Contacts of the strand formed by residues 172 - 178 (chain A) in PDB entry 2O9B
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 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A PHE* 3.2 1.7 - - - +
171A ASP* 1.3 79.3 - - + +
173A VAL* 1.3 66.9 + - - +
174A MET* 3.8 14.8 - - + -
189A GLU* 2.8 33.5 + - + +
190A ALA 3.5 8.1 - - - +
191A ARG* 3.8 9.4 - - + +
195A LEU* 3.9 22.1 - - + +
196A HIS* 2.6 53.5 + - - -
198A PHE* 3.7 28.4 - - - +
288A ALA 4.5 0.4 - - - -
289A CYS* 3.2 4.9 - - - +
290A HIS* 2.8 57.3 + - + +
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A THR* 3.6 28.7 - - - +
164A VAL* 3.8 11.2 - - + -
165A ARG* 3.7 30.7 - - + +
170A PHE* 4.1 14.6 - - + -
172A ARG* 1.3 78.8 - - - +
174A MET* 1.3 61.9 + - - +
189A GLU* 3.3 2.8 - - - -
190A ALA 2.8 40.4 + - - +
287A ILE* 3.7 28.5 - - + -
288A ALA 3.5 2.5 - - - -
289A CYS* 4.1 10.1 - - - -
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Residues in contact with MET 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A THR* 3.7 4.7 - - - -
172A ARG* 3.8 15.7 - - - -
173A VAL* 1.3 78.4 - - - +
175A LEU* 1.3 63.0 + - - +
176A TYR* 3.8 3.1 - - + +
186A VAL* 3.9 24.5 - - + -
188A ALA 3.3 7.9 - - - +
189A GLU* 3.9 16.4 - - + +
198A PHE* 4.1 6.5 - - - -
287A ILE* 3.3 8.7 - - - +
288A ALA* 2.7 58.7 + - + +
290A HIS* 3.4 37.2 - - + +
328A LBV 3.5 28.7 - - + +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 5.9 0.7 - - + -
157A ALA* 3.3 32.8 - - + +
160A ALA* 5.5 1.3 - - + -
161A THR* 3.5 15.1 - - + +
174A MET* 1.3 75.2 - - - +
176A TYR* 1.3 58.4 + - - +
186A VAL* 3.6 1.2 - - - -
187A ILE* 2.9 48.2 + - + +
188A ALA* 3.0 12.0 + - + -
277A VAL* 4.2 7.2 - - + -
284A TRP* 4.0 22.0 - - + -
286A LEU 3.6 16.4 - - - +
287A ILE* 3.9 20.4 - - + -
312A LEU* 4.0 21.5 - - + -
316A VAL* 5.8 0.9 - - + -
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A MET* 3.8 3.1 - - + -
175A LEU* 1.3 74.9 - - - +
177A LYS* 1.3 58.8 + - - +
178A PHE* 3.7 31.4 - + - -
182A ALA 5.5 0.5 + - - -
184A GLY* 3.3 25.8 + - - -
185A GLU 3.5 19.7 - - - -
186A VAL* 4.1 13.0 - - + +
203A PHE* 3.3 37.1 + + - +
204A PRO 4.4 4.2 + - - -
208A ILE* 3.8 15.7 - - + +
285A GLY* 3.0 4.5 - - - -
286A LEU* 2.7 50.8 + - + +
288A ALA* 4.8 11.4 - - + -
328A LBV 3.4 32.6 - + + +
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Residues in contact with LYS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU 3.9 0.8 + - - -
176A TYR* 1.3 72.4 - - - +
178A PHE* 1.3 76.0 + - - +
179A ALA 3.9 0.2 + - - -
184A GLY* 3.3 3.3 - - - -
185A GLU* 3.0 34.3 + - + +
187A ILE* 4.1 29.8 - - + -
284A TRP* 3.6 56.6 - - + +
285A GLY* 4.2 0.9 - - - -
320A GLU* 4.1 7.6 + - - -
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Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A TYR* 3.7 22.9 - + - -
177A LYS* 1.3 94.5 + - - +
179A ALA* 1.3 66.5 + - - +
180A PRO* 4.9 0.5 - - - +
182A ALA* 3.8 21.5 - - + -
183A THR 3.3 4.3 - - - +
208A ILE* 3.8 26.9 - - + -
213A ARG* 4.0 22.2 - - + -
283A LEU* 3.4 44.2 - - + +
284A TRP 3.0 15.2 + - - +
285A GLY* 3.5 28.7 - - - -
286A LEU* 4.1 7.0 - - + -
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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