Contacts of the strand formed by residues 77 - 83 (chain F) in PDB entry 2OV2
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 VAL 77 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4F ILE* 4.0 7.9 - - + -
5F LYS 3.1 1.2 + - - -
6F CYS* 3.3 28.8 - - + +
7F VAL 3.0 23.6 + - - -
75F THR* 3.3 8.1 - - - +
76F ASP* 1.3 79.7 - - - +
78F PHE* 1.3 67.4 + - - +
79F LEU* 4.9 1.3 - - + -
108F THR* 4.3 0.7 - - - -
109F PRO* 3.5 16.2 - - + +
111F LEU* 3.7 27.6 - - + -
172F ALA* 4.0 22.2 - - + +
175F ALA* 4.3 4.5 - - + -
176F VAL* 3.9 19.5 - - + -
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Residues in contact with PHE 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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7F VAL* 3.3 28.5 - - + -
9F VAL* 4.7 4.0 - - + -
72F TYR* 3.7 29.8 - + - -
75F THR* 3.7 15.5 - - + -
77F VAL* 1.3 76.3 - - - +
79F LEU* 1.3 65.6 + - - +
80F ILE* 3.8 4.7 - - + -
101F VAL* 3.7 34.3 - - + -
105F CYS* 3.5 32.3 - - + -
108F THR* 3.6 29.6 - - + -
109F PRO 2.9 11.4 + - - +
110F ILE* 3.5 13.1 - - + -
111F LEU* 2.8 28.1 + - - +
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Residues in contact with LEU 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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6F CYS* 3.8 15.5 - - - -
7F VAL 3.0 7.3 + - - -
8F VAL* 3.5 16.9 - - + +
9F VAL* 2.9 28.9 + - - +
19F LEU* 4.2 15.5 - - + -
77F VAL* 4.2 1.7 + - + -
78F PHE* 1.3 75.2 - - - +
80F ILE* 1.3 60.0 + - - +
81F CYS* 3.7 5.8 + - - -
111F LEU* 3.4 37.0 - - + -
113F VAL* 4.2 9.9 - - + -
168F VAL* 3.8 23.6 - - + -
169F PHE* 4.0 22.7 - - + -
172F ALA* 4.4 11.7 - - + -
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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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9F VAL* 3.5 16.4 - - + +
78F PHE* 3.8 4.9 - - + -
79F LEU* 1.3 71.8 - - - +
81F CYS* 1.3 61.2 + - - +
93F VAL* 4.1 25.4 - - + -
97F TRP* 3.7 28.3 - - + +
98F TYR* 4.1 24.0 - - - +
101F VAL* 4.5 6.5 - - + -
110F ILE* 3.6 39.7 - - + -
111F LEU 2.9 8.9 + - - +
112F LEU* 3.4 11.6 - - + +
113F VAL 2.9 24.4 + - - -
149F ILE* 4.3 7.4 - - + -
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Residues in contact with CYS 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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8F VAL* 3.5 31.2 - - - -
9F VAL 2.8 13.2 + - - +
10F GLY* 3.5 18.9 - - - -
11F ASP 4.2 2.1 + - - -
14F VAL* 4.0 18.6 - - + +
16F LYS* 4.1 6.1 - - + -
19F LEU* 4.4 11.0 - - - -
79F LEU* 3.9 7.9 - - - -
80F ILE* 1.3 81.3 - - - +
82F PHE* 1.3 62.8 + - - +
89F SER 5.0 1.2 - - - +
93F VAL* 4.7 1.6 - - - +
97F TRP* 5.1 1.0 - - - -
113F VAL* 3.3 23.1 - - - +
115F THR* 4.1 9.0 - - + -
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Residues in contact with PHE 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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14F VAL* 4.1 7.0 - - - -
81F CYS* 1.3 74.0 - - - +
83F SER* 1.3 71.4 + - - +
84F LEU* 3.5 21.5 - - + -
89F SER* 3.5 27.1 - - - +
90F PHE* 3.5 42.4 - + + +
93F VAL* 4.0 4.0 - - + -
112F LEU* 4.0 24.5 - - + -
113F VAL 3.0 11.3 + - - +
114F GLY* 3.8 13.9 - - - -
115F THR* 2.8 28.4 + - - -
137F ILE* 3.9 11.4 - - + -
154F TYR* 3.7 35.4 - + - -
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Residues in contact with SER 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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13F ALA 5.1 0.4 - - - -
14F VAL* 3.7 15.2 - - - +
82F PHE* 1.3 81.2 - - - +
84F LEU* 1.3 62.8 + - - +
85F VAL* 3.0 30.5 + - - +
86F SER* 3.0 30.1 + - - +
89F SER* 2.9 11.8 + - - -
115F THR* 3.1 13.6 + - - -
116F LYS* 3.5 18.6 + - - +
137F ILE* 4.3 0.7 - - - +
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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