Contacts of the strand formed by residues 179 - 185 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C SER* 3.3 5.9 - - - -
146C ASP* 2.8 33.3 + - + +
177C ASP* 3.7 1.7 + - - -
178C GLU* 1.3 79.4 - - - +
180C CYS* 1.3 61.5 + - - +
195C ASP* 2.8 36.2 + - - +
196C ILE* 3.5 12.6 + - - +
197C HIS* 3.6 23.8 - - - +
198C CYS* 3.3 3.4 - - - -
151G ARG* 3.2 40.5 - - - +
153G TRP* 3.7 20.4 - - + -
174G ASN* 2.8 30.4 + - - +
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Residues in contact with CYS 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C TRP* 3.3 40.6 - - + -
141C PHE* 3.9 14.1 - - + -
144C LEU 3.7 3.4 - - - -
145C SER* 3.9 7.0 - - - +
179C ARG* 1.3 75.7 - - - +
181C ALA* 1.3 62.6 + - - +
195C ASP* 3.4 0.9 - - - -
196C ILE* 2.9 36.9 + - - +
198C CYS* 2.0 49.4 - - - -
153G TRP* 4.3 4.3 - - - -
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Residues in contact with ALA 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C PHE* 3.6 8.1 - - - -
142C LEU* 3.0 36.7 + - + +
144C LEU* 2.9 46.2 + - + +
180C CYS* 1.3 72.5 - - - +
182C ILE* 1.3 62.3 + - - +
193C TRP* 5.0 0.7 - - + -
194C ASN 3.3 6.3 - - - +
195C ASP* 4.5 1.1 - - - +
153G TRP* 4.3 1.6 - - + -
168G TRP* 3.9 15.7 - - + -
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Residues in contact with ILE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B PRO* 4.2 8.3 - - + -
139C SER* 3.4 10.5 - - - +
140C TYR 3.1 10.8 - - - +
141C PHE* 3.4 33.7 - - + -
142C LEU* 4.3 4.0 - - - -
181C ALA* 1.3 73.0 - - - +
183C ILE* 1.3 60.1 + - - +
184C ASN* 3.2 27.3 + - - +
193C TRP* 3.1 7.3 - - - +
194C ASN* 2.8 49.0 + - + +
196C ILE* 3.8 28.5 - - + -
202C GLN* 3.4 22.7 - - + +
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Residues in contact with ILE 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE* 5.0 0.4 - - + -
127C GLN* 3.7 33.7 - - - +
130C ILE* 4.8 6.7 - - + -
131C ILE* 4.3 11.0 - - + -
134C LEU* 4.0 16.6 - - + -
139C SER* 3.6 2.1 - - - -
140C TYR* 2.8 41.5 + - + +
142C LEU* 3.6 26.4 - - + +
182C ILE* 1.3 73.4 - - - +
184C ASN* 1.3 64.6 + - - +
191C TRP* 3.8 12.8 - - + -
192C GLY 3.4 12.3 - - - +
193C TRP* 4.1 8.3 - - + +
205C ILE* 3.8 19.1 - - + -
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Residues in contact with ASN 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B PRO* 3.8 16.6 - - + +
138C SER 4.1 2.9 - - - +
139C SER* 3.1 30.4 + - - +
182C ILE* 3.2 24.2 - - - +
183C ILE* 1.3 74.8 - - - +
185C PHE* 1.3 64.8 + - - +
186C ARG* 4.5 4.3 + - - +
191C TRP* 3.4 14.3 - - - -
192C GLY 3.1 16.3 + - - -
194C ASN* 4.6 8.1 + - - +
169G HIS* 2.9 39.9 + - - -
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Residues in contact with PHE 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLN* 5.6 3.8 + - - -
136C ARG* 3.7 52.1 + - + +
138C SER 4.7 1.4 + - - -
184C ASN* 1.3 79.0 - - - +
186C ARG* 1.3 69.6 + - - +
187C SER* 4.0 26.0 + - - -
190C GLU* 3.4 39.3 - - + -
191C TRP* 3.5 39.9 - + + -
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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