Contacts of the strand formed by residues 181 - 188 (chain C) in PDB entry 3WHD
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 ASN 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C ARG* 3.4 5.5 - - - +
147C ASP* 2.8 60.9 + - - +
150C ALA* 3.5 20.7 + - - +
154C TRP* 3.7 25.3 - - + -
176C ASN* 2.7 47.9 + - + +
177C SER* 5.0 0.3 - - - -
178C GLN 4.6 0.7 + - - -
179C GLY 3.6 7.7 - - - +
180C GLU* 1.3 70.8 - - - +
182C CYS* 1.3 60.3 + - - +
196C ASP* 4.7 1.7 + - - +
197C VAL 3.8 2.9 - - - -
199C CYS* 3.5 2.0 - - - -
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Residues in contact with CYS 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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105C TRP* 3.1 42.2 - - + -
142C PHE* 3.9 8.3 - - + -
145C LEU 3.6 4.9 - - - -
146C ARG* 3.7 7.4 - - - -
181C ASN* 1.3 71.5 - - - +
183C VAL* 1.3 66.6 + - - +
196C ASP* 3.1 7.3 - - - +
197C VAL* 2.7 36.8 + - - +
199C CYS* 2.0 50.6 - - - -
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Residues in contact with VAL 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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142C PHE* 3.6 5.7 - - - -
143C LEU* 2.8 45.4 + - + +
145C LEU* 3.3 39.9 + - + +
154C TRP* 3.7 18.8 - - + -
169C TRP* 4.0 10.8 - - + -
182C CYS* 1.3 80.2 - - - +
184C VAL* 1.3 76.1 + - - +
194C TRP* 4.0 25.4 - - + -
195C ASN 3.4 7.0 - - - +
197C VAL 4.7 0.2 - - - +
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Residues in contact with VAL 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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140C SER* 3.8 29.2 - - - +
141C TYR 3.1 16.2 - - - +
142C PHE* 3.5 33.4 - - + +
143C LEU* 4.6 0.9 - - - -
183C VAL* 1.3 78.4 - - - +
185C LEU* 1.3 65.8 + - - +
186C VAL* 4.2 1.3 - - + -
194C TRP* 3.3 5.0 - - - -
195C ASN* 2.9 59.9 + - + +
197C VAL* 4.4 13.2 - - + -
203C ALA* 4.3 5.6 - - + -
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Residues in contact with LEU 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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122C ILE* 4.1 11.2 - - + -
128C GLN* 3.7 27.6 - - + +
131C ILE* 3.8 22.7 - - + -
132C ILE* 4.1 9.2 - - + -
135C LEU* 3.7 24.7 - - + -
140C SER* 3.3 4.3 - - - -
141C TYR* 2.8 36.1 + - + +
143C LEU* 4.3 14.6 - - + +
184C VAL* 1.3 72.4 - - - +
186C VAL* 1.3 57.6 + - - +
192C TRP* 3.7 14.9 - - + -
193C ALA 3.6 16.6 - - - +
194C TRP* 3.8 11.0 - - + -
206C ILE* 4.1 8.7 - - + -
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Residues in contact with VAL 186 (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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139C LEU 4.5 5.2 - - - +
140C SER* 3.5 21.3 - - - +
170C HIS* 3.0 39.0 + - + +
184C VAL* 4.2 3.6 - - + -
185C LEU* 1.3 75.1 - - - +
187C TYR* 1.3 70.6 + - - +
188C ASN* 4.8 7.0 - - + +
192C TRP* 3.3 8.0 - - - -
193C ALA 3.0 15.0 + - - +
195C ASN* 3.6 32.5 - - + +
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Residues in contact with TYR 187 (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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137C ARG* 3.5 71.8 + - + +
139C LEU 4.7 1.6 + - - -
186C VAL* 1.3 77.5 - - - +
188C ASN* 1.3 67.3 + - - +
190C ASP* 3.3 39.7 + - - +
191C LYS* 3.5 21.8 - - - -
192C TRP* 3.4 44.1 - + + -
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Residues in contact with ASN 188 (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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170C HIS* 3.3 27.8 + - + +
186C VAL* 3.7 9.2 + - + +
187C TYR* 1.3 79.4 + - - +
189C GLN* 1.3 95.9 + - - +
190C ASP 3.2 1.6 - - - +
191C LYS* 3.0 18.5 + - - +
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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