Contacts of the strand formed by residues 165 - 169 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139E TYR 4.7 2.8 + - - +
140E PHE* 3.2 21.0 - - + +
141E TYR* 2.7 33.3 + - - +
163E GLU* 5.0 0.4 + - - +
164E ARG* 1.3 91.9 - - - +
166E PHE* 1.3 57.1 + - - +
192E ARG* 3.6 37.7 - - + +
194E ARG* 3.3 44.6 - - + +
219E GLU* 4.2 3.1 - - - +
322E ASP 4.3 10.1 - - - +
323E GLY* 4.3 1.6 - - - -
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Residues in contact with PHE 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E TYR* 3.8 25.8 - + + -
143E LEU* 4.3 14.6 - - + -
155E ALA* 3.7 9.9 - - - -
158E GLY 3.9 4.7 - - - -
159E HIS* 3.5 35.2 - - - -
163E GLU* 3.7 25.4 - - + -
164E ARG 4.4 0.9 - - - -
165E VAL* 1.3 76.1 - - - +
167E TYR* 1.3 56.0 + - - +
184E VAL* 5.0 0.2 - - + -
188E ILE* 3.6 34.1 - - + -
191E ALA* 3.7 19.5 - - + -
192E ARG 3.0 20.8 + - - +
193E LEU* 3.4 15.1 - - + +
194E ARG* 2.7 35.7 + - - +
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Residues in contact with TYR 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PHE* 3.4 43.1 - + + -
141E TYR 3.1 13.5 + - - +
142E PHE* 3.9 22.6 - + - -
143E LEU* 3.2 29.7 + - - +
166E PHE* 1.3 73.1 - - - +
168E LEU* 1.3 62.2 + - - +
169E LYS* 4.4 1.6 + - + -
194E ARG* 3.5 27.6 - - + -
196E ASP* 3.2 41.1 + - + -
220E PHE* 4.9 1.3 - + - -
222E GLU* 3.0 42.3 + - + -
247E ASP* 4.6 0.2 + - - -
325E GLN* 3.5 14.3 + - - -
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Residues in contact with LEU 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E LEU* 4.0 17.0 - - + -
151E LEU* 3.8 37.0 - - + -
166E PHE 4.1 0.4 - - - -
167E TYR* 1.3 75.2 - - - +
169E LYS* 1.3 70.6 + - - +
170E VAL* 3.7 1.2 + - + -
172E ARG* 4.3 1.1 - - - +
180E ILE* 3.9 7.4 - - + +
181E THR* 3.9 24.7 - - + +
184E VAL* 3.8 22.7 - - + -
193E LEU* 4.1 5.8 - - + -
194E ARG 2.9 9.7 + - - +
195E LEU* 3.2 29.7 - - + +
196E ASP* 2.8 32.3 + - - -
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Residues in contact with LYS 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E HIS 4.9 10.7 + - - -
24E TRP* 5.9 1.8 - - - +
142E PHE* 6.4 2.2 - - + -
143E LEU 5.9 1.2 + - - -
146E GLU* 5.5 3.0 + - - -
167E TYR* 4.4 2.1 + - + -
168E LEU* 1.3 76.6 - - - +
170E VAL* 1.3 85.7 + - - +
172E ARG* 2.7 63.1 + - + +
180E ILE* 3.6 6.4 - - - +
196E ASP* 3.6 21.1 - - + +
198E ASN* 4.9 15.6 - - + +
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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