Contacts of the strand formed by residues 227 - 231 (chain A) in PDB entry 4AOR
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 GLY 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A CYS* 3.2 5.9 - - - +
186A ALA 3.1 30.1 + - - -
194A ASP* 3.4 13.4 + - - -
216A TRP 3.9 1.6 - - - -
226A PRO* 1.3 75.6 - - - +
228A VAL* 1.3 58.1 + - - -
229A TYR* 3.3 12.6 - - - -
32D ARG* 3.4 28.5 - - - -
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Residues in contact with VAL 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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175A TYR* 3.6 39.0 - - + -
179A ILE* 4.0 6.3 - - + -
183A MET* 3.8 23.3 - - + -
184A PHE 3.6 6.1 - - - +
185A CYS* 4.0 5.4 - - - -
215A SER* 3.4 8.2 + - - -
216A TRP* 2.8 80.0 + - + +
226A PRO 3.9 1.1 - - - +
227A GLY* 1.3 74.4 - - - +
229A TYR* 1.3 66.4 + - - +
32D ARG* 4.7 0.5 + - - +
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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
----------------------------------------------------------
141A ILE* 3.5 19.7 - - + +
183A MET* 3.2 7.3 - - - -
184A PHE* 2.9 55.0 + + + +
186A ALA* 3.7 30.6 + - + -
194A ASP* 3.7 9.7 + - - -
195A SER* 2.8 31.2 + - - -
204A VAL* 3.3 26.7 - - + -
213A ILE 3.3 9.6 - - - +
214A VAL* 3.5 28.3 - - + -
215A SER* 4.2 1.8 - - - -
227A GLY* 3.3 27.6 - - - -
228A VAL* 1.3 78.4 - - - +
230A THR* 1.3 63.5 + - - +
32D ARG* 4.6 0.2 - - - -
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Residues in contact with THR 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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107A ASP* 2.9 50.7 + - - +
108A ILE* 4.2 7.9 - - + -
182A ASN 3.5 9.0 - - - +
183A MET* 4.7 2.2 - - - +
184A PHE* 3.8 0.4 - - - -
212A GLY* 3.2 21.3 - - - -
213A ILE* 3.1 22.6 + - + +
215A SER* 3.8 10.9 - - - -
229A TYR* 1.3 69.2 - - - +
231A LYS* 1.3 61.9 + - - +
232A VAL* 3.2 7.3 + - - +
235A TYR* 3.9 24.5 - - + +
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Residues in contact with LYS 231 (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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132A CYS* 3.7 16.6 - - - +
133A ALA 5.6 3.7 + - - +
181A SER 3.8 19.3 + - - +
182A ASN* 2.8 24.5 + - - +
183A MET 4.0 9.7 + - - +
184A PHE* 3.9 23.4 - - + +
211A GLN 3.8 4.3 - - - +
229A TYR 3.4 1.0 + - - -
230A THR* 1.3 69.9 - - - +
232A VAL* 1.3 63.5 + - - +
233A CYS* 3.6 28.9 - - - -
234A ASN* 3.1 19.5 + - - +
235A TYR* 3.2 15.0 - - - -
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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