Contacts of the strand formed by residues 117 - 125 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B LYS* 3.1 8.0 - - - -
114B PHE 2.9 29.4 + - - +
115B MET* 4.2 24.0 - - + +
116B GLY* 1.3 82.6 - - - +
118B ASP* 1.3 70.8 + - - +
119B THR* 4.2 1.2 - - - -
139B ARG* 4.2 15.7 - - - +
143B ARG* 4.1 37.7 - - - +
144B GLN* 5.7 4.3 - - - +
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ARG 4.0 3.1 - - - -
113B LYS* 3.7 23.5 - - - +
117B MET* 1.3 71.9 - - - +
119B THR* 1.3 52.7 + - - +
139B ARG* 2.5 37.2 + - - +
144B GLN* 6.0 1.6 - - - +
145B LEU* 3.8 20.2 - - + +
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ILE* 5.6 0.7 - - + -
111B GLU* 3.2 6.8 - - - +
112B ARG* 2.7 68.7 + - + +
114B PHE* 4.4 19.1 - - + +
117B MET 4.2 3.1 - - - -
118B ASP* 1.3 78.1 - - - +
120B ALA* 1.3 61.1 + - - +
121B SER* 5.2 3.6 - - - +
136B PHE* 3.6 29.4 - - + -
139B ARG* 3.6 13.9 + - - +
145B LEU* 4.0 7.1 - - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ILE 3.2 9.4 - - - +
111B GLU* 4.2 13.0 - - + +
119B THR* 1.3 75.9 + - - +
121B SER* 1.3 62.9 + - - +
136B PHE* 3.5 4.8 - - - -
137B LEU* 3.0 59.3 + - + -
145B LEU* 4.0 14.8 - - + +
150B VAL* 5.2 1.1 - - + -
153B PHE* 4.2 8.1 - - + -
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ALA 3.7 0.5 - - - +
109B LEU* 3.4 3.6 - - - -
110B ILE* 2.8 56.2 + - - +
119B THR* 5.2 1.9 - - - +
120B ALA* 1.3 76.2 - - - +
122B ILE* 1.3 65.0 + - - +
123B LEU* 3.4 16.4 - - - +
135B ILE 3.2 11.7 - - - -
136B PHE* 3.6 28.7 - - - -
137B LEU* 4.9 0.7 - - - -
153B PHE* 3.5 4.3 - - - -
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 3.8 26.5 - - + -
54B VAL* 3.4 33.4 - - + -
57B TRP* 4.1 15.9 - - + -
107B ILE* 3.9 15.9 - - + -
108B ALA 3.2 4.5 - - - +
109B LEU* 4.0 9.0 - - + -
121B SER* 1.3 78.3 - - - +
123B LEU* 1.3 64.3 + - - +
124B PHE* 3.8 16.4 - - + -
133B LEU 4.1 0.3 - - - +
134B LYS* 3.3 4.0 - - - -
135B ILE* 2.8 48.7 + - + +
137B LEU* 5.1 1.8 - - + -
153B PHE* 4.0 13.2 - - + -
156B LEU* 4.8 4.0 - - + -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 5.7 2.2 - - + -
29B LEU* 4.0 19.1 - - + -
33B VAL* 4.4 10.3 - - + -
107B ILE* 3.3 7.3 - - - +
108B ALA* 2.9 35.0 + - + +
110B ILE* 4.7 10.1 - - + -
121B SER* 3.4 29.6 - - - +
122B ILE* 1.3 81.5 - - - +
124B PHE* 1.3 61.6 + - - +
125B PHE* 3.6 35.0 - - + -
131B ALA* 4.3 2.2 - - + -
133B LEU 3.7 2.9 - - - +
134B LYS* 3.7 35.4 - - + +
136B PHE* 5.3 0.7 - - + -
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B PHE* 3.7 37.2 - + - -
50B VAL* 3.9 25.8 - - + -
51B TRP* 3.9 21.8 - + - -
54B VAL* 5.9 1.8 - - + -
99B ILE* 6.3 0.9 - - + -
104B CYS* 4.3 13.7 - - - -
106B HIS 3.8 2.9 - - - -
107B ILE* 3.8 25.1 - - + -
122B ILE* 3.8 15.5 - - + -
123B LEU* 1.3 74.1 - - - +
125B PHE* 1.3 57.4 + - - +
131B ALA* 3.3 2.8 - - - -
132B MET* 2.7 38.6 + - + +
133B LEU* 3.0 38.0 + - + +
135B ILE* 4.1 21.3 - - + -
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Residues in contact with PHE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 3.7 16.6 - - + -
30B LEU* 3.5 54.7 - - + -
33B VAL* 4.0 9.4 - - + -
104B CYS* 3.1 5.9 - - - +
105B THR 2.9 23.9 + - - -
106B HIS* 2.7 33.0 + - + +
108B ALA* 3.8 14.8 - - + -
123B LEU* 3.6 39.9 - - + -
124B PHE* 1.3 75.6 - - - +
126B ASN* 1.3 66.8 + - - +
129B GLY* 3.4 19.1 - - - -
130B SER 3.3 12.1 - - - -
131B ALA* 3.8 3.4 - - - -
132B MET* 4.0 3.6 - - - -
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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