Contacts of the strand formed by residues 182 - 187 (chain V) in PDB entry 3FKS
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 SER 182 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92V LEU* 4.8 1.2 - - - +
175V ALA* 4.2 19.3 + - - +
178V HIS* 5.1 1.0 - - - -
180V GLY 4.1 4.7 + - - -
181V PHE* 1.3 78.4 + - - +
183V VAL* 1.3 65.3 + - - +
214V LYS* 4.1 10.0 + - - +
215V VAL* 3.1 21.2 - - - +
216V ALA* 2.9 24.4 + - - +
252V LEU* 3.2 24.3 - - - +
254V PHE* 4.5 10.1 - - - -
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Residues in contact with VAL 183 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182V SER* 1.3 79.9 - - - +
184V PHE* 1.3 61.4 + - - +
185V THR* 4.1 8.1 - - - +
216V ALA* 3.3 19.1 - - + +
218V VAL* 4.6 6.5 - - + -
236V GLY* 3.8 24.5 - - - +
239V ILE* 3.6 28.0 - - + -
240V ALA* 4.5 9.6 - - + +
243V PHE* 4.4 13.9 - - + -
251V VAL* 5.0 2.2 - - + -
252V LEU 2.9 9.5 + - - +
253V LEU* 3.3 15.3 - - + +
254V PHE* 2.8 28.5 + - - +
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Residues in contact with PHE 184 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167V ILE* 4.8 15.0 - - + -
171V ILE* 5.1 11.7 - - + -
182V SER 4.2 0.6 - - - -
183V VAL* 1.3 69.9 - - - +
185V THR* 1.3 75.4 + - - +
186V GLY* 4.4 4.0 - - - -
189V GLU* 5.7 2.5 - - + -
197V LEU* 3.7 37.0 - - + -
201V MET* 5.8 3.1 - - + -
215V VAL* 4.3 8.1 - - + +
216V ALA 3.0 8.9 + - - -
217V LEU* 3.7 18.8 - - + +
218V VAL 3.0 24.3 + - - +
219V PHE* 4.2 17.4 - + - -
254V PHE* 3.8 30.5 - + + -
256V ASP* 4.0 27.8 - - + -
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Residues in contact with THR 185 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183V VAL* 4.1 1.7 - - - +
184V PHE* 1.3 79.3 - - - +
186V GLY* 1.3 62.5 + - - +
187V VAL* 3.5 17.6 + - + -
218V VAL* 3.5 13.8 - - + +
232V VAL* 3.4 26.9 - - + +
233V ALA* 4.3 5.5 + - - +
236V GLY* 3.3 24.0 - - - -
253V LEU* 3.9 9.4 - - - +
254V PHE 2.8 17.7 + - - +
255V ILE* 3.9 8.0 - - + -
256V ASP* 3.1 26.3 + - - +
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Residues in contact with GLY 186 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184V PHE* 3.9 4.4 + - - -
185V THR* 1.3 73.0 - - - +
187V VAL* 1.3 60.0 + - - -
189V GLU* 4.5 2.7 - - - -
218V VAL 2.7 17.3 + - - -
219V PHE* 4.1 17.7 - - - -
220V GLY 2.9 27.9 + - - +
221V GLN* 3.0 12.1 - - - +
232V VAL* 4.2 0.6 - - - +
256V ASP 3.1 8.1 - - - -
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Residues in contact with VAL 187 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185V THR* 3.7 15.0 - - + +
186V GLY* 1.3 67.8 - - - +
188V GLY* 1.3 67.2 + - - +
189V GLU 3.2 1.6 - - - -
229V ARG* 3.5 24.2 - - + +
232V VAL* 3.6 9.2 - - + -
233V ALA* 3.7 31.6 - - + -
255V ILE* 4.5 13.7 - - + -
256V ASP 2.7 7.7 + - - -
257V ASN 2.7 42.1 + - - +
260V ARG* 3.3 9.3 - - + +
261V PHE* 4.0 20.6 - - + +
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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