Contacts of the strand formed by residues 233 - 238 (chain B) in PDB entry 1ZQ1
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 VAL 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ALA* 3.6 20.6 - - - +
188B LEU* 3.5 30.7 - - + +
189B SER* 3.7 14.8 + - - +
192B LEU* 4.0 10.1 - - + -
195B LEU* 4.2 3.8 - - + +
199B VAL* 3.2 26.5 - - + +
201B LEU* 3.7 25.4 - - + -
232B GLU* 1.3 77.6 - - - +
234B MSE 1.3 65.7 + - - +
250B ARG* 3.9 2.1 - - - +
251B GLY* 2.9 21.3 + - - -
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Residues in contact with MSE 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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198B PRO* 4.5 7.0 - - + -
199B VAL 2.9 9.4 + - - +
200B VAL* 3.3 33.1 - - + -
201B LEU* 2.9 29.6 + - - +
225B MSE 3.6 44.2 - - + +
230B VAL* 3.8 13.0 - - + -
232B GLU* 3.7 11.0 - - + +
233B VAL* 1.3 81.6 - - - +
235B VAL* 1.3 70.8 + - - +
236B VAL* 4.1 4.0 - - + -
248B ALA* 4.2 3.4 - - - -
249B HIS 3.1 12.3 - - - +
251B GLY 3.9 1.3 - - - +
273B ILE* 3.3 33.9 - - + -
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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
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181B MSE 3.8 24.5 - - + +
182B GLY* 5.4 1.3 - - - -
185B ALA* 3.8 27.8 - - + -
201B LEU* 3.8 9.9 - - + +
234B MSE 1.3 78.1 - - - +
236B VAL* 1.3 63.7 + - - +
237B MSE 3.8 23.3 - - + -
247B LEU 3.2 1.8 - - - +
248B ALA* 3.3 2.4 - - - -
249B HIS* 2.6 37.2 + - + +
251B GLY* 4.6 0.4 - - - -
254B VAL* 3.9 34.1 - - + -
265B PHE* 4.6 5.8 - - + -
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Residues in contact with VAL 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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200B VAL* 3.9 17.5 - - + -
201B LEU 3.5 4.9 + - - +
202B VAL* 3.6 21.1 - - - +
218B ASN* 4.2 3.0 - - - +
221B CYS* 3.8 15.9 - - + -
222B SER* 3.6 15.9 - - - +
225B MSE 3.8 24.0 - - + -
234B MSE 4.7 4.0 - - + -
235B VAL* 1.3 79.8 - - - +
237B MSE 1.3 66.3 + - - +
246B CYS* 3.9 7.2 - - + -
247B LEU 3.1 3.8 - - - +
248B ALA* 4.0 12.3 - - + -
276B ILE* 3.7 24.5 - - + -
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Residues in contact with MSE 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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178B THR* 6.2 0.4 - - - -
181B MSE 4.6 6.3 - - - +
203B GLY* 2.9 35.4 - - - +
204B ALA* 4.9 0.7 - - - -
205B GLN* 4.9 3.8 - - + +
214B ASP* 3.4 11.9 - - - +
218B ASN* 2.8 42.2 - - - +
235B VAL* 3.8 20.4 - - + -
236B VAL* 1.3 79.8 - - - +
238B HIS* 1.3 69.0 + - - +
246B CYS* 3.1 6.6 - - - -
247B LEU* 2.6 38.3 + - - +
249B HIS* 4.8 3.2 + - - +
262B ARG* 4.6 7.0 - - - +
265B PHE* 3.9 35.0 - - + -
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Residues in contact with HIS 238 (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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214B ASP* 3.2 37.4 + - + +
217B MSE 3.8 22.2 - - + -
218B ASN* 3.1 31.1 + - - -
237B MSE 1.3 82.5 - - - +
239B GLY* 1.3 60.9 + - - +
240B GLU 3.5 15.7 - - - +
242B GLY 3.2 23.6 - - - -
243B ASP* 2.9 25.8 + - - -
245B TYR 3.9 5.8 - - - -
246B CYS* 4.0 3.8 - - - -
247B LEU* 4.7 2.1 - - - +
249B HIS* 4.9 0.3 + - - -
262B ARG* 3.5 38.8 + - + +
263B ASP* 4.5 0.3 - - - -
265B PHE 4.7 5.2 - - - +
266B ARG* 4.2 5.5 + - - -
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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
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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