Contacts of the strand formed by residues 191 - 196 (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 TRP 191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C GLN* 4.7 4.3 + - - +
131C ILE* 3.5 51.0 + - + +
134C LEU* 3.5 37.5 - - + -
135C LYS 3.3 24.9 - - - -
136C ARG* 3.7 29.5 - - + +
138C SER 4.0 7.4 - - - -
140C TYR* 4.2 1.1 - + - -
183C ILE* 3.8 14.1 - - + -
184C ASN* 3.4 40.6 - - - -
185C PHE* 3.5 29.4 - + + -
190C GLU* 1.3 85.0 + - + +
192C GLY* 1.3 57.3 + - - +
167G PHE* 4.8 0.9 - - - +
169G HIS* 3.5 2.7 + - - -
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Residues in contact with GLY 192 (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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127C GLN* 4.5 5.2 - - - -
183C ILE* 3.4 4.9 - - - +
184C ASN* 3.1 26.5 + - - +
191C TRP* 1.3 75.9 - - - +
193C TRP* 1.3 68.2 + - - -
167G PHE 3.2 12.6 - - - -
169G HIS* 3.1 25.1 + - - -
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Residues in contact with TRP 193 (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* 4.1 19.5 - - + +
127C GLN* 3.2 21.6 + - - +
142C LEU* 3.6 24.4 - - + +
144C LEU* 4.0 18.2 - - + -
181C ALA* 5.0 0.4 - - + -
182C ILE 3.1 7.2 - - - +
183C ILE* 4.1 12.0 - - + +
192C GLY* 1.3 79.5 - - - -
194C ASN* 1.3 60.1 + - - +
155G TRP* 3.8 21.8 - + - -
161G TYR* 4.8 0.2 - + - -
165G VAL 4.2 4.3 - - - -
166G THR* 3.6 28.5 - - + -
167G PHE* 2.7 53.0 + + + +
168G TRP* 3.5 39.2 - + + -
169G HIS* 2.8 31.4 + - - +
172G GLU* 3.7 2.4 - - - +
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Residues in contact with ASN 194 (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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199B HIS* 5.7 7.3 + - - +
181C ALA* 3.3 3.5 - - - -
182C ILE* 2.8 50.1 + - + +
184C ASN* 4.6 9.1 + - - +
186C ARG* 3.1 25.5 - - - +
192C GLY 4.2 0.2 + - - -
193C TRP* 1.3 74.2 - - - +
195C ASP* 1.3 77.3 + - - +
196C ILE* 4.8 5.4 - - - +
168G TRP* 3.8 7.0 - - - -
169G HIS* 4.6 3.1 - - + -
172G GLU* 3.1 27.7 + - - +
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Residues in contact with ASP 195 (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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179C ARG* 2.8 41.0 + - - +
180C CYS 3.4 3.6 - - - -
194C ASN* 1.3 80.8 + - - +
196C ILE* 1.3 68.2 + - - +
151G ARG* 5.2 1.6 + - - -
153G TRP* 3.4 32.4 - - + -
168G TRP* 3.9 3.2 - - + -
172G GLU* 3.7 5.2 - - - +
173G PRO* 3.2 13.1 - - + +
174G ASN* 3.0 39.4 + - - +
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Residues in contact with ILE 196 (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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200B VAL* 3.7 45.3 - - + -
141C PHE* 3.8 20.0 - - + -
179C ARG* 3.5 15.7 - - - +
180C CYS 2.9 39.2 + - - +
182C ILE* 3.8 35.4 - - + -
194C ASN* 4.8 5.8 - - - +
195C ASP* 1.3 81.6 - - - +
197C HIS* 1.3 75.6 + - - +
198C CYS 3.5 0.2 + - - -
200C VAL* 4.1 4.9 - - + -
202C GLN* 4.0 6.5 - - + -
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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