Contacts of the helix formed by residues 167 - 173 (chain B) in PDB entry 2B9R
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 MET 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ARG* 2.7 26.0 + - - -
42B ILE* 3.6 21.2 - - + +
46B VAL* 4.0 10.1 - - + -
59B MET* 3.6 40.8 - - + +
60B TYR* 3.7 39.5 - - + -
63B VAL* 4.0 28.0 - - + +
163B MET 4.8 0.7 - - - +
164B GLU* 3.0 38.2 + - + +
166B THR* 1.3 76.9 + - - +
168B LEU* 1.3 54.1 + - + +
236B VAL* 4.8 1.6 - - + -
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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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35B GLY 5.6 0.2 - - - +
38B ARG* 3.6 7.1 + - - +
39B ALA* 4.2 26.0 - - + +
42B ILE* 3.1 42.6 - - + -
43B ASP* 3.8 19.5 - - + +
46B VAL* 5.1 0.4 - - + -
164B GLU 5.2 0.2 - - - +
165B LEU* 4.0 20.9 - - + +
166B THR 2.6 5.5 + - - -
167B MET* 1.3 78.9 - - + +
169B ASP* 1.3 61.4 + - - +
170B TYR* 3.3 5.2 + - - +
222B ASN* 5.4 7.0 - - - +
226B VAL* 6.1 1.3 - - + -
231B THR* 4.9 6.5 - - + -
233B HIS* 3.9 33.2 - - + +
236B VAL* 5.0 20.9 - - + -
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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
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38B ARG* 4.1 1.6 - - - -
165B LEU 4.5 0.4 + - - -
166B THR* 2.9 12.0 + - - +
168B LEU* 1.3 75.6 - - - +
170B TYR* 1.3 63.3 + - - +
171B ASP* 3.6 19.5 + - - +
172B MET* 3.1 45.2 + - + +
173B VAL* 3.5 13.7 + - - +
218B HIS* 4.0 1.9 - - - -
221B LYS* 3.2 25.3 + - - -
222B ASN* 3.4 28.9 + - - +
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Residues in contact with TYR 170 (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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26B LYS* 3.0 27.8 + - + -
27B TYR* 4.0 20.0 - + - -
28B LEU* 2.9 56.6 + - + +
29B LEU* 3.1 5.7 + - - -
35B GLY* 4.1 26.2 - - - -
38B ARG* 4.2 16.4 - - - +
39B ALA* 6.6 0.2 - - + -
168B LEU 3.3 5.7 + - - +
169B ASP* 1.3 69.1 + - - +
171B ASP* 1.3 67.0 + - - +
172B MET 3.0 9.2 + - - -
173B VAL* 3.2 29.7 - - + +
174B HIS* 5.5 0.5 - - - -
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Residues in contact with ASP 171 (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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169B ASP* 3.1 20.9 - - - +
170B TYR* 1.3 89.1 + - - +
172B MET* 1.3 58.9 + - - +
173B VAL 3.9 0.2 - - - -
174B HIS* 4.1 12.0 + - - -
218B HIS* 3.6 25.3 + - + +
221B LYS* 4.4 12.7 + - - +
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Residues in contact with MET 172 (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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166B THR* 3.9 33.0 - - + +
169B ASP* 3.1 36.4 + - + +
170B TYR 3.0 1.0 - - - -
171B ASP* 1.3 83.1 - - - +
173B VAL* 1.3 62.8 + - - +
174B HIS* 3.3 6.9 + - - -
175B PHE* 3.4 48.2 + - + +
180B ILE* 3.8 21.1 - - + +
215B VAL* 3.9 24.2 - - + +
218B HIS* 3.6 14.4 - - + -
219B LEU* 4.4 5.2 - - + -
222B ASN* 4.5 3.8 - - - +
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Residues in contact with VAL 173 (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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22B ALA 5.0 0.3 - - - +
23B VAL* 3.9 19.8 - - + +
24B ARG 4.5 4.5 - - - +
26B LYS 5.1 3.6 - - - +
27B TYR* 4.3 16.2 - - + -
38B ARG* 3.6 33.7 - - - +
67B ASP* 3.8 10.3 - - - +
166B THR 5.8 0.2 - - - +
169B ASP 3.5 15.9 - - - +
170B TYR* 3.2 31.9 - - + +
171B ASP 3.9 0.2 - - - -
172B MET* 1.3 76.7 - - - +
174B HIS* 1.3 69.1 + - + +
175B PHE 3.3 8.5 - - - +
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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
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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