Contacts of the strand formed by residues 179 - 185 (chain F) in PDB entry 3WBR
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 ARG 179 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145F SER* 3.3 6.2 - - - -
146F ASP* 2.8 33.4 + - + +
177F ASP 3.9 0.2 + - - -
178F GLU* 1.3 77.8 + - - +
180F CYS* 1.3 62.1 + - - +
195F ASP* 3.0 44.3 + - + -
196F ILE* 3.6 14.8 + - - +
197F HIS* 3.4 28.3 - - - +
198F CYS* 3.3 6.7 - - - -
151H ARG* 3.6 39.9 - - - +
153H TRP* 3.6 18.8 - - + -
174H ASN* 4.3 13.7 + - - +
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Residues in contact with CYS 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F TRP* 3.3 41.3 - - + -
141F PHE* 3.9 13.5 - - + -
144F LEU 3.8 4.3 - - - -
145F SER* 3.9 6.7 - - - -
179F ARG* 1.3 75.4 - - - +
181F ALA* 1.3 61.0 + - - +
182F ILE 4.1 0.3 + - - -
195F ASP* 3.3 2.8 - - - -
196F ILE* 2.8 38.5 + - - +
198F CYS* 2.0 46.4 - - - -
153H TRP* 4.1 4.3 - - - -
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Residues in contact with ALA 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F PHE* 3.6 5.4 - - - -
142F LEU* 2.9 35.8 + - + +
144F LEU* 3.0 34.2 + - + +
180F CYS* 1.3 74.5 - - - +
182F ILE* 1.3 64.5 + - - +
194F ASN 3.2 9.2 - - - +
195F ASP* 4.5 0.2 - - - +
153H TRP* 4.2 1.3 - - + -
168H TRP* 3.8 25.4 - - + -
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Residues in contact with ILE 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D PRO* 4.2 4.9 - - + -
139F SER* 3.3 22.0 - - - +
140F TYR 3.1 11.4 - - - +
141F PHE* 3.4 35.4 - - + -
142F LEU* 4.2 4.7 - - - +
181F ALA* 1.3 73.6 - - - +
183F ILE* 1.3 60.0 + - - +
184F ASN* 3.4 16.1 + - - +
193F TRP* 3.1 6.6 - - - +
194F ASN* 2.7 45.7 + - + +
196F ILE* 3.7 33.2 - - + -
202F GLN* 3.4 22.2 - - + +
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Residues in contact with ILE 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F ILE* 5.0 0.7 - - + -
127F GLN* 3.8 24.7 - - - +
130F ILE* 4.9 6.5 - - + -
131F ILE* 3.8 29.4 - - + -
134F LEU* 4.1 11.0 - - + -
139F SER* 3.5 1.8 - - - -
140F TYR* 2.8 39.2 + - + +
142F LEU* 3.6 26.2 - - + +
182F ILE* 1.3 74.3 - - - +
184F ASN* 1.3 65.3 + - - +
191F TRP* 4.1 9.6 - - + -
192F GLY 3.3 14.8 - - - +
193F TRP* 4.1 8.1 - - + +
205F ILE* 3.9 18.6 - - + -
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Residues in contact with ASN 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D PRO* 3.9 12.7 - - + +
138F SER 3.8 5.4 - - - +
139F SER* 3.0 30.4 + - - +
182F ILE* 3.4 22.0 - - - +
183F ILE* 1.3 75.7 - - - +
185F PHE* 1.3 64.8 + - - +
186F ARG* 4.6 5.6 + - - +
191F TRP* 3.4 14.8 - - - -
192F GLY 3.1 17.0 + - - -
194F ASN* 4.7 6.9 - - - +
169H HIS* 3.0 41.9 + - - -
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Residues in contact with PHE 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F ARG* 3.3 78.8 + - + +
138F SER 4.4 2.2 + - - -
184F ASN* 1.3 78.3 - - - +
186F ARG* 1.3 81.1 + - - +
187F SER* 4.1 10.3 - - - -
188F SER 5.2 0.2 - - - -
190F GLU* 3.3 37.2 - - + -
191F TRP* 3.6 33.4 - + + -
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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