Contacts of the strand formed by residues 236 - 241 (chain B) in PDB entry 1I9R
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 SER 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B GLN* 3.0 28.8 + - - +
161B LEU 3.1 5.4 - - - -
162B THR* 2.9 25.8 - - - -
195B LEU* 3.5 1.1 - - - +
196B LYS* 2.6 54.8 + - - +
234B GLY 4.2 3.4 - - - -
235B ALA* 1.3 76.3 - - - +
237B VAL* 1.3 60.8 + - - +
238B PHE* 4.5 1.0 - - - -
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Residues in contact with VAL 237 (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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160B GLN* 2.9 18.7 - - - +
161B LEU* 2.7 34.2 + - + +
171B ILE* 4.2 22.4 - - + -
193B LEU* 3.9 10.8 - - + -
194B CYS 3.1 12.6 - - - +
195B LEU* 3.7 21.3 - - + -
205B LEU* 4.9 1.3 - - + -
231B LEU* 4.9 6.1 - - + -
236B SER* 1.3 79.3 - - - +
238B PHE* 1.3 64.5 + - - +
256B PHE* 3.4 23.6 - - + -
258B LEU* 4.2 15.0 - - + -
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Residues in contact with PHE 238 (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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137B VAL* 4.3 20.4 - - + -
159B LYS* 3.5 19.5 - - + +
160B GLN* 3.9 10.1 - - + +
192B SER 3.5 0.3 - - - +
193B LEU* 3.6 2.0 - - - -
194B CYS* 2.6 81.9 + - + -
195B LEU 4.1 4.0 - - - -
196B LYS* 4.2 18.6 - - + -
202B GLU* 3.9 28.3 - - + -
236B SER* 4.5 3.8 - - - -
237B VAL* 1.3 80.5 - - - +
239B VAL* 1.3 62.8 + - - +
240B ASN* 4.4 15.0 - - + -
256B PHE* 4.0 4.5 - - - -
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Residues in contact with VAL 239 (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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137B VAL* 3.7 4.5 - - - +
138B LEU* 2.9 45.4 + - + +
140B TRP* 3.4 28.8 - - + +
159B LYS 4.5 1.8 + - - -
173B ALA* 3.6 26.9 - - + -
175B VAL* 4.4 9.9 - - + -
191B ALA* 5.1 2.2 - - + -
192B SER 3.3 13.5 - - - +
193B LEU* 4.6 3.1 - - - +
225B LEU* 5.9 1.3 - - + -
238B PHE* 1.3 74.3 - - - +
240B ASN* 1.3 63.6 + - - +
241B VAL* 4.3 7.2 - - + -
256B PHE* 3.6 19.3 - - + -
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Residues in contact with ASN 240 (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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136B SER* 2.4 53.9 + - - +
137B VAL* 4.0 6.3 - - - +
138B LEU 4.4 0.2 - - - +
191B ALA* 3.4 0.2 - - - -
192B SER* 2.7 43.1 + - - +
194B CYS* 4.3 18.4 - - - -
238B PHE* 4.4 10.0 - - + -
239B VAL* 1.3 76.7 - - - +
241B VAL* 1.3 67.1 + - - +
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B SER* 2.6 38.8 + - - +
138B LEU* 3.7 36.6 - - + -
175B VAL* 5.1 3.4 - - + -
189B PHE* 3.7 24.5 - - + -
190B ILE 3.6 7.2 - - - +
191B ALA* 3.9 15.9 - - + -
239B VAL* 4.3 1.6 - - + -
240B ASN* 1.3 83.5 - - - +
242B THR* 1.3 62.2 + - - +
243B ASP 3.4 15.5 - - - +
244B PRO* 3.5 17.7 - - + -
247B VAL* 4.4 0.2 - - + -
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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