Contacts of the strand formed by residues 177 - 181 (chain B) in PDB entry 1WBB
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 GLU 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B THR* 2.8 28.1 + - - -
116B PRO* 3.7 11.3 - - + +
117B GLY* 2.8 23.2 + - - +
118B THR* 4.1 0.2 - - - +
132B LEU 3.5 1.6 + - - -
133B LEU* 3.5 15.5 - - + +
134B ALA* 2.8 30.5 + - - +
175B PRO* 3.1 4.2 - - - +
176B ALA* 1.3 80.9 - - - +
178B LEU* 1.3 60.0 + - - +
179B LEU 4.1 0.2 - - - -
195B GLY* 3.5 16.4 - - - +
197B ARG* 3.1 21.7 + - + +
243B TYR* 2.7 34.0 + - + -
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ALA* 3.5 10.5 - - + +
135B ALA 4.3 0.4 - - - -
136B ILE* 3.5 27.1 - - + +
145B TYR* 4.7 2.5 - - + -
170B LEU* 3.9 9.4 - - + -
175B PRO* 4.2 15.0 - - + +
177B GLU* 1.3 71.6 - - - +
179B LEU* 1.3 85.2 + - - +
180B TYR* 3.7 3.5 + - + -
190B ILE* 3.6 33.2 - - + -
193B ARG* 3.8 22.9 - - - +
194B ARG 4.6 4.9 + - - +
195B GLY 2.9 11.0 + - - +
196B LEU* 3.5 15.0 - - + -
197B ARG* 3.0 26.8 + - - -
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Residues in contact with LEU 179 (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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133B LEU* 4.3 7.4 - - + -
134B ALA 2.8 19.1 + - - +
135B ALA* 3.2 7.0 - - + -
136B ILE 2.8 27.4 + - - +
178B LEU* 1.3 76.5 - - - +
180B TYR* 1.3 58.5 + - - +
197B ARG* 3.4 29.8 - - + -
199B ARG* 4.0 14.4 - - + -
204B PHE* 5.0 0.9 - - - -
239B CYS* 3.6 22.0 - - - -
240B LEU* 3.7 16.8 - - + -
243B TYR* 3.5 52.3 - - + -
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Residues in contact with TYR 180 (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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136B ILE* 3.5 26.5 - - + +
178B LEU* 4.0 4.5 - - + -
179B LEU* 1.3 74.5 - - - +
181B ALA* 1.3 81.3 + - - +
184B PHE* 4.4 5.6 - + + -
187B MET* 3.7 32.5 - - + +
190B ILE* 3.6 20.2 - - + -
196B LEU* 3.9 20.6 - - + +
197B ARG 3.3 30.4 + - - +
198B ARG* 3.8 40.5 + - + +
199B ARG* 2.8 29.8 + - - +
204B PHE* 4.0 6.3 - - - -
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Residues in contact with ALA 181 (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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136B ILE 3.9 4.6 + - - -
137B TRP* 4.4 14.4 - - + -
180B TYR* 1.3 87.7 - - - +
182B GLU* 1.3 66.6 + - - +
183B ASP 3.4 13.9 - - - +
184B PHE* 3.2 19.1 - - + +
199B ARG 3.5 6.5 - - - +
200B PRO 5.1 0.2 - - - +
201B LEU* 4.3 13.7 - - + -
204B PHE* 3.6 25.8 - - + -
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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
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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