Contacts of the strand formed by residues 165 - 172 (chain B) in PDB entry 2FGY
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 PHE 165 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B PHE* 2.9 36.8 + - - +
161B LEU* 3.3 9.5 + - - +
163B CYS* 3.8 20.0 - - + -
164B GLY* 1.3 83.4 - - - +
166B HIS* 1.3 59.8 + - - +
167B ALA 3.9 13.2 - - - +
168B VAL* 4.4 7.2 - - + -
233B THR* 4.2 3.4 - - - -
234B ARG 3.2 8.3 - - - +
236B LEU* 3.8 23.3 - - + -
289B ASP* 3.3 25.8 - - + -
364B MET* 3.5 41.3 - - + -
367B PHE* 3.6 41.1 - + + -
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Residues in contact with HIS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ILE* 5.6 1.2 - - - +
160B PHE* 5.5 3.1 - - - -
161B LEU* 4.0 8.1 - - + -
165B PHE* 1.3 72.9 - - - +
167B ALA* 1.3 70.3 + - + +
193B PHE* 3.9 12.1 - - - +
213B TRP* 5.0 2.1 + - - -
216B ASN* 4.9 10.0 + - + +
217B GLU* 3.5 14.2 + - - -
220B ARG* 3.5 34.0 - - + +
226B PRO* 3.5 26.0 - - + +
227B ASN* 3.7 15.0 - - - +
233B THR* 3.0 27.1 + - - +
234B ARG* 3.1 12.6 + - - -
235B TYR* 3.4 35.0 + + + +
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PHE* 5.4 0.9 - - - -
165B PHE* 3.5 3.2 - - - +
166B HIS* 1.3 81.9 - - + +
168B VAL* 1.3 68.7 + - - +
169B ASP 4.1 0.2 - - - -
193B PHE* 3.5 13.0 - - + +
195B TYR* 4.2 4.5 - - + -
216B ASN* 3.6 24.7 - - - +
234B ARG 4.2 0.6 + - - -
235B TYR* 3.6 27.4 - - + -
236B LEU* 3.0 24.7 + - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PHE* 3.7 45.3 - - + -
165B PHE* 4.4 6.7 - - + -
167B ALA* 1.3 78.6 - - - +
169B ASP* 1.3 61.8 + - - +
170B ILE* 4.0 13.2 - - + -
188B LEU* 4.6 5.4 - - + -
193B PHE 2.8 9.3 + - - +
194B THR* 3.4 5.0 - - + +
195B TYR* 2.8 26.7 + - - +
236B LEU* 3.7 15.3 - - + -
238B ILE* 3.8 27.6 - - + -
367B PHE* 4.3 11.0 - - + -
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Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL* 1.3 75.0 - - - +
170B ILE* 1.3 58.0 + - - +
195B TYR* 3.8 12.7 - - + +
197B LYS* 2.9 34.0 + - - -
209B ASP* 3.9 5.7 - - - +
212B GLN* 4.7 0.2 - - - +
235B TYR* 2.7 35.9 + - + +
236B LEU 2.8 16.6 + - - +
237B LYS* 3.0 29.2 + - + +
238B ILE 2.7 32.9 + - - +
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL* 4.0 11.4 - - + -
169B ASP* 1.3 79.0 + - - +
171B SER* 1.3 63.7 + - - +
172B PRO* 3.5 3.1 - - + +
181B LEU* 3.6 27.4 - - + -
182B LEU* 4.0 21.5 - - + -
186B LEU* 4.3 6.3 - - + -
188B LEU* 3.7 29.2 - - + -
194B THR* 4.6 4.3 - - + -
195B TYR 2.9 15.4 + - - +
196B ARG* 3.2 5.5 - - - -
197B LYS 2.9 25.1 + - - -
238B ILE* 3.3 27.6 - - + +
240B VAL* 4.0 15.5 - - + -
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ILE* 1.3 70.9 + - - +
172B PRO* 1.3 66.8 - - - +
197B LYS* 2.9 21.5 + - - +
199B TYR* 4.7 1.1 - - - -
202B SER* 4.2 6.4 - - - -
204B PHE* 3.4 30.5 - - - +
237B LYS* 2.6 30.1 + - - +
238B ILE 2.8 10.4 + - - -
239B ALA* 3.4 5.7 - - - +
240B VAL 3.0 22.1 + - - +
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Residues in contact with PRO 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ILE* 3.5 15.7 - - + +
171B SER* 1.3 87.2 - - - +
173B CYS* 1.3 70.8 + - - +
178B LEU* 3.8 22.4 - - + +
181B LEU* 4.0 24.2 - - + -
196B ARG* 5.0 5.4 - - + -
197B LYS 3.7 11.6 - - - +
198B ALA* 3.2 15.5 - - + -
199B TYR 3.2 19.2 + - - +
202B SER* 4.0 5.3 - - - -
240B VAL* 3.7 12.3 - - + +
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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