Contacts of the strand formed by residues 225 - 229 (chain F) in PDB entry 3KDO
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 THR 225 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150F LEU* 4.0 20.9 - - + -
181F LEU* 4.7 2.3 - - - +
186F ASP 3.2 3.4 + - - +
187F TYR* 3.1 38.5 - - + -
188F MET 3.2 4.3 + - - -
209F MET* 4.6 3.5 - - - +
213F ILE* 3.7 12.3 - - - +
224F LYS* 1.3 75.5 - - - +
226F TRP* 1.3 68.6 + - - +
227F PHE* 3.8 6.1 - - + -
250F LYS* 3.9 16.0 + - - +
251F HIS* 2.7 44.9 + - + +
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Residues in contact with TRP 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F PHE* 4.3 4.4 - + - -
188F MET* 3.2 30.7 - - + -
189F KCX 4.3 0.7 - - - -
190F ASP* 3.1 40.3 + - - +
202F PHE* 4.4 8.3 - + - -
205F ARG* 3.8 19.7 - - + -
206F ALA* 3.4 37.9 - - + -
209F MET* 3.6 39.4 - - + +
213F ILE* 4.2 5.8 - - + +
225F THR* 1.3 81.5 + - - +
227F PHE* 1.3 63.9 + - - +
228F ALA* 3.0 35.4 + - + -
244F LEU* 3.7 11.4 - - + -
249F LEU* 3.7 15.4 - - + +
251F HIS* 3.4 18.8 + - - +
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Residues in contact with PHE 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F LEU* 6.2 1.3 - - + -
157F ILE* 5.8 1.8 - - + -
187F TYR* 3.2 51.8 - + - -
188F MET 2.8 10.0 + - - -
189F KCX 3.7 22.2 - - + -
190F ASP* 3.0 25.1 + - - +
225F THR* 3.8 11.2 - - + -
226F TRP* 1.3 69.6 + - - +
228F ALA* 1.3 63.4 + - - +
229F ASN 3.5 1.2 + - - -
251F HIS* 3.6 44.4 - + + -
253F MET* 3.8 16.8 - - + +
279F HIS* 3.8 23.6 - + + -
312F GLN* 3.4 21.5 - - - -
387F VAL* 4.7 5.2 - - + -
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Residues in contact with ALA 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ASP* 3.3 6.5 - - - -
202F PHE* 3.7 6.7 - - + -
226F TRP* 3.0 46.6 + - + -
227F PHE* 1.3 68.5 - - - +
229F ASN* 1.3 58.5 + - - +
230F ILE* 3.1 11.4 + - - +
244F LEU* 3.6 20.6 - - + -
251F HIS 4.0 3.4 + - - +
252F ALA* 3.7 0.3 - - - -
253F MET* 2.7 27.0 + - - +
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Residues in contact with ASN 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F ASP* 2.8 24.5 + - + +
191F ASP 3.5 4.9 + - - -
192F GLU 3.1 26.7 + - - -
194F LEU 2.8 30.7 + - - +
195F THR* 4.3 8.2 - - - +
202F PHE* 3.4 17.5 - - - -
205F ARG* 4.3 1.2 + - - -
227F PHE 3.5 2.4 + - - -
228F ALA* 1.3 67.6 - - - +
230F ILE* 1.3 60.9 + - - +
231F THR* 2.5 34.5 + - - -
240F ARG* 4.9 1.2 + - - -
253F MET* 3.6 23.6 - - - +
255F ASP* 3.8 2.6 - - - +
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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