Contacts of the strand formed by residues 226 - 233 (chain B) in PDB entry 2PZI
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 PRO 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B GLY 4.6 2.6 - - - +
188B ASP 5.4 0.2 - - - -
189B ALA* 4.1 31.6 - - + +
192B GLN* 3.4 17.8 + - + +
218B GLU* 4.1 25.4 - - + +
219B HIS 3.8 7.9 - - - +
220B THR* 4.5 4.7 - - - +
224B GLY 4.0 7.2 - - - +
225B ASP* 1.4 89.7 - - + +
227B VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN* 5.8 1.8 - - + +
182B GLY* 5.7 2.7 - - - -
184B VAL 5.8 3.8 - - - +
192B GLN* 3.7 16.6 - - - +
218B GLU* 3.3 5.3 - - - -
219B HIS 2.7 38.9 + - - +
220B THR 5.3 0.2 - - - -
221B ASP* 3.6 33.4 - - + +
225B ASP* 3.8 2.7 - - + +
226B PRO* 1.3 80.3 - - - +
228B GLY* 1.3 66.6 + - - +
229B TYR* 3.4 32.0 - - + +
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Residues in contact with GLY 228 (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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182B GLY* 3.7 3.5 - - - -
183B LEU* 3.4 28.5 + - - +
192B GLN* 3.0 22.3 + - - +
196B MET* 4.2 19.3 - - - -
217B VAL 3.3 6.1 - - - -
218B GLU* 4.3 2.0 - - - -
227B VAL* 1.3 76.7 - - - +
229B TYR* 1.3 64.8 + - - -
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Residues in contact with TYR 229 (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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140B GLN* 3.5 27.4 + - + +
141B LEU* 3.7 18.4 - - + +
166B TYR* 3.8 22.2 - + - -
180B LEU* 4.0 26.5 - - + -
181B LYS* 3.3 26.7 - - - +
182B GLY* 3.7 11.0 - - - -
183B LEU* 4.1 6.7 - - - +
216B PHE* 3.4 6.2 - - - +
217B VAL* 2.7 43.3 + - + +
219B HIS* 4.2 21.8 - - + -
220B THR 5.6 0.7 + - - -
221B ASP* 6.0 1.0 - - - +
227B VAL* 3.4 40.2 - - + +
228B GLY* 1.3 72.5 - - - -
230B ILE* 1.3 61.2 + - - +
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Residues in contact with ILE 230 (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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179B VAL 3.4 1.0 - - - +
180B LEU* 3.1 7.7 - - - -
181B LYS* 2.9 39.0 + - + +
182B GLY 5.0 1.1 - - - +
183B LEU* 3.8 20.4 - - + +
199B ARG* 5.9 0.2 - - - -
202B LEU* 4.3 12.1 - - + -
213B ILE* 3.5 37.2 - - + -
215B ASN 3.7 6.1 - - - +
216B PHE* 3.5 27.1 - - + -
229B TYR* 1.3 73.8 - - - +
231B VAL* 1.3 66.1 + - - +
232B MET* 3.7 22.9 - - + -
294B LEU* 5.6 4.0 - - + -
295B GLY* 5.8 4.3 - - - +
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Residues in contact with VAL 231 (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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151B TYR* 3.9 36.1 - - + +
178B VAL* 4.0 16.6 - - + -
179B VAL 3.2 4.9 - - - +
180B LEU* 4.1 14.4 - - + -
213B ILE* 3.8 5.0 - - - +
214B PHE* 2.8 46.1 + - + -
215B ASN* 2.9 38.0 + - + +
217B VAL* 4.2 13.2 - - + -
230B ILE* 1.3 75.1 - - - +
232B MET* 1.3 57.9 + - - +
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Residues in contact with MET 232 (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 VAL* 3.4 11.3 - - - +
179B VAL* 2.7 40.2 + - + +
181B LYS* 3.8 20.6 - - + -
211B VAL* 4.1 7.6 - - + -
212B GLN 3.4 6.7 - - - +
213B ILE* 3.6 26.0 - - + -
214B PHE* 3.7 7.0 - - - -
230B ILE* 3.7 28.5 - - + -
231B VAL* 1.3 73.2 - - - +
233B GLU* 1.3 66.0 + - - +
292B ILE 3.7 10.3 - - - +
293B ASP* 5.2 4.9 - - - +
294B LEU 5.8 1.3 - - - +
752B AXX 3.4 40.2 - - + -
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Residues in contact with GLU 233 (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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179B VAL* 4.1 0.4 - - - +
210B ILE 4.5 0.9 - - - +
211B VAL* 3.6 18.8 - - + +
212B GLN* 3.0 49.9 + - - +
214B PHE* 3.6 23.6 - - + -
232B MET* 1.3 73.9 - - - +
234B TYR* 1.3 70.5 + - - +
235B VAL* 3.5 10.0 + - - +
290B LYS* 3.5 24.8 + - - -
752B AXX 2.8 25.6 + - - -
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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