +
79F PRO* 1.3 76.0 - - + +
82F GLY* 4.0 3.4 - - - -
83F HIS* 3.7 21.8 - - - +
84F ILE* 3.6 35.4 - - + -
109F LYS* 4.0 9.0 + - - +
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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