Contacts of the helix formed by residues 169 - 174 (chain B) in PDB entry 4AU8
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 PRO 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B VAL* 5.0 0.2 - - + -
167B TYR 3.9 5.4 - - - +
168B ARG* 1.4 85.8 - - - +
170B PRO* 1.4 71.0 - - + +
171B ASP* 3.3 20.6 - - - +
172B VAL* 3.2 27.4 + - + -
173B LEU* 3.0 19.7 + - - +
183B ILE* 3.8 27.4 - - + +
186B TRP* 3.5 15.2 - - + -
274B ARG* 3.4 22.2 - - - +
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Residues in contact with PRO 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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169B PRO* 1.4 85.8 - - + +
171B ASP* 1.4 57.1 + - - +
173B LEU* 3.3 12.6 + - + +
174B PHE* 2.9 34.2 + - + +
186B TRP* 3.8 21.5 - - + -
212B LEU* 4.1 5.2 - - + -
215B ILE* 3.9 18.6 - - + -
216B PHE* 4.2 12.8 - - + -
227B TRP* 4.0 20.6 - - + -
269B CYS* 3.9 26.5 - - + +
274B ARG* 4.0 6.7 - - - +
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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 PRO* 3.3 11.3 - - - +
170B PRO* 1.4 71.7 - - - +
172B VAL* 1.3 70.7 + - - +
174B PHE* 3.1 11.3 + - - +
175B GLY 3.4 0.7 + - - -
176B ALA* 3.0 35.0 + - + +
178B LEU 5.0 0.5 - - - +
179B TYR* 4.1 15.8 - - - +
182B SER* 5.0 0.3 + - - -
183B ILE* 5.8 0.3 - - - +
227B TRP* 3.6 29.5 - - + -
233B LEU* 4.1 8.3 - - + +
271B PRO* 3.7 22.8 - - + +
274B ARG* 2.7 29.0 + - - -
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Residues in contact with VAL 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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162B VAL* 3.9 28.3 - - + -
163B VAL* 5.6 0.4 - - + -
168B ARG* 4.1 16.1 + - + -
169B PRO* 3.2 29.5 + - + +
171B ASP* 1.3 76.7 - - - +
173B LEU* 1.3 60.8 + - - +
175B GLY* 3.0 19.8 + - - -
176B ALA* 4.0 10.8 + - + +
179B TYR* 3.6 35.9 - - + -
183B ILE* 4.0 9.0 - - + -
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Residues in contact with LEU 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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165B LEU* 4.1 10.3 - - + -
168B ARG* 3.5 49.6 - - + +
169B PRO 3.0 16.4 + - - +
170B PRO* 3.3 6.7 + - + +
172B VAL* 1.3 75.9 - - - +
174B PHE* 1.3 58.4 + - - +
175B GLY 3.2 3.5 + - - -
208B VAL* 3.5 28.0 - - + +
211B GLN* 3.6 35.2 - - + -
212B LEU* 3.8 27.2 - - + +
215B ILE* 3.7 15.5 - - + -
235B ASP* 4.5 8.0 - - - +
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Residues in contact with PHE 174 (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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170B PRO 2.9 22.7 + - - +
171B ASP 3.1 7.6 + - - +
173B LEU* 1.3 76.1 - - - +
175B GLY* 1.3 51.8 + - - +
212B LEU* 3.8 21.5 - - + -
216B PHE* 3.7 37.9 - + - -
227B TRP* 4.6 1.3 - + - -
230B MET* 3.8 24.0 - - + -
233B LEU* 3.5 29.8 - - + +
234B PRO 3.4 9.2 - - - -
235B ASP* 2.8 44.5 + - - -
236B TYR* 3.6 12.1 - + - +
237B LYS* 3.6 32.1 - - + -
239B TYR* 3.9 6.1 - + - -
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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
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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