Contacts of the helix formed by residues 170 - 175 (chain C) in PDB entry 2WFY
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 170 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C TYR 3.8 1.0 + - - -
169C ARG* 1.3 76.8 - - - +
171C PRO* 1.3 70.6 - - + +
172C GLU* 3.3 29.4 - - - +
173C ILE* 3.1 23.6 + - + +
174C LEU* 3.3 10.8 + - - +
184C VAL* 4.1 15.3 + - + +
187C TRP* 3.6 25.1 - - + -
274C ARG* 4.2 0.2 - - - +
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Residues in contact with PRO 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C ARG 3.8 0.6 - - - +
170C ALA* 1.3 83.1 - - - +
172C GLU* 1.3 70.8 + - - +
174C LEU* 3.2 13.3 + - + +
175C LEU* 2.8 36.2 + - + +
187C TRP* 3.5 44.2 - - + -
212C LEU* 4.8 5.8 - - + -
215C ILE* 4.9 5.8 - - + -
216C PHE* 6.3 0.2 - - + -
227C TRP* 3.8 17.3 - - + -
269C TYR* 3.9 24.2 - - + +
274C ARG* 4.1 2.9 - - - +
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Residues in contact with GLU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ALA* 3.3 23.6 - - - +
171C PRO* 1.3 79.7 - - - +
173C ILE* 1.3 57.9 + - + +
175C LEU 3.6 0.5 + - - -
176C GLY 3.4 3.3 + - - -
177C CYS* 2.9 45.3 + - + +
181C SER* 5.3 0.5 + - - -
183C ALA* 4.9 0.3 - - - +
184C VAL* 3.7 15.8 + - - +
227C TRP* 3.6 24.7 - - + -
233C MET* 3.7 5.0 - - + +
271C PRO* 3.5 31.5 - - + +
274C ARG* 2.5 38.0 + - - -
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Residues in contact with ILE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C THR* 5.0 13.7 - - + +
159C TYR 6.0 0.7 - - - +
169C ARG* 3.4 40.2 - - + +
170C ALA* 3.1 17.1 + - + +
172C GLU* 1.3 77.1 - - - +
174C LEU* 1.3 60.3 + - - +
176C GLY* 2.9 20.3 + - - -
177C CYS* 4.4 10.7 - - - +
180C TYR* 3.5 33.0 - - + +
184C VAL* 3.5 37.2 - - + -
208C GLU* 5.4 0.5 - - - +
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Residues in contact with LEU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C LEU* 4.9 2.5 - - + -
169C ARG* 3.7 35.4 - - + +
170C ALA 3.3 10.5 + - - +
171C PRO* 3.2 7.3 + - + +
173C ILE* 1.3 75.9 - - - +
175C LEU* 1.3 59.0 + - - +
176C GLY 3.0 3.9 + - - -
208C GLU* 3.8 35.7 - - + +
211C GLN* 3.5 32.8 - - + -
212C LEU* 3.7 43.1 - - + +
215C ILE* 4.1 13.5 - - + -
235C ASP* 3.7 13.5 - - - +
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Residues in contact with LEU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C PRO* 2.8 22.3 + - + +
173C ILE 3.2 0.4 - - - -
174C LEU* 1.3 74.6 - - - +
176C GLY* 1.3 61.1 + - - +
177C CYS 3.6 1.1 + - - -
212C LEU* 4.1 23.3 - - + -
216C PHE* 5.2 3.4 - - + -
222C PRO* 5.3 5.4 - - + -
227C TRP* 3.5 30.5 - - + -
230C VAL* 4.3 12.8 - - + -
233C MET* 3.8 26.5 - - + +
234C PRO* 3.8 3.1 - - - +
235C ASP* 3.0 45.1 + - - +
236C TYR* 4.2 15.9 - - + +
240C PHE* 4.3 10.8 - - + -
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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