Contacts of the strand formed by residues 165 - 169 (chain B) in PDB entry 2QQ6
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 ALA 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ARG* 4.0 15.5 - - - +
122B LEU 3.9 7.9 - - - +
123B TYR* 3.3 27.0 - - + -
124B ALA* 2.8 31.6 + - - +
163B PHE* 3.6 2.3 - - - +
164B ASP* 1.3 81.3 - - - +
166B ILE* 1.3 62.6 + - - +
210B GLU* 3.1 12.3 - - + +
237B LEU* 5.1 6.5 - - + -
339B VAL* 4.6 3.4 - - + -
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Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TYR* 4.9 2.7 - - - -
124B ALA* 3.4 2.9 - - + +
126B CYS* 3.7 28.7 - - - -
155B ALA* 4.3 13.2 - - + +
158B ALA* 3.9 21.5 - - + -
159B VAL* 4.7 4.7 - - + -
163B PHE* 4.4 6.5 - - + +
165B ALA* 1.3 90.3 - - - +
167B LYS* 1.3 68.7 + - - +
168B LEU* 4.3 11.4 - - + -
201B VAL* 5.0 6.3 - - + -
205B VAL* 5.9 2.9 - - + -
209B VAL* 4.2 15.5 - - + -
210B GLU 2.6 12.7 + - - +
211B VAL* 3.3 17.5 - - + -
212B ALA* 2.8 27.2 + - - +
237B LEU* 5.7 1.2 - - - +
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Residues in contact with LYS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TYR* 3.1 42.6 + - + -
124B ALA 2.8 9.5 + - - -
125B ASP* 3.0 31.5 + - - +
126B CYS* 2.7 34.7 + - - +
166B ILE* 1.3 75.5 - - - +
168B LEU* 1.3 68.5 + - - +
169B ASP* 5.4 0.7 - - - +
212B ALA* 3.3 14.4 - - + +
213B ILE 5.6 0.2 - - - -
214B ASP* 3.6 15.9 - - + +
238B TRP* 5.3 1.6 - - + +
240B GLU* 2.9 43.1 + - - -
316B HIS* 3.9 4.2 + - - -
341B GLU* 3.8 13.1 + - - +
409B MG 3.4 7.1 - - - -
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Residues in contact with LEU 168 (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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125B ASP* 6.1 0.2 - - - -
126B CYS* 4.2 9.9 - - + +
127B ASN* 3.5 23.3 - - - +
151B TYR* 3.7 27.8 - - + +
155B ALA* 5.6 0.7 - - + -
166B ILE* 4.3 11.2 - - + -
167B LYS* 1.3 77.7 - - - +
169B ASP* 1.3 70.4 + - - +
170B VAL* 5.5 1.3 - - + -
197B ARG* 4.7 9.0 - - + +
198B VAL* 6.4 0.2 - - - -
201B VAL* 3.5 43.1 - - + -
211B VAL* 5.1 4.0 - - + -
212B ALA 2.9 11.6 + - - +
213B ILE* 3.1 17.0 - - + +
214B ASP* 2.7 32.4 + - - -
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Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASP* 5.1 5.6 - - - +
127B ASN* 3.0 38.1 - - - +
137B HIS* 2.9 30.9 + - + +
167B LYS* 5.4 0.3 - - - -
168B LEU* 1.3 82.5 - - - +
170B VAL* 1.3 74.1 + - - +
171B ASP* 4.0 1.8 - - - +
197B ARG* 4.1 12.2 + - - +
214B ASP* 3.5 16.2 - - - +
216B HIS* 3.1 30.1 + - - -
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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