Contacts of the strand formed by residues 82 - 88 (chain A) in PDB entry 1OFV
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 LYS 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ASP 3.1 6.1 + - - +
49A TYR* 3.4 22.1 + - + -
50A LEU 3.1 22.7 + - - +
80A GLY 4.8 4.0 - - - +
81A LYS* 1.3 73.9 - - - +
83A VAL* 1.3 65.9 - - - +
115A GLN* 3.3 35.2 - - + +
117A VAL* 4.3 9.2 - - + -
166A GLU* 2.9 48.2 + - - +
167A PHE* 4.1 15.3 - - + -
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 3.3 22.0 - - + +
52A ILE* 3.9 15.7 - - + -
78A PHE* 4.7 0.7 - - + -
81A LYS* 4.2 9.0 - - + -
82A LYS* 1.3 81.1 - - - +
84A ALA* 1.3 69.4 - - - +
85A TYR* 3.4 35.1 - - + +
109A ILE* 4.2 9.0 - - + -
114A SER* 3.6 26.5 - - - +
115A GLN 2.9 9.2 + - - +
116A THR* 3.2 7.0 - - - +
117A VAL* 3.1 24.2 + - - +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU 2.9 11.0 + - - +
51A ILE* 3.2 6.9 - - + -
52A ILE 2.9 22.7 + - - -
83A VAL* 1.3 76.7 - - - +
85A TYR* 1.3 67.9 + - - +
117A VAL 3.4 17.5 - - - +
159A TRP* 3.9 7.2 - - + -
163A LEU* 3.9 34.8 - - + -
167A PHE* 4.1 6.9 - - + -
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Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ILE* 3.2 34.3 - - + +
83A VAL* 3.4 30.6 - - + +
84A ALA* 1.3 77.0 - - - +
86A PHE* 1.3 64.3 + - - +
102A MET* 3.9 24.5 - - + -
105A LEU* 4.1 6.1 - - + -
106A GLU* 3.4 52.0 + - + +
109A ILE* 3.4 32.0 - - + +
110A SER 4.2 1.6 + - - -
114A SER* 4.7 0.9 + - - -
116A THR* 3.7 20.6 + - + -
117A VAL 4.6 0.6 + - - -
139A VAL 4.1 3.4 - - - +
140A GLY* 3.1 9.9 - - - -
141A LEU 2.9 21.3 + - - -
159A TRP* 3.2 10.4 - - - -
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Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.9 10.1 - - + -
7A TYR* 4.3 0.9 - - + -
14A THR* 3.7 26.7 - - + -
17A ILE* 3.5 33.7 - - + -
18A ALA* 3.7 25.8 - - + -
21A ILE* 3.7 12.1 - - + -
51A ILE* 3.6 29.2 - - + -
52A ILE 2.9 7.2 + - - +
53A GLY* 3.1 27.3 - - - -
54A CYS* 3.0 22.3 + - - +
85A TYR* 1.3 75.5 - - - +
87A GLY* 1.3 63.0 + - - +
102A MET* 3.7 9.4 - - - +
141A LEU* 3.3 25.1 - - + +
143A ILE* 5.8 0.7 - - + -
159A TRP* 4.3 3.6 - - + -
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 5.4 0.7 - - - -
17A ILE* 4.9 3.8 - - - -
54A CYS 3.3 17.9 - - - -
86A PHE* 1.3 80.0 - - - +
88A ALA* 1.3 58.2 + - - -
99A GLN* 3.1 18.3 + - - -
102A MET* 3.7 4.7 - - - -
141A LEU 2.9 8.3 + - - +
143A ILE* 2.9 30.3 + - - +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.9 16.4 - - + -
14A THR* 3.6 20.6 + - - +
17A ILE* 4.0 8.1 - - + -
55A PRO* 3.2 7.0 - - + +
56A THR* 3.2 23.9 + - - -
87A GLY* 1.3 73.6 - - - -
89A GLY* 1.3 58.3 + - - +
99A GLN* 3.7 5.8 - - - +
143A ILE* 3.5 7.6 - - + +
145A GLU 5.8 0.9 - - - +
170A FMN 3.5 26.5 + - - +
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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