Contacts of the strand formed by residues 117 - 125 (chain A) in PDB entry 2OVI
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 MET 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A LYS* 3.9 3.8 - - - +
114A PHE* 3.0 34.5 + - + +
115A MET* 3.2 21.9 + - + +
116A GLY* 1.3 82.9 - - - +
118A ASP* 1.3 70.1 + - - +
119A THR* 3.5 2.9 + - - -
139A ARG* 4.3 19.6 + - - +
143A ARG* 4.1 26.5 - - - +
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Residues in contact with ASP 118 (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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112A ARG 3.8 5.3 - - - -
113A LYS* 4.1 22.5 + - - +
117A MET* 1.3 71.8 - - - +
119A THR* 1.3 59.5 + - - +
139A ARG* 2.9 28.4 + - - +
145A LEU* 3.7 19.4 - - + +
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Residues in contact with THR 119 (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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110A ILE* 5.6 1.8 - - + +
111A GLU* 3.2 7.7 - - - +
112A ARG* 2.8 60.6 + - + +
114A PHE* 4.5 15.4 - - + +
117A MET 4.2 4.3 - - - -
118A ASP* 1.3 77.6 - - - +
120A ALA* 1.3 64.5 + - - +
121A SER* 5.5 3.1 - - - +
136A PHE* 3.9 25.1 - - + -
139A ARG* 4.2 10.1 + - - +
145A LEU* 4.4 4.0 - - - -
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Residues in contact with ALA 120 (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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110A ILE 3.3 6.1 - - - +
111A GLU* 4.0 17.0 - - + +
119A THR* 1.3 76.0 + - - +
121A SER* 1.3 64.0 + - - +
136A PHE* 3.4 3.9 - - - -
137A LEU* 3.0 54.7 + - + +
145A LEU* 4.4 13.8 - - + +
150A VAL* 5.7 2.5 - - + -
153A PHE* 4.1 11.9 - - + -
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Residues in contact with SER 121 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ALA 3.7 0.5 - - - +
109A LEU* 3.5 3.6 - - - -
110A ILE* 3.0 52.0 + - - +
119A THR* 5.5 2.1 - - - +
120A ALA* 1.3 77.5 - - - +
122A ILE* 1.3 66.5 + - - +
123A LEU* 3.5 11.6 - - - +
134A LYS* 5.6 0.2 - - - -
135A ILE 3.1 13.0 - - - -
136A PHE* 3.4 32.4 - - - -
153A PHE* 3.5 5.2 - - - -
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A VAL* 3.9 14.4 - - + -
54A VAL* 4.2 14.1 - - + -
57A TRP* 3.9 24.2 - - + -
107A ILE* 4.0 9.2 - - + -
108A ALA 3.2 7.9 - - - +
109A LEU* 3.9 20.6 - - + -
121A SER* 1.3 76.5 - - - +
123A LEU* 1.3 64.7 + - - +
124A PHE* 3.7 29.7 - - + -
133A LEU 4.2 0.2 - - - +
134A LYS* 3.3 4.7 - - - +
135A ILE* 2.6 53.2 + - + +
137A LEU* 4.2 6.3 - - + -
153A PHE* 3.9 15.0 - - + -
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 5.7 1.1 - - + -
29A LEU* 3.6 32.8 - - + -
33A VAL* 4.3 10.8 - - + -
107A ILE* 3.3 6.8 - - - +
108A ALA* 2.8 39.8 + - + +
110A ILE* 4.1 16.6 - - + -
121A SER* 3.5 28.0 - - - +
122A ILE* 1.3 78.5 - - - +
124A PHE* 1.3 62.7 + - - +
125A PHE* 3.5 24.2 - - + -
131A ALA* 4.6 2.7 - - + -
133A LEU 3.9 2.9 - - - +
134A LYS* 3.9 26.5 - - + +
136A PHE* 6.0 0.2 - - + -
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Residues in contact with PHE 124 (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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47A PHE* 3.7 38.1 - + - -
50A VAL* 3.9 15.9 - - + -
51A TRP* 3.8 22.9 - + - -
54A VAL* 5.9 2.7 - - + -
99A ILE* 6.5 0.4 - - + -
104A CYS* 4.1 7.6 - - - -
106A HIS 3.8 3.4 - - - -
107A ILE* 3.9 22.7 - - + -
122A ILE* 3.7 25.1 - - + -
123A LEU* 1.3 72.6 - - - +
125A PHE* 1.3 55.4 + - - +
131A ALA* 3.4 3.6 - - - -
132A MET* 2.6 42.5 + - + +
133A LEU* 3.1 37.1 + - + +
135A ILE* 4.0 21.3 - - + -
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Residues in contact with PHE 125 (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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29A LEU* 3.8 15.5 - - + -
30A LEU* 3.4 48.0 - - + -
33A VAL* 3.9 11.4 - - + -
104A CYS* 3.3 6.4 - - - -
105A THR 3.0 24.4 + - - -
106A HIS* 2.8 32.2 + - + +
108A ALA* 3.8 18.6 - - + -
123A LEU* 3.5 43.7 - - + -
124A PHE* 1.3 75.6 - - - +
126A ASN* 1.3 65.9 + - - +
129A GLY* 3.3 22.9 - - - -
130A SER 3.3 10.3 - - - -
131A ALA* 4.0 0.9 - - - -
132A MET* 3.8 3.1 - - - -
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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