Contacts of the strand formed by residues 110 - 115 (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 ILE 110 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F PHE* 3.5 15.5 - - + +
80F ILE* 3.6 36.8 - - + -
98F TYR* 4.5 3.8 - - + -
101F VAL* 4.3 10.1 - - + -
102F ARG* 3.2 45.1 - - + +
108F THR 3.8 3.1 - - - +
109F PRO* 1.3 77.1 - - - +
111F LEU* 1.3 76.6 + - - +
112F LEU 4.3 0.4 - - - +
149F ILE* 4.3 23.6 - - + +
150F GLY 5.2 0.6 + - - -
151F SER* 3.0 11.1 + - - +
152F VAL* 2.8 35.6 + - - +
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Residues in contact with LEU 111 (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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77F VAL* 3.7 20.2 - - + -
78F PHE 2.8 7.5 + - - -
79F LEU* 3.4 21.9 - - + -
80F ILE 2.9 25.8 + - - -
110F ILE* 1.3 82.5 - - - +
112F LEU* 1.3 62.0 + - - +
113F VAL* 3.8 5.4 + - + +
152F VAL* 4.1 12.3 - - + -
153F LYS* 3.7 17.9 - - + +
155F LEU* 3.9 10.1 - - + -
168F VAL 3.9 7.6 - - - +
171F GLU* 3.8 15.3 - - + +
172F ALA* 3.5 30.1 - - - +
175F ALA* 4.0 16.6 - - + -
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Residues in contact with LEU 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ILE* 3.4 17.5 - - + +
82F PHE* 4.0 24.7 - - + -
93F VAL* 3.9 25.1 - - + -
111F LEU* 1.3 72.0 - - - +
113F VAL* 1.3 60.3 + - - +
142F GLY 3.6 11.2 - - - +
145F MET* 3.5 19.3 - - + -
146F ALA* 3.4 32.1 - - + +
149F ILE* 4.1 8.1 - - + -
151F SER* 3.3 14.8 + - - +
153F LYS 3.1 8.6 + - - +
154F TYR* 3.4 10.7 - - + -
155F LEU 3.0 25.3 + - - -
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Residues in contact with VAL 113 (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 LEU* 4.7 4.0 - - + -
79F LEU* 4.2 17.5 - - + -
80F ILE 2.9 12.2 + - - +
81F CYS* 3.3 12.8 - - - +
82F PHE* 3.0 30.9 + - - +
111F LEU* 4.2 12.8 - - + +
112F LEU* 1.3 76.5 - - - +
114F GLY* 1.3 61.7 + - - +
115F THR* 3.7 11.1 + - + -
155F LEU* 3.3 11.2 - - + +
157F CYS* 4.0 26.7 - - - -
168F VAL* 4.0 29.8 - - + -
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Residues in contact with GLY 114 (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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82F PHE* 3.4 27.3 - - - -
84F LEU* 3.9 14.7 - - - +
113F VAL* 1.3 72.0 - - - +
115F THR* 1.3 61.1 + - - -
154F TYR* 4.1 3.4 - - - -
155F LEU 2.8 14.1 + - - -
156F GLU* 3.3 2.3 - - - -
157F CYS* 2.8 29.1 + - - +
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Residues in contact with THR 115 (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 2.6 29.0 + - - +
15F GLY* 4.9 11.0 - - - +
19F LEU* 5.4 4.7 - - + -
81F CYS* 4.1 16.6 - - + -
82F PHE 2.8 21.9 + - - +
83F SER* 3.1 7.6 - - - -
84F LEU* 2.9 27.6 + - - +
113F VAL* 4.1 20.0 - - + +
114F GLY* 1.3 74.1 - - - -
116F LYS* 1.3 67.8 + - - +
117F LEU 3.3 2.9 - - - -
157F CYS* 3.6 10.1 - - - -
200F GCP 5.8 1.1 - - - -
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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
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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