Contacts of the strand formed by residues 181 - 188 (chain A) in PDB entry 1FR8
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 LYS 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A SER 5.0 6.1 - - - +
179A PRO 3.6 4.2 + - - +
180A HIS* 1.3 71.4 - - - +
182A VAL* 1.3 60.0 + - - +
212A ASP* 3.3 15.7 - - + +
243A TYR* 3.4 35.4 + - + +
244A ASP* 2.7 43.4 + - - +
245A TYR* 3.5 18.7 - - - -
246A ASN* 3.0 42.1 + - - +
247A CYS 3.1 8.3 + - - +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A HIS* 3.8 25.1 - - + +
181A LYS* 1.3 75.6 - - - +
183A ALA* 1.3 67.2 + - - +
184A ILE* 3.9 9.6 - - + -
211A LEU* 4.4 8.5 - - + -
212A ASP 3.0 6.7 + - - -
213A TYR* 3.0 33.0 - - + +
214A GLY 3.1 4.2 + - - -
245A TYR* 3.7 3.6 - - - -
247A CYS* 3.5 21.8 - - - +
249A VAL* 3.4 33.0 - - + -
264A TYR 3.7 16.4 - - - +
265A ARG* 4.3 1.6 - - - -
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A VAL* 1.3 73.0 - - - +
184A ILE* 1.3 62.6 + - - +
185A ILE* 3.7 6.9 + - + +
214A GLY 3.7 5.2 - - - -
216A TYR* 4.2 2.5 - - + -
239A ALA* 4.0 8.1 - - + -
245A TYR* 3.5 37.0 - - + -
247A CYS 3.1 6.3 + - - -
248A PHE* 3.4 21.9 - - + -
249A VAL 3.0 22.3 + - - +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A VAL* 3.9 16.4 - - + -
183A ALA* 1.3 71.2 - - - +
185A ILE* 1.3 65.6 + - - +
186A ILE* 4.1 11.7 - - + -
198A TRP* 3.9 29.8 - - + -
206A LEU* 4.4 14.4 - - + -
211A LEU* 5.7 0.2 - - + -
213A TYR* 4.0 20.4 - - + -
214A GLY 3.0 18.7 + - - +
215A ILE* 4.0 15.4 - - + +
216A TYR* 2.9 28.6 + - - +
249A VAL* 3.4 26.9 - - + +
251A SER* 4.5 8.3 - - - -
264A TYR* 4.6 7.9 - - + +
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Residues in contact with ILE 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ALA* 4.0 23.1 - - + +
184A ILE* 1.3 82.0 - - - +
186A ILE* 1.3 65.9 + - - +
187A PRO* 3.9 2.0 - - - +
216A TYR* 3.7 13.9 - - + -
218A ILE* 3.9 13.2 - - + -
232A LEU* 3.9 23.1 - - + +
235A GLY* 3.7 41.3 - - - +
236A PHE 4.4 0.2 - - - +
239A ALA* 4.3 1.1 - - + -
248A PHE* 4.4 5.8 - - + -
249A VAL 2.7 16.3 + - - +
250A PHE* 3.5 23.1 - - + -
251A SER 3.0 25.8 + - - +
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Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ILE* 4.1 10.8 - - + +
185A ILE* 1.3 82.6 - - - +
187A PRO* 1.3 73.5 - - - +
188A PHE* 3.3 5.2 + - + +
195A LEU* 4.5 7.0 - - + -
198A TRP* 3.8 48.9 - - + +
215A ILE* 4.5 10.3 - - + -
216A TYR 2.9 16.1 + - - +
217A VAL* 3.7 7.4 - - + -
218A ILE 2.9 25.8 + - - -
251A SER* 3.5 14.6 - - - +
253A VAL* 3.4 31.9 - - + +
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Residues in contact with PRO 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GDU 3.0 31.6 + - - +
186A ILE* 1.3 89.1 - - - +
188A PHE* 1.3 57.8 + - - +
218A ILE* 3.8 5.2 - - + +
226A PHE* 4.0 14.6 - - + -
228A ARG* 3.8 37.0 - - + +
231A LEU* 4.3 8.5 - - + -
232A LEU* 3.5 23.5 - - + -
251A SER 3.2 16.4 - - - +
252A ASP* 4.2 4.3 - - - +
253A VAL* 4.5 1.0 - - - +
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Residues in contact with PHE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GDU 3.6 4.5 - - - -
186A ILE* 3.9 1.6 - - + +
187A PRO* 1.3 75.8 - - - +
189A ARG* 1.3 75.4 + - - +
190A ASN* 3.7 12.6 - - - -
191A ARG* 3.2 50.0 - - + -
192A GLN* 3.6 22.2 - - + -
195A LEU* 4.4 8.7 - - + -
217A VAL* 3.2 35.4 - - + -
218A ILE 2.8 12.7 + - - +
219A ASN* 3.2 21.1 - - + -
220A GLN 3.0 23.0 + - - -
226A PHE* 3.5 7.2 - - - -
253A VAL* 4.4 13.9 - - + -
393A LYS* 4.3 16.8 - - - -
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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