Contacts of the strand formed by residues 181 - 184 (chain B) in PDB entry 2OG9
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 ILE 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ASN* 3.1 28.3 - - - +
154B THR 4.8 5.2 - - - +
155B SER* 3.3 13.5 - - - +
166B LEU* 5.1 0.2 - - + -
170B ALA* 3.9 23.1 - - + +
173B SER* 4.3 2.9 - - - -
174B ILE* 4.2 12.1 - - + -
178B ILE* 4.7 0.2 - - + -
180B GLY* 1.3 77.6 - - - +
182B LYS* 1.3 61.7 + - - +
183B LEU* 3.8 26.0 - - + -
200B VAL* 4.9 1.8 - - + -
204B LEU* 3.9 22.0 - - + -
208B VAL* 4.5 1.8 - - + -
209B PRO 3.1 7.2 + - - +
210B LEU* 3.3 19.3 - - + +
211B MSE 3.0 27.9 + - - -
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 3.8 28.1 + - + -
153B ASN 2.8 11.5 + - - +
154B THR* 3.4 43.1 - - + +
157B GLY* 5.5 0.3 - - - +
181B ILE* 1.3 75.9 - - - +
183B LEU* 1.3 64.0 + - - +
184B LYS* 4.1 10.6 + - - +
211B MSE 3.3 25.8 - - + +
212B VAL 4.4 1.1 - - - -
213B ASP* 3.1 36.7 + - + -
237B TRP* 4.5 0.4 - - - +
239B GLU* 3.2 28.8 + - - +
315B HIS* 4.7 9.9 + - - -
335B GLU* 4.2 16.2 + - - -
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B THR 5.5 0.7 - - - +
166B LEU* 3.5 40.2 - - + -
181B ILE* 3.8 15.0 - - + -
182B LYS* 1.3 76.6 - - - +
184B LYS* 1.3 65.2 + - - +
185B VAL* 3.6 1.0 + - + -
196B ARG* 5.0 1.6 - - + -
197B VAL* 4.0 26.2 - - + +
200B VAL* 3.8 24.7 - - + -
210B LEU* 3.7 30.1 - - + -
211B MSE 2.8 12.8 + - - +
212B VAL* 3.2 10.6 - - + +
213B ASP 2.9 24.1 + - - -
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Residues in contact with LYS 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B THR* 4.8 14.1 - - + -
157B GLY 3.6 22.2 + - - +
158B PHE* 4.2 24.6 - - + -
159B LEU* 3.4 34.8 - - + +
166B LEU* 6.0 2.4 - - - +
182B LYS* 4.1 10.0 + - - +
183B LEU* 1.3 74.5 - - - +
185B VAL* 1.3 65.8 + - - +
193B ASP* 4.3 0.7 - - - +
196B ARG* 4.8 7.8 + - - -
213B ASP* 3.6 21.8 + - + -
215B ASN* 3.5 33.0 + - - +
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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
------------------------------------------------------------
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