Contacts of the strand formed by residues 171 - 175 (chain C) in PDB entry 5Y7K
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 ASP 171 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C TYR 3.7 0.3 - - - +
167C VAL* 3.2 5.2 - - - +
168C TRP 2.9 33.2 + - - +
169C ASN* 3.3 5.9 - - - +
170C ASN* 1.3 79.5 - - - +
172C ILE* 1.3 63.8 + - - +
173C TYR* 3.8 15.0 + - + +
184C ARG* 2.7 25.3 + - - +
186C THR* 3.0 33.8 + - - +
187C TRP 3.6 0.9 + - - +
189C GLY* 2.8 36.6 + - - +
196C ASN* 3.6 1.7 + - - -
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Residues in contact with ILE 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C ALA* 4.8 0.7 - - + -
166C TYR 3.5 6.5 - - - +
167C VAL* 4.1 3.1 - - + +
171C ASP* 1.3 68.5 - - - +
173C TYR* 1.3 73.6 + - - +
185C ILE* 2.7 50.8 + - + -
186C THR* 2.9 10.8 + - + +
196C ASN* 3.5 19.5 - - + +
197C GLY* 3.6 9.9 - - - +
214C LEU* 3.5 24.0 - - + -
223C LEU* 4.2 16.6 - - + -
225C TYR* 3.3 47.1 - - + -
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Residues in contact with TYR 173 (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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149C PRO* 5.0 3.6 - - + -
165C ALA* 3.2 4.5 - - - +
166C TYR* 2.8 79.3 + + + +
168C TRP* 3.6 42.2 + + + -
171C ASP* 4.1 13.2 - - + +
172C ILE* 1.3 85.6 - - - +
174C VAL* 1.3 65.1 + - - +
182C SER* 3.9 13.2 - - - -
183C TYR 3.4 4.3 - - - +
184C ARG* 3.3 59.0 + - + -
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C LYS* 5.3 0.4 - - + -
164C LEU 3.2 7.2 - - - +
165C ALA* 4.1 3.4 - - + -
172C ILE* 4.5 0.4 - - + -
173C TYR* 1.3 82.8 - - - +
175C LYS* 1.3 66.4 + - - +
176C ILE* 4.2 11.9 - - + -
182C SER* 3.3 2.4 - - - -
183C TYR* 2.7 44.2 + - + +
185C ILE* 3.5 26.9 - - + -
216C TRP* 4.5 8.1 - - + -
223C LEU* 3.6 26.2 - - + -
273C THR* 4.4 11.2 - - + -
276C LEU* 3.9 22.7 - - + -
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Residues in contact with LYS 175 (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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134C ILE* 5.1 2.2 - - + -
146C GLU* 3.2 30.4 + - - +
147C ARG 4.8 3.8 + - - -
148C ILE* 5.1 5.8 - - + +
162C HIS 4.3 0.5 - - - +
163C LYS* 3.6 2.6 - - - +
164C LEU* 2.5 59.4 + - + +
166C TYR* 3.5 21.0 + - + -
174C VAL* 1.3 72.0 - - - +
176C ILE* 1.3 66.3 + - - +
177C GLU 3.6 15.7 - - - +
178C PRO* 3.9 14.6 - - + +
180C LEU 3.3 22.8 + - - +
181C PRO 4.9 1.8 - - - -
182C SER* 3.1 36.2 + - - +
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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