Contacts of the strand formed by residues 165 - 169 (chain B) in PDB entry 2W5X
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 PHE 165 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B THR 3.1 2.7 + - - +
126B GLY* 3.2 9.8 - - - -
127B VAL 3.1 19.7 + - - -
128B VAL* 4.1 6.7 - - + -
163B LEU* 3.6 6.7 - - - +
164B ASP* 1.3 81.3 - - - +
166B PHE* 1.3 82.6 + - - +
167B ALA* 4.1 9.4 - - + -
205B ILE* 4.3 7.4 - - + -
211B MET* 3.2 16.4 - - + -
213B PHE* 4.0 33.7 - + - -
234B ALA* 4.0 8.7 - - - -
237B LEU* 4.2 13.7 - - + -
238B ALA* 3.6 41.7 - - + -
241B PHE* 3.8 20.4 - + + -
242B LEU* 3.8 19.1 - - + -
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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
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127B VAL 3.0 14.1 - - - +
133B ILE* 4.1 24.2 - - + -
158B MET* 3.8 31.0 - - + -
163B LEU* 4.3 10.3 - - + -
165B PHE* 1.3 82.6 - - - +
167B ALA* 1.3 64.2 + - - +
174B PHE* 5.2 1.1 - + - -
187B LEU* 4.1 22.2 - - + -
192B PHE* 3.6 32.3 - + - -
194B ILE* 4.2 4.3 - - + -
211B MET 3.0 7.8 + - - +
212B GLY* 3.4 19.4 - - - -
213B PHE* 2.9 32.6 + - - +
214B LEU* 3.9 29.4 - - + -
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL 3.0 5.7 + - - -
128B VAL* 3.3 6.5 - - + +
129B ALA 3.0 24.1 + - - +
133B ILE* 3.7 6.6 - - - +
165B PHE* 4.1 10.3 - - + -
166B PHE* 1.3 76.4 - - - +
168B GLY* 1.3 57.6 + - - +
199B LEU* 4.6 1.1 - - + -
213B PHE* 3.4 22.2 - - + -
230B PHE* 4.0 8.7 - - + -
234B ALA* 4.0 26.7 - - + -
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Residues in contact with GLY 168 (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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129B ALA 3.3 17.0 - - - -
131B SER 4.1 2.0 - - - -
133B ILE* 4.5 7.7 - - - +
166B PHE* 4.9 0.8 - - - -
167B ALA* 1.3 75.1 - - - +
169B GLY* 1.3 64.8 + - - -
213B PHE* 3.0 11.4 + - - +
214B LEU* 3.4 2.4 - - - -
215B LEU* 3.0 22.9 + - - +
220B MET* 4.0 6.8 - - - +
230B PHE* 4.0 7.8 - - - -
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Residues in contact with GLY 169 (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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131B SER 3.0 14.7 + - - -
132B SER* 3.5 4.3 - - - -
133B ILE* 2.9 15.9 + - - +
168B GLY* 1.3 76.8 - - - +
170B GLY* 1.3 59.3 + - - -
171B LEU 3.7 0.2 - - - -
214B LEU* 3.6 13.6 - - - +
216B ALA* 3.6 19.7 - - - -
218B GLU 3.1 14.8 - - - -
220B MET* 3.9 6.2 - - - +
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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