Contacts of the strand formed by residues 226 - 231 (chain B) in PDB entry 2ESN
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 GLU 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B LEU 5.1 8.5 + - - +
199B GLU 4.3 11.5 + - - +
200B ARG* 3.4 17.4 - - + +
201B HIS* 3.0 28.7 + - - -
224B ARG* 3.0 37.8 + - - +
225B ARG* 1.3 71.0 - - - +
227B VAL* 1.3 60.4 + - - +
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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
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200B ARG* 4.6 2.9 + - - -
201B HIS* 3.7 5.4 - - + +
203B VAL* 3.9 21.1 - - + -
215B ASP* 4.5 14.1 - - - +
224B ARG* 5.1 1.0 - - - +
225B ARG* 3.7 14.8 + - + +
226B GLU* 1.3 75.2 + - - +
228B ALA* 1.3 60.8 + - - +
229B VAL 3.8 22.7 - - - +
230B GLN* 4.0 16.6 - - + +
129D ARG* 3.1 55.7 + - - +
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Residues in contact with ALA 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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200B ARG* 3.4 39.2 - - + +
201B HIS 2.9 11.2 + - - +
226B GLU 3.9 2.2 + - - -
227B VAL* 1.3 74.3 - - - +
229B VAL* 1.3 60.3 + - + +
246B PHE* 3.6 29.8 - - + -
128D VAL 4.4 0.2 - - - +
129D ARG* 3.2 8.9 - - - +
130D LEU 2.9 25.1 + - - -
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B HIS 3.5 3.4 + - - +
202B ALA* 3.5 2.9 - - - -
203B VAL 2.8 30.8 + - - -
227B VAL* 3.8 5.3 - - - +
228B ALA* 1.3 86.2 - - + +
230B GLN* 1.3 71.3 + - - +
231B LEU* 4.1 3.8 - - + +
240B LEU* 3.9 25.4 - - + -
246B PHE* 4.1 17.9 - - + -
114D LEU* 3.9 26.7 - - + -
118D MET* 4.1 20.4 - - + -
130D LEU* 3.1 18.2 - - + +
132D LEU* 5.1 0.9 - - + -
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Residues in contact with GLN 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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203B VAL* 3.2 15.8 - - + +
205B THR* 3.9 20.9 - - + +
209B GLU 4.6 1.5 + - - -
210B ASP 3.3 25.0 + - - +
211B SER* 4.2 5.2 + - - -
215B ASP* 5.5 0.5 - - - +
227B VAL* 4.0 15.2 - - + +
229B VAL* 1.3 80.7 - - - +
231B LEU* 1.3 63.5 + - - +
100D THR* 6.1 0.6 - - - +
129D ARG* 4.3 18.7 + - - +
130D LEU 3.0 6.7 + - - -
131D ARG* 3.5 45.6 - - + +
132D LEU 2.8 25.7 + - - -
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Residues in contact with LEU 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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203B VAL 2.9 21.2 + - - +
204B VAL* 3.1 9.8 - - + -
205B THR* 2.8 22.5 + - - -
229B VAL* 4.1 16.2 - - + +
230B GLN* 1.3 78.0 - - - +
232B PRO* 1.3 72.9 - - + +
233B THR* 3.6 24.9 - - - +
236B ALA* 4.1 12.8 - - + -
237B ALA* 3.8 32.3 - - + +
240B LEU* 4.5 7.2 - - + -
110D ALA* 4.3 2.9 - - + -
114D LEU* 3.8 21.1 - - + -
132D LEU* 3.8 14.1 - - + -
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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