Contacts of the strand formed by residues 194 - 197 (chain B) in PDB entry 7UUT
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 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B VAL* 3.3 8.1 - - + +
172B VAL* 4.3 17.7 - - + -
183B VAL* 3.7 31.0 - - + +
186B ALA* 3.8 7.6 - - + -
187B LYS* 3.6 33.2 - - + +
191B ALA* 3.8 14.8 - - + -
192B GLY 3.5 1.4 + - - -
193B ARG* 1.3 76.5 - - - +
195B ILE* 1.3 63.9 + - - +
211B GLY 3.8 14.1 - - - +
212B ALA* 3.6 4.9 - - + -
213B THR* 2.8 37.7 + - - +
214B ASP 3.2 3.3 + - - -
313C ARG* 3.6 20.4 - - - +
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Residues in contact with ILE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B THR* 4.4 6.5 - - + -
170B VAL 2.8 14.5 + - - +
171B ALA* 3.2 7.3 - - + +
172B VAL 2.8 31.7 + - - +
193B ARG* 4.1 21.3 - - + +
194B ILE* 1.3 75.0 - - - +
196B ALA* 1.3 58.4 + - - +
197B VAL* 4.8 1.7 - - + +
214B ASP* 3.5 21.8 - - + +
216B VAL* 3.7 29.4 - - + -
227B ILE* 4.4 15.5 - - + -
230B LEU* 4.1 18.4 - - + -
231B THR* 4.1 24.2 - - + -
236B VAL* 4.4 8.1 - - + -
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL* 3.7 5.4 - - - +
175B ILE* 3.7 22.9 - - + -
183B VAL* 4.4 8.5 - - + -
194B ILE 3.8 0.8 + - - -
195B ILE* 1.3 73.8 - - - +
197B VAL* 1.3 56.1 + - - +
198B GLY 3.9 0.7 + - - -
207B ALA* 4.2 2.7 - - + -
212B ALA* 3.9 14.1 - - + -
214B ASP 2.8 7.2 + - - +
215B ILE* 3.3 25.7 - - + +
216B VAL* 2.8 31.5 + - - +
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ALA* 5.7 0.2 - - + -
172B VAL 3.0 12.6 + - - +
173B LEU* 3.6 30.1 - - + -
174B GLY* 3.2 25.6 + - - +
175B ILE* 3.8 6.8 + - - +
195B ILE* 4.8 3.1 - - + +
196B ALA* 1.3 76.8 - - - +
198B GLY* 1.3 60.8 + - - +
216B VAL* 3.4 25.4 - - + +
218B TYR 5.8 1.3 - - - +
223B ILE* 3.6 41.3 - - + -
227B ILE* 4.0 8.7 - - + -
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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