Contacts of the strand formed by residues 226 - 231 (chain F) in PDB entry 1XPU
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 GLU 226 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F ALA* 3.5 23.7 - - + +
72F TYR* 3.0 24.5 + - - -
203F VAL* 6.0 3.4 - - + -
204F LEU 3.0 12.2 + - - +
205F MET* 3.4 21.1 - - + +
206F VAL* 2.9 25.9 + - - +
223F VAL* 5.4 0.2 - - - -
225F GLY* 1.3 70.3 - - - -
227F VAL* 1.3 63.0 + - - +
228F VAL* 3.9 12.7 + - + +
249F LYS* 3.3 26.2 + - - -
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Residues in contact with VAL 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F ALA 4.7 5.7 - - - +
71F SER* 4.4 2.3 + - - -
206F VAL* 3.4 14.4 - - + +
208F LEU* 4.2 11.7 - - + -
216F VAL* 5.1 1.6 - - + +
219F MET* 3.9 33.2 - - + +
220F GLN* 4.1 39.3 + - + +
223F VAL* 3.6 34.5 - - + +
225F GLY 3.7 7.3 + - - +
226F GLU* 1.3 75.9 - - - +
228F VAL* 1.3 65.6 + - - +
229F ALA* 4.2 2.4 + - + -
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Residues in contact with VAL 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F ALA 4.7 5.6 - - - +
71F SER* 3.7 17.0 - - - -
72F TYR* 3.6 40.2 - - + +
205F MET* 4.8 2.7 - - + -
206F VAL 2.8 11.3 + - - +
207F LEU* 3.3 9.8 - - - +
208F LEU 3.0 22.0 + - - -
226F GLU* 4.1 20.0 - - + +
227F VAL* 1.3 77.2 - - - +
229F ALA* 1.3 62.0 + - - +
242F VAL* 3.4 24.7 - - + -
246F VAL* 3.8 15.7 - - + -
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Residues in contact with ALA 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F SER* 3.0 29.0 + - - +
208F LEU* 3.1 29.2 - - + +
216F VAL* 3.8 35.5 - - + +
220F GLN* 6.0 1.3 - - - +
227F VAL* 4.2 2.6 + - + -
228F VAL* 1.3 76.3 - - - +
230F SER* 1.3 60.3 + - - +
231F THR* 4.2 1.3 + - - +
234F GLU* 4.7 0.7 - - - +
238F ARG* 4.5 1.6 + - - -
242F VAL* 4.7 3.1 - - - -
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Residues in contact with SER 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F LEU 2.8 9.5 + - - +
209F ILE* 3.7 9.9 - - - +
210F ASP 2.8 34.0 + - - -
211F GLU* 3.1 5.7 + - - -
229F ALA* 1.3 75.2 - - - +
231F THR* 1.3 59.3 + - - +
234F GLU* 3.4 15.5 - - - -
238F ARG* 4.2 4.9 - - - -
239F HIS* 2.9 30.0 + - - -
242F VAL* 3.8 22.8 - - - +
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Residues in contact with THR 231 (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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210F ASP* 4.2 0.4 - - - -
211F GLU 3.0 13.9 - - - +
213F PRO* 3.8 29.8 - - + -
216F VAL* 3.9 15.9 - - + -
229F ALA 5.6 1.3 - - - +
230F SER* 1.3 73.2 - - - +
232F PHE* 1.3 64.1 + - - +
233F ASP* 2.6 27.2 + - - -
234F GLU* 3.2 24.9 + - - +
239F HIS* 3.2 19.6 - - - -
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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