Contacts of the strand formed by residues 182 - 185 (chain C) in PDB entry 3HYW
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 MET 182 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C VAL* 3.4 13.0 - - + +
148C ILE* 4.1 20.4 - - + -
164C ALA* 3.2 32.5 - - + +
167C LEU* 4.2 9.6 - - + -
168C HIS* 4.0 20.2 - - + +
171C LEU* 4.0 7.6 - - - -
177C ARG* 3.5 39.1 - - - +
180C VAL* 3.9 6.3 - - + +
181C PRO* 1.3 78.7 - - - +
183C THR* 1.3 66.6 + - - +
214C ASN 4.1 1.2 + - - +
215C ILE* 3.8 18.6 - - + -
216C ASP* 2.9 29.2 + - - +
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Residues in contact with THR 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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146C VAL* 3.0 11.4 + - - +
147C VAL* 3.4 12.9 - - - +
148C ILE* 2.9 28.5 + - - +
181C PRO* 5.4 2.4 - - - +
182C MET* 1.3 78.1 + - - +
184C PHE* 1.3 63.8 + - - +
185C ILE* 3.9 23.3 - - + -
215C ILE* 4.7 2.0 - - - -
216C ASP* 3.2 25.0 + - + +
218C ILE* 3.9 17.9 - - + -
243C VAL* 4.5 11.4 - - + +
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Residues in contact with PHE 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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148C ILE* 3.1 20.4 - - + -
149C GLY* 4.2 5.2 - - - -
150C ALA* 5.9 1.1 - - + -
157C PHE* 6.0 1.3 - + - -
160C ALA* 3.6 39.7 - - + -
161C TYR* 3.5 46.4 - + - -
164C ALA* 4.1 8.1 - - + -
183C THR* 1.3 72.9 - - - +
185C ILE* 1.3 64.2 + - - +
186C THR* 3.8 20.4 - - - -
188C GLU* 4.8 0.2 - - - -
191C LEU* 4.2 9.6 - - + -
210C PHE* 3.6 34.1 - + + -
215C ILE* 4.1 4.3 - - + -
216C ASP 2.7 12.1 + - - +
217C TRP* 3.1 3.7 - - + +
218C ILE 2.8 26.9 + - - +
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Residues in contact with ILE 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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147C VAL* 3.7 24.0 - - + -
148C ILE 2.8 9.9 + - - -
149C GLY* 3.1 4.8 - - - -
150C ALA 2.9 26.1 + - - +
183C THR* 3.9 13.9 - - + -
184C PHE* 1.3 77.3 - - - +
186C THR* 1.3 63.5 + - - +
218C ILE* 3.3 17.7 - - + +
221C VAL* 3.5 28.0 - - + -
223C VAL* 3.6 20.4 - - + -
231C VAL* 4.1 11.4 - - + -
233C TYR* 3.9 24.9 - - + -
243C VAL* 4.5 7.2 - - + -
250C PHE* 3.9 5.4 - - + -
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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