Contacts of the strand formed by residues 225 - 228 (chain A) in PDB entry 4PEI
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 TYR 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ASP 3.1 11.1 + - - +
176A ILE* 4.4 10.1 - - + -
177A SER 2.9 23.9 + - - -
223A PRO* 3.3 12.3 - - - +
224A LYS* 1.3 100.3 - - + +
226A TRP* 1.3 60.3 + - - +
227A ILE* 4.4 13.9 - - + -
242A THR* 4.2 0.9 - - - -
243A HIS* 3.3 40.7 + + + +
245A ILE* 3.9 17.3 - - + -
259A LEU* 4.1 24.7 - - + +
261A LEU* 4.0 31.3 - - + +
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Residues in contact with TRP 226 (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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129A VAL* 4.6 2.7 - - + -
177A SER* 3.2 37.7 - - - -
178A LEU 4.7 0.9 - - - -
179A SER* 2.8 28.9 + - - -
183A PRO* 3.3 16.3 - - + +
214A ASN* 3.6 37.5 - - + -
217A ILE* 3.6 25.1 - - + -
218A LEU* 3.5 49.4 - - + -
221A LEU* 5.7 0.4 - - + -
223A PRO* 3.7 10.8 - - + -
225A TYR* 1.3 73.1 - - - +
227A ILE* 1.3 67.1 + - - +
228A SER* 3.3 14.2 + - - -
242A THR* 4.0 6.4 - - + +
243A HIS 3.0 7.7 + - - +
244A PHE* 3.4 9.8 - + + -
245A ILE 3.0 25.1 + - - -
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Residues in contact with ILE 227 (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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11A ILE* 3.4 37.7 - - + -
12A VAL 5.4 0.2 - - - +
41A ILE* 5.8 1.6 - - + -
43A THR* 3.6 19.9 - - + +
176A ILE* 3.8 21.8 - - + -
177A SER 2.8 12.6 + - - +
178A LEU* 3.4 9.1 - - + -
179A SER 3.0 25.3 + - - +
225A TYR* 4.4 4.9 - - + -
226A TRP* 1.3 81.9 - - - +
228A SER* 1.3 65.9 + - - +
245A ILE* 3.3 16.2 - - + +
247A LEU* 4.1 20.4 - - + -
259A LEU* 4.0 13.9 - - + -
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Residues in contact with SER 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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43A THR* 3.9 6.3 + - - +
179A SER* 2.8 27.9 + - - -
180A HIS 3.5 12.1 - - - -
181A ASP 3.7 2.5 + - - -
182A TRP* 3.7 20.6 - - - -
183A PRO* 3.7 0.7 - - - +
226A TRP* 3.3 11.6 + - - -
227A ILE* 1.3 74.0 + - - +
229A GLY* 1.3 58.9 + - - +
230A HIS 4.2 0.2 - - - -
244A PHE* 3.4 11.4 - - - -
245A ILE 3.0 6.9 + - - +
246A ALA* 3.2 7.1 - - - +
247A LEU* 2.9 26.0 + - - +
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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