Contacts of the strand formed by residues 182 - 187 (chain B) in PDB entry 2GB0
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 182 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B HIS* 5.7 3.4 - - - -
177B ASP 4.9 0.2 - - - -
179B SER* 2.8 44.7 + - - +
181B ASP* 1.3 85.9 + - - +
183B VAL* 1.3 71.2 + - - +
184B LYS* 5.9 0.5 - - - +
193B THR* 5.5 5.2 - - - +
194B ALA 3.4 14.1 - - - -
195B ASP* 4.6 2.2 - - - -
335B ASN* 3.8 2.9 - - - +
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 5.0 4.7 - - + -
177B ASP 3.7 5.6 - - - -
178B ILE* 4.1 15.0 - - + -
182B SER* 1.3 83.3 - - - +
184B LYS* 1.3 63.5 + - - +
185B ILE* 6.3 0.7 - - + -
193B THR* 3.1 7.3 - - - -
194B ALA* 2.8 49.8 + - + +
195B ASP 4.0 4.7 - - - +
196B LYS 3.7 17.7 - - - +
197B LEU* 3.9 20.2 - - + -
335B ASN* 3.7 35.9 - - - +
336B VAL* 4.4 0.4 - - + -
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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
----------------------------------------------------------
7B ILE* 5.5 0.4 - - - -
176B PHE* 3.5 6.6 - - - +
177B ASP* 2.9 58.3 + - + +
178B ILE* 4.7 0.9 - - - +
182B SER* 5.9 0.7 - - - +
183B VAL* 1.3 78.9 - - - +
185B ILE* 1.3 74.8 + - - +
186B GLU* 2.7 34.2 + - + -
191B SER* 4.0 12.3 + - - -
192B TYR 3.2 12.8 - - - +
193B THR* 3.9 17.3 - - + -
197B LEU* 5.9 0.4 - - - +
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Residues in contact with ILE 185 (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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7B ILE* 3.9 25.1 - - + -
9B VAL* 4.2 8.5 - - + -
32B VAL* 4.0 19.5 - - + -
173B VAL* 4.0 26.7 - - + -
175B ASP 3.9 4.7 - - - -
176B PHE* 3.9 23.8 - - + -
183B VAL* 6.3 0.9 - - + -
184B LYS* 1.3 81.8 - - - +
186B GLU* 1.3 63.3 + - - +
187B THR* 4.6 5.2 - - + -
191B SER* 3.3 5.4 - - - -
192B TYR* 2.7 62.9 + - + +
197B LEU* 4.7 7.9 - - + -
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Residues in contact with GLU 186 (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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172B ARG 4.8 0.7 - - - +
173B VAL* 4.7 2.9 - - - +
174B GLU* 4.5 19.8 + - + +
175B ASP* 4.1 15.8 + - + +
184B LYS* 2.7 36.9 + - + -
185B ILE* 1.3 75.3 - - - +
187B THR* 1.3 73.2 + - - +
190B GLY 4.2 1.9 - - - -
191B SER* 3.6 17.0 + - - -
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Residues in contact with THR 187 (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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32B VAL* 5.0 0.2 - - + -
168B LEU* 4.6 2.6 - - + +
171B THR* 3.5 32.2 - - + +
172B ARG 5.2 4.0 - - - +
173B VAL* 4.9 6.3 - - + -
174B GLU* 6.2 1.6 - - - -
185B ILE* 4.6 11.2 - - + -
186B GLU* 1.3 84.9 + - - +
188B ALA* 1.3 69.8 + - - +
189B ASN* 3.9 2.9 + - - +
190B GLY* 2.4 49.0 + - - +
192B TYR* 3.3 23.4 + - + -
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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
------------------------------------------------------------
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