Contacts of the strand formed by residues 226 - 233 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A GLY 4.8 3.1 - - - +
189A ALA* 3.9 32.4 + - + +
192A GLN* 3.4 19.3 + - + +
218A GLU* 3.4 33.0 - - + +
219A HIS 3.5 4.3 - - - +
220A THR* 4.2 10.7 - - - +
224A GLY 3.8 7.2 - - - +
225A ASP* 1.3 92.0 - - + +
227A VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A GLN* 6.0 2.9 - - + +
182A GLY* 5.7 2.2 - - - -
184A VAL 5.9 2.5 - - - +
192A GLN* 3.6 15.3 - - - +
218A GLU* 3.4 2.7 - - - -
219A HIS* 2.6 44.8 + - + +
221A ASP* 3.9 27.1 - - + +
225A ASP* 3.9 5.8 - - + +
226A PRO* 1.3 79.5 - - - +
228A GLY* 1.3 66.7 + - - +
229A TYR* 3.7 32.3 - - + +
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Residues in contact with GLY 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLY* 3.7 5.4 - - - -
183A LEU* 3.2 32.4 + - - +
192A GLN* 3.1 24.2 + - - +
196A MET* 4.1 14.6 - - - -
217A VAL 3.4 7.0 - - - -
218A GLU* 4.5 0.7 - - - -
227A VAL* 1.3 75.4 - - - +
229A TYR* 1.3 63.7 + - - -
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Residues in contact with TYR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLN* 3.5 27.1 + - + +
141A LEU* 3.8 32.2 - - + +
147A VAL* 4.8 1.6 - - + -
166A TYR* 4.1 10.8 - + - -
180A LEU* 4.1 20.0 - - + -
181A LYS* 3.4 22.7 - - - +
182A GLY* 3.6 14.6 - - - -
183A LEU* 4.1 5.9 - - - +
216A PHE* 3.5 7.4 - - - +
217A VAL* 2.7 41.4 + - + +
219A HIS* 3.7 28.8 - - + -
227A VAL* 3.7 31.8 - - + +
228A GLY* 1.3 74.9 - - - -
230A ILE* 1.3 61.7 + - - +
231A VAL* 5.3 0.2 - - + -
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Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL 3.4 1.4 - - - +
180A LEU* 3.2 7.3 - - - +
181A LYS* 2.9 45.9 + - + +
182A GLY 5.0 1.3 - - - +
183A LEU* 3.8 19.8 - - + +
199A ARG* 5.8 0.2 - - - -
202A LEU* 4.8 9.4 - - + -
213A ILE* 3.5 42.6 - - + -
215A ASN 3.9 2.9 - - - +
216A PHE* 3.6 25.4 - - + -
229A TYR* 1.3 74.3 - - - +
231A VAL* 1.3 65.1 + - - +
232A MET* 3.7 20.1 + - + -
294A LEU* 5.5 2.7 - - + +
295A GLY* 5.6 7.4 - - - +
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A TYR* 3.6 36.6 - - + +
178A VAL* 3.6 33.0 - - + -
179A VAL 3.3 3.1 - - - +
180A LEU* 4.0 14.4 - - + -
213A ILE* 3.6 4.7 - - - +
214A PHE* 2.7 39.6 + - + -
215A ASN* 3.0 25.9 + - + +
217A VAL* 4.2 14.6 - - + -
230A ILE* 1.3 76.7 - - - +
232A MET* 1.3 57.2 + - - +
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Residues in contact with MET 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A VAL* 3.4 9.4 - - - +
179A VAL* 2.7 43.1 + - + +
181A LYS* 4.0 15.3 - - + -
211A VAL* 4.0 6.1 - - + -
212A GLN 3.3 6.7 - - - +
213A ILE* 3.4 28.9 - - + -
214A PHE* 3.6 7.4 - - - -
230A ILE* 3.7 32.3 - - + +
231A VAL* 1.3 74.5 - - - +
233A GLU* 1.3 66.1 + - - +
292A ILE 3.7 11.9 - - - +
293A ASP* 5.3 3.6 - - - +
294A LEU 5.7 1.3 - - - -
753A AXX 3.6 41.5 - - + +
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Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 4.3 0.6 - - - +
210A ILE 4.5 1.6 - - - +
211A VAL* 3.7 12.9 - - + +
212A GLN* 2.9 53.5 + - - +
214A PHE* 3.3 25.3 - - + -
232A MET* 1.3 73.0 - - - +
234A TYR* 1.3 75.3 + - - +
235A VAL* 4.1 10.4 - - + +
290A LYS* 3.5 22.0 + - - -
753A AXX 3.0 23.6 + - - -
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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