Contacts of the strand formed by residues 167 - 172 (chain B) in PDB entry 2RVE
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 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B GLU* 6.0 4.0 - - - -
100B ASN* 5.6 10.5 - - - +
135B GLY 4.4 0.2 - - - -
136B TYR* 3.4 1.2 - - - -
137B VAL* 2.6 49.4 + - + +
165B GLY 4.6 7.6 - - - +
166B VAL* 1.3 71.2 - - - +
168B VAL* 1.4 69.6 + - - +
196B TYR* 3.5 58.3 - - + +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.9 28.5 - - + +
12B TYR* 2.8 44.7 - - + -
134B ILE* 5.2 2.2 - - + -
135B GLY 3.3 10.8 - - - +
136B TYR* 3.2 36.8 - - + -
166B VAL* 3.9 10.8 - - + +
167B LYS* 1.4 82.3 - - - +
169B PHE* 1.3 57.7 - - - +
196B TYR* 2.8 15.7 + - - -
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Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 5.0 3.1 - - - -
12B TYR* 3.4 11.4 - - - +
105B PHE* 3.4 42.6 - + - -
133B ILE* 4.6 6.5 - - + -
134B ILE* 3.3 8.7 - - - +
135B GLY* 3.1 43.5 + - - -
137B VAL* 4.6 4.5 - - + -
168B VAL* 1.3 77.3 - - - +
170B LEU* 1.3 63.1 + - - +
171B GLN* 3.8 27.4 - - + -
176B ILE* 4.5 8.3 - - + -
196B TYR* 3.9 18.4 - + - -
199B PHE* 3.7 33.4 - + + -
200B VAL* 3.4 26.0 - - + -
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Residues in contact with LEU 170 (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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4B ARG* 3.6 40.2 + - + +
7B LEU* 3.8 31.6 - - + -
8B ILE* 3.5 25.9 - - + +
11B LEU* 4.1 8.1 - - + -
12B TYR* 4.0 6.7 + - - -
89B ILE* 5.3 0.4 - - + -
132B TRP* 3.9 33.0 - - + -
133B ILE 3.3 9.2 - - - +
134B ILE* 3.5 24.9 - - + -
169B PHE* 1.3 74.3 - - - +
171B GLN* 1.3 68.1 + - - +
200B VAL* 5.2 1.9 - - - +
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Residues in contact with GLN 171 (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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4B ARG* 3.7 14.1 + - - +
132B TRP* 4.8 3.4 - - - -
133B ILE* 3.0 35.0 + - - +
169B PHE* 3.8 11.4 - - + -
170B LEU* 1.3 77.1 + - - +
172B ASP* 1.3 84.5 + - - +
175B VAL* 4.2 10.5 - - + +
176B ILE* 3.1 35.9 - - + -
199B PHE 3.0 24.1 + - - +
200B VAL 3.2 19.0 + - - -
201B GLU 4.1 0.8 - - - -
202B GLY* 3.4 17.9 - - - -
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Residues in contact with ASP 172 (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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4B ARG* 2.4 36.4 + - - -
130B ALA* 5.3 2.8 - - - +
131B HIS 3.8 11.3 + - - +
132B TRP* 4.0 13.7 + - - -
171B GLN* 1.3 82.8 + - - +
173B LYS* 1.3 69.0 + - - +
174B TRP* 4.2 17.3 + - + -
175B VAL* 3.1 28.5 + - + +
176B ILE* 3.4 10.0 + - - +
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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