Contacts of the strand formed by residues 259 - 265 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ARG* 2.8 36.3 + - - +
201B ASP* 4.5 3.9 + - - +
202B CYS* 3.4 23.1 - - + -
203B VAL* 2.9 27.7 + - - +
257B LYS 4.4 1.7 - - - +
258B LYS* 1.3 75.4 - - - +
260B VAL* 1.3 61.4 + - - +
261B ILE* 6.1 0.7 - - + -
311B GLY* 3.2 23.2 - - - -
312B SER* 3.1 24.1 + - - +
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 3.5 13.9 - - + +
205B MET* 4.8 7.2 - - - -
250B ALA* 3.9 20.9 - - + +
253B LEU* 3.9 23.3 - - + -
254B VAL* 3.8 19.7 - - + -
258B LYS 3.9 2.7 - - - +
259B ASP* 1.3 77.7 - - - +
261B ILE* 1.3 67.1 + - - +
262B ILE* 4.1 10.3 - - + -
312B SER 2.9 9.7 + - - +
313B LEU* 3.7 24.6 - - + -
314B THR* 3.0 32.3 + - - +
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LEU* 3.8 24.7 - - + -
168B ILE* 5.9 0.7 - - + -
170B ARG* 5.7 0.9 - - + -
195B ILE* 4.4 19.1 - - + -
202B CYS* 3.9 27.1 - - + -
203B VAL 3.1 7.3 + - - +
204B LEU* 3.8 23.7 - - + +
205B MET* 2.8 33.3 + - - +
259B ASP* 6.1 0.7 - - + -
260B VAL* 1.3 75.2 - - - +
262B ILE* 1.3 61.1 + - - +
263B LEU* 4.2 18.6 - - + -
314B THR* 3.4 35.7 - - + +
316B ILE* 5.2 2.9 - - + -
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B MET* 3.2 16.6 - - + +
207B LEU* 4.3 11.4 - - + -
246B VAL* 4.0 27.1 - - + +
247B ILE* 4.4 15.0 - - + -
250B ALA* 3.6 28.7 - - + -
260B VAL* 4.1 10.1 - - + -
261B ILE* 1.3 77.2 - - - +
263B LEU* 1.3 70.3 + - - +
264B LEU* 4.5 0.9 - - + +
300B PHE* 4.5 11.9 - - + -
313B LEU* 3.9 11.0 - - + -
314B THR 2.8 10.3 + - - -
315B ILE* 3.2 18.3 - - + +
316B ILE 2.9 25.6 + - - -
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU* 3.9 40.6 - - + +
191B ILE* 4.2 17.5 - - + -
192B ALA* 4.0 20.2 - - + +
195B ILE* 5.4 0.2 - - + -
204B LEU* 4.0 25.4 - - + -
205B MET 3.0 6.3 + - - -
206B VAL* 3.4 18.2 - - + +
207B LEU 2.7 32.0 + - - +
261B ILE* 4.2 11.2 - - + -
262B ILE* 1.3 72.2 - - - +
264B LEU* 1.3 56.9 + - - +
265B ASP 4.0 0.3 + - - -
316B ILE* 3.3 34.1 - - + +
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B LEU* 4.1 3.3 - - - +
207B LEU* 3.2 31.9 - - + +
209B ILE* 3.6 29.2 - - + -
262B ILE* 3.7 5.4 + - + -
263B LEU* 1.3 73.0 - - - +
265B ASP* 1.3 61.3 + - - +
266B SER 3.8 6.1 - - - +
267B ILE* 3.8 24.9 - - + -
270B LEU* 4.1 6.5 - - + -
300B PHE* 3.7 23.8 - - + -
315B ILE* 4.7 7.2 - - + -
316B ILE 3.1 8.6 + - - +
317B ALA* 3.3 24.3 - - + -
318B THR* 2.9 31.7 + - - +
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Residues in contact with ASP 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B LYS* 3.1 33.2 - - - +
185B THR* 4.3 5.0 + - - +
188B LEU* 4.2 12.2 - - + +
207B LEU 2.5 11.5 + - - +
208B LEU* 3.5 27.8 - - + +
209B ILE 3.7 8.7 + - - -
211B GLU* 2.9 29.6 - - - +
219B MET* 5.2 0.3 - - - +
263B LEU 4.0 0.8 + - - -
264B LEU* 1.3 75.4 - - - +
266B SER* 1.3 76.9 + - - +
318B THR* 3.5 1.1 - - - -
2601B MG 3.9 5.9 - - - -
2701B FPD 3.0 17.5 + - - +
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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
------------------------------------------------------------
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