Contacts of the strand formed by residues 233 - 237 (chain B) in PDB entry 2Z1Z
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 ILE 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 4.1 14.6 - - + +
24A VAL* 3.7 29.6 - - + -
139B PHE* 4.1 33.0 - - + -
200B ASP 2.8 12.1 + - - +
201B ILE* 3.2 9.4 - - + +
202B ILE 2.7 30.6 + - - -
232B SER* 1.3 74.1 - - - +
234B ILE* 1.4 70.4 + - - +
235B VAL* 4.5 1.8 - - + -
261B VAL 3.4 5.4 - - - +
263B MET* 4.3 4.9 - - + -
288B LEU* 4.2 20.0 - - + -
290B TYR* 4.2 2.9 - - + -
296B VAL* 4.2 24.2 - - + -
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Residues in contact with ILE 234 (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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202B ILE* 3.4 22.2 - - + +
204B PHE* 4.3 4.5 - - + -
223B LEU* 3.8 40.6 - - + +
224B VAL* 4.1 16.8 - - + +
227B ALA* 3.5 29.8 - - + -
232B SER 4.0 0.2 - - - -
233B ILE* 1.4 72.5 - - - +
235B VAL* 1.3 64.6 + - - +
236B TYR* 3.9 24.0 - - + +
252B ILE* 4.8 3.1 - - + -
261B VAL* 2.8 21.2 + - + +
262B ALA* 4.1 8.5 - - + -
263B MET* 3.1 31.0 + - - +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 5.6 1.6 - - + -
135B LEU* 3.8 22.9 - - + -
139B PHE* 4.0 18.4 - - + -
155B TYR* 5.8 1.3 - - + -
201B ILE* 3.6 24.9 - - + -
202B ILE 2.8 9.4 + - - +
203B PHE* 3.5 29.4 - - + -
204B PHE 2.8 31.9 + - - +
233B ILE* 4.5 1.3 - - + -
234B ILE* 1.3 73.7 - - - +
236B TYR* 1.3 56.7 + - - +
237B ASP* 3.8 1.6 + - + +
263B MET* 3.8 16.2 - - + -
265B THR* 4.1 19.5 - - + +
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Residues in contact with TYR 236 (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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204B PHE* 3.2 22.9 - + + -
206B SER* 3.6 37.2 + - - -
220B LEU* 3.9 27.6 - - + +
223B LEU* 5.4 0.2 - - + -
234B ILE* 3.6 8.7 - - + -
235B VAL* 1.3 73.5 - - - +
237B ASP* 1.3 54.5 + - - +
238B SER* 4.0 17.3 - - - -
244B MET* 5.5 0.3 - - - +
249B PRO 3.8 17.2 + - - -
250B ARG* 4.1 2.6 - - - -
251B SER* 4.0 4.7 + - - -
252B ILE* 3.6 45.1 - - + -
263B MET 2.9 17.5 + - - +
264B GLU* 3.2 26.8 - - + +
265B THR* 2.7 33.0 + - - +
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Residues in contact with ASP 237 (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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128B ALA* 5.2 1.3 - - - +
132B ILE* 4.4 2.6 - - - +
155B TYR* 2.6 36.8 + - + +
204B PHE 2.7 15.8 + - - +
205B CYS* 3.6 12.5 - - - -
206B SER 3.3 24.9 + - - +
207B PRO 4.7 0.2 - - - +
235B VAL* 3.8 2.2 + - + +
236B TYR* 1.3 71.0 - - - +
238B SER* 1.3 57.5 + - - +
239B ALA* 3.2 29.1 + - - +
240B TYR 5.0 0.2 + - - -
265B THR* 3.5 22.8 - - + +
501B PLP 3.2 21.2 + - - -
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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