Contacts of the strand formed by residues 165 - 169 (chain B) in PDB entry 2PGW
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 VAL 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B TYR 4.4 3.2 + - - +
140B PHE* 3.3 20.1 - - + +
141B TYR* 2.7 34.6 + - - +
163B GLU* 5.3 0.2 + - - -
164B ARG* 1.3 94.0 - - + +
166B PHE* 1.3 57.9 + - - +
192B ARG* 3.5 38.6 - - + +
194B ARG* 3.4 43.1 - - + +
219B GLU* 4.4 3.1 - - - +
322B ASP 4.3 9.6 - - - +
323B GLY* 4.3 2.2 - - - -
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 3.8 30.1 - + + -
143B LEU* 4.2 14.8 - - + -
155B ALA* 3.7 17.7 - - - -
158B GLY 3.9 1.1 - - - -
159B HIS* 3.5 28.9 - - - -
163B GLU* 3.7 24.0 - - + -
164B ARG 4.4 0.7 - - - -
165B VAL* 1.3 74.9 - - - +
167B TYR* 1.3 55.7 + - - +
168B LEU 4.1 0.4 - - - -
184B VAL* 5.0 0.2 - - + -
188B ILE* 3.6 28.3 - - + -
191B ALA* 3.5 26.2 - - + -
192B ARG 3.0 21.0 + - - +
193B LEU* 3.5 15.9 - - + +
194B ARG* 2.7 35.3 + - - +
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Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B PHE* 3.4 39.5 - + + -
141B TYR 3.1 13.0 + - - +
142B PHE* 4.0 21.4 - + - -
143B LEU* 3.2 28.5 + - - +
166B PHE* 1.3 74.8 - - - +
168B LEU* 1.3 63.4 + - - +
169B LYS* 4.4 2.2 + - + -
194B ARG* 3.4 26.7 - - + -
196B ASP* 3.3 40.0 - - + +
220B PHE* 4.9 3.4 - + - -
222B GLU* 3.0 41.4 + - + -
247B ASP* 4.6 0.5 + - - -
298B HIS* 5.8 0.2 - - - -
325B GLN* 3.3 17.8 + - + -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.8 17.5 - - + +
151B LEU* 3.8 37.9 - - + -
167B TYR* 1.3 75.8 - - - +
169B LYS* 1.3 77.7 + - - +
170B VAL* 3.6 1.0 + - + -
172B ARG* 4.0 1.3 - - - +
180B ILE* 4.1 7.0 - - + +
181B THR* 3.7 33.0 - - - +
184B VAL* 3.9 22.0 - - + -
193B LEU* 4.2 5.8 - - + -
194B ARG 2.8 9.5 + - - +
195B LEU* 3.1 22.4 - - + +
196B ASP* 2.8 25.8 + - - -
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Residues in contact with LYS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 5.9 3.4 - - - +
23B HIS 5.5 7.8 + - - +
24B TRP* 6.3 1.6 - - - +
142B PHE* 6.4 3.6 - - + -
143B LEU 5.7 4.0 + - - +
167B TYR* 4.4 3.0 + - + -
168B LEU* 1.3 75.7 - - - +
170B VAL* 1.3 72.0 + - - +
171B GLY 5.8 1.0 + - - -
172B ARG* 2.9 51.2 + - - +
180B ILE* 3.7 7.4 - - - +
196B ASP* 3.5 22.9 - - + +
198B ASN* 4.1 24.8 - - + +
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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
------------------------------------------------------------
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