Contacts of the strand formed by residues 183 - 187 (chain D) in PDB entry 2Q5E
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 PHE 183 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B VAL* 4.4 6.6 - - - +
205B ARG* 3.3 17.6 + - - -
106D ILE* 4.2 11.0 - - + -
112D LEU* 4.1 15.9 - - + -
150D LEU* 4.0 30.1 - - + -
159D CYS* 3.5 22.0 - - + -
160D VAL 3.7 15.0 - - - -
161D LEU* 3.5 32.5 - - + -
174D THR* 3.7 18.6 - - + -
177D LEU* 5.1 2.7 - - + -
178D ASP* 3.1 36.4 + - + +
181D GLY 3.4 0.4 - - - -
182D VAL* 1.3 75.2 - - + +
184D ARG* 1.3 65.4 + - - +
185D ALA* 3.1 12.4 + - - +
186D ARG* 4.6 12.4 + - - +
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Residues in contact with ARG 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B CYS 4.3 3.2 - - - +
193B VAL* 3.6 8.7 - - - -
194B PHE* 3.2 19.9 + - - +
205B ARG* 4.4 6.5 - - - +
95D THR* 6.5 0.9 - - + -
97D GLU* 4.4 15.6 + - - +
98D ASP* 3.1 35.6 + - - +
101D ARG* 3.0 12.5 - - - +
154D GLY* 2.7 33.2 + - - -
157D PHE 3.0 18.2 + - - -
158D GLU* 4.0 15.0 - - + +
159D CYS 3.2 16.4 + - - +
160D VAL* 5.7 0.2 - - + -
181D GLY 4.8 6.0 + - - -
182D VAL* 3.1 22.2 + - - -
183D PHE* 1.3 73.5 - - - +
185D ALA* 1.3 60.1 + - + +
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Residues in contact with ALA 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B VAL* 4.9 0.2 - - - -
194B PHE* 3.1 19.1 - - + +
91D LEU* 3.9 28.0 - - + -
92D PRO* 5.7 0.2 - - + -
158D GLU* 6.0 1.8 - - - +
159D CYS 4.1 1.4 + - - -
160D VAL* 3.9 15.8 - - + -
161D LEU 3.2 19.6 + - - -
183D PHE* 3.1 5.8 - - - +
184D ARG* 1.3 82.1 - - + +
186D ARG* 1.3 70.9 + - - +
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Residues in contact with ARG 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B VAL* 4.5 6.2 - - + +
194B PHE* 2.7 11.8 + - - +
195B HIS* 3.5 8.7 - - + -
196B GLN 3.0 26.9 + - - -
202B ASP* 4.8 5.3 + - - -
205B ARG* 4.8 5.9 - - - +
225B PHE* 3.7 20.3 - - - -
161D LEU* 3.6 28.0 - - + -
171D ASP* 2.9 42.2 + - - +
174D THR* 3.7 23.8 - - - +
175D ASP* 3.0 30.7 + - - +
178D ASP* 4.7 7.9 + - - +
183D PHE* 4.6 9.2 + - + +
185D ALA* 1.3 81.2 - - - +
187D LEU* 1.3 64.0 + - - +
188D PHE* 3.8 16.1 - - + -
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Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B PHE* 4.1 12.8 - - + -
196B GLN* 4.1 7.2 - - - -
90D LEU* 3.8 29.4 - - + +
91D LEU* 4.1 17.9 - - + -
160D VAL* 4.1 11.4 - - + -
161D LEU* 2.9 12.4 + - - +
162D PHE* 3.5 37.9 - - + -
163D THR* 3.0 28.2 + - - +
186D ARG* 1.3 80.8 - - - +
188D PHE* 1.3 65.5 + - - +
191D SER* 4.1 13.0 - - - +
206D LEU* 4.1 15.0 - - + -
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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
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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