Contacts of the strand formed by residues 186 - 190 (chain B) in PDB entry 6UQY
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 ARG 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLN* 3.4 11.8 - - - +
27B ALA* 2.8 33.2 + - - +
28B PRO 2.9 20.8 + - - -
29B VAL* 3.8 18.5 - - - +
136B GLY 3.9 9.2 - - - +
137B GLN* 3.2 39.6 + - - +
138B ALA 3.6 10.1 + - - +
139B LEU* 4.1 6.9 - - + +
140B HIS* 2.8 33.8 + - - +
184B ALA 3.9 0.4 - - - -
185B ARG* 1.3 84.6 - - + +
187B PHE* 1.3 64.0 + - - +
235B GLU* 2.9 46.9 + - + +
305B TYR* 4.1 4.4 - - - -
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Residues in contact with PHE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 3.5 9.7 - - - +
140B HIS* 3.2 27.1 - - + +
142B ILE* 4.3 4.7 - - + -
176B VAL* 3.6 44.0 - - + -
179B LEU* 3.8 22.2 - - + -
180B GLY 3.9 1.8 - - - -
184B ALA* 3.7 35.7 - - + -
185B ARG 4.1 2.2 - - - -
186B ARG* 1.3 82.6 - - - +
188B LEU* 1.3 59.4 + - - +
189B VAL* 4.6 4.0 - - + -
234B LEU* 3.9 25.6 - - + -
235B GLU* 2.7 12.5 + - - +
236B LEU* 3.4 20.5 - - + -
237B SER* 2.9 26.3 + - - -
305B TYR* 3.9 0.9 + - - -
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 4.1 24.2 - - + -
139B LEU* 3.7 12.0 - - + +
140B HIS 3.0 6.1 + - - +
141B PHE* 3.3 12.5 - - + -
142B ILE 2.9 25.6 + - - +
187B PHE* 1.3 74.3 - - - +
189B VAL* 1.3 68.4 + - - +
190B VAL* 3.7 26.2 - - + -
237B SER* 3.3 11.9 - - - +
238B TRP 5.7 0.2 - - - -
239B PHE* 4.1 13.0 - - + -
301B MET* 4.3 14.6 - - + +
305B TYR* 3.8 32.3 - - + +
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ILE* 3.4 18.4 - - + +
172B ILE* 4.1 19.3 - - + -
176B VAL* 4.2 21.8 - - + -
187B PHE* 4.6 3.4 - - + -
188B LEU* 1.3 79.4 - - - +
190B VAL* 1.3 72.7 + - - +
221B LEU* 4.3 2.2 - - + -
225B LEU* 3.8 32.3 - - + -
236B LEU* 4.4 13.0 - - + -
237B SER 2.9 9.5 + - - +
238B TRP* 3.4 12.4 - - + -
239B PHE 2.9 23.2 + - - -
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PHE* 3.7 25.4 - - + -
142B ILE 2.8 14.0 + - - +
143B PHE* 3.6 38.7 - - + -
144B VAL 4.8 5.7 + - - +
172B ILE* 5.7 0.9 - - - +
188B LEU* 3.7 21.3 - - + -
189B VAL* 1.3 83.0 - - - +
191B SER* 1.3 76.3 + - - +
221B LEU* 4.7 3.8 - - - +
238B TRP* 4.2 2.4 - - - -
239B PHE* 3.6 14.4 - - + +
241B HIS* 4.0 16.8 - - + -
301B MET* 4.0 6.5 - - + -
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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