Contacts of the strand formed by residues 205 - 208 (chain B) in PDB entry 1U8R
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 VAL 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 3.6 47.6 - - + +
155B THR* 5.4 0.9 - - - -
157B LEU* 6.1 1.1 - - + -
197B VAL* 4.0 22.7 - - + -
198B GLU 3.6 8.5 - - - +
199B THR* 4.7 8.7 - - - +
200B THR* 4.0 2.8 - - - +
203B GLY 4.8 1.6 - - - +
204B GLY* 1.3 84.2 - - - +
206B THR* 1.3 67.9 + - - +
207B ILE* 4.1 3.0 + - + +
215B VAL 4.2 0.2 - - - +
216B THR* 3.3 3.5 - - - +
217B LEU* 2.8 38.0 + - + +
222B ALA* 4.1 18.6 - - + -
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Residues in contact with THR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B THR 3.7 0.3 - - - +
197B VAL* 3.2 4.9 - - - -
198B GLU* 2.8 44.9 + - - +
200B THR* 4.3 11.6 + - - -
205B VAL* 1.3 74.6 - - - +
207B ILE* 1.3 70.6 + - - +
208B VAL* 3.9 7.8 + - + +
214B ASN* 4.5 17.9 - - + +
215B VAL 3.8 4.7 - - - +
216B THR* 3.4 25.3 + - - +
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Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 4.8 5.4 - - + -
167B VAL* 6.0 0.2 - - + -
184B LEU* 4.6 3.8 - - + -
189B VAL* 4.1 20.9 - - + -
195B VAL* 3.3 38.4 - - + -
196B THR 3.4 4.3 - - - +
197B VAL* 3.9 13.5 - - + -
205B VAL* 4.6 7.2 - - + -
206B THR* 1.3 76.3 - - - +
208B VAL* 1.3 60.0 + - - +
209B ILE* 3.1 19.6 - - + +
214B ASN* 3.3 4.7 - - - +
215B VAL* 2.8 47.2 + - + +
217B LEU* 3.9 29.8 - - + -
225B VAL* 5.9 2.0 - - + -
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PRO* 6.1 4.7 - - + -
195B VAL* 2.7 22.7 - - - +
196B THR* 2.7 39.2 + - - +
197B VAL* 5.5 0.7 - - - -
198B GLU* 5.8 4.5 - - + +
206B THR* 4.4 11.9 - - + +
207B ILE* 1.3 71.9 - - - +
209B ILE* 1.3 60.9 + - - +
210B PRO* 3.6 5.5 - - + +
214B ASN* 3.1 24.7 - - - +
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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
------------------------------------------------------------
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