Contacts of the strand formed by residues 259 - 265 (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 ASP 259 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170F ARG* 3.1 42.5 + - - +
201F ASP* 4.0 13.1 + - - +
202F CYS* 3.4 15.8 - - - +
203F VAL* 3.0 25.5 + - - +
258F LYS* 1.3 72.2 - - - +
260F VAL* 1.3 60.9 + - - +
261F ILE* 4.3 3.1 - - + -
306F ASN* 4.9 0.2 - - - +
311F GLY* 3.4 8.5 - - - -
312F SER* 2.8 34.4 + - - +
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Residues in contact with VAL 260 (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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203F VAL* 3.6 20.0 - - + +
205F MET* 4.4 9.6 - - + -
250F ALA* 3.7 41.1 - - + +
253F LEU* 3.9 21.1 - - + -
254F VAL* 4.0 2.0 - - + -
258F LYS* 3.9 11.0 - - + +
259F ASP* 1.3 78.3 - - - +
261F ILE* 1.3 59.5 + - - +
262F ILE* 4.1 8.5 - - + -
312F SER* 2.7 13.1 + - - +
313F LEU* 3.4 12.0 - - + +
314F THR* 2.8 34.3 + - - +
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Residues in contact with ILE 261 (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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145F LEU* 3.7 26.5 - - + -
168F ILE* 6.3 0.2 - - + -
170F ARG* 5.1 0.7 - - + +
195F ILE* 4.8 11.0 - - + -
202F CYS* 3.5 34.3 - - + -
203F VAL 3.1 7.8 + - - +
204F LEU* 3.7 22.4 - - + +
205F MET* 2.7 33.1 + - - +
259F ASP* 4.2 6.1 - - + +
260F VAL* 1.3 76.1 - - - +
262F ILE* 1.3 59.1 + - - +
263F LEU* 4.2 18.6 - - + -
314F THR* 3.2 29.8 - - + +
316F ILE* 4.8 6.5 - - + -
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Residues in contact with ILE 262 (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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205F MET* 3.1 20.2 - - + +
207F LEU* 4.5 11.2 - - + -
246F VAL* 4.4 13.9 - - + -
247F ILE* 3.8 22.0 - - + -
250F ALA* 3.7 24.7 - - + -
260F VAL* 4.3 4.0 - - + -
261F ILE* 1.3 75.5 - - - +
263F LEU* 1.3 63.8 + - - +
264F LEU* 3.5 19.1 + - + +
300F PHE* 4.7 6.7 - - + -
313F LEU* 3.8 17.7 - - + -
314F THR 2.7 12.7 + - - +
315F ILE* 3.3 13.3 - - + +
316F ILE 2.9 27.4 + - - -
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Residues in contact with LEU 263 (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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188F LEU* 3.9 25.5 - - + +
191F ILE* 3.8 14.1 - - + -
192F ALA* 3.8 38.6 - - + +
204F LEU* 3.8 18.4 - - + -
205F MET 2.8 8.9 + - - -
206F VAL* 3.5 24.2 - - + +
207F LEU 2.9 23.9 + - - +
261F ILE* 4.2 7.4 - - + -
262F ILE* 1.3 69.0 - - - +
264F LEU* 1.3 63.5 + - - +
265F ASP* 3.8 0.3 + - - +
316F ILE* 3.6 39.0 - - + +
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Residues in contact with LEU 264 (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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188F LEU* 4.5 2.9 - - - +
207F LEU* 3.4 22.0 - - + +
209F ILE* 3.7 30.1 - - + -
262F ILE* 3.5 13.8 + - + -
263F LEU* 1.3 74.0 - - - +
265F ASP* 1.3 76.9 + - - +
266F SER 4.2 2.5 - - - +
267F ILE* 3.7 25.6 - - + -
270F LEU* 4.4 2.9 - - + -
300F PHE* 3.6 23.1 - - + -
315F ILE* 4.7 3.4 - - + -
316F ILE 3.1 8.3 + - - +
317F ALA* 3.4 28.4 - - + -
318F THR* 3.2 24.6 + - - +
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Residues in contact with ASP 265 (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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184F LYS* 3.3 16.8 - - - +
185F THR* 5.1 5.0 + - - +
188F LEU* 3.5 15.7 - - + +
207F LEU 2.7 18.9 + - - +
208F LEU* 3.4 25.8 - - + +
209F ILE* 3.7 14.5 + - - +
211F GLU* 3.4 17.2 - - - +
219F MET* 4.6 4.3 - - - +
263F LEU 3.8 0.2 + - - -
264F LEU* 1.3 73.3 - - - +
266F SER* 1.3 77.4 + - - +
318F THR* 3.2 11.3 + - - -
6701F FPD 3.0 24.4 + - - +
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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