Contacts of the helix formed by residues 168 - 171 (chain C) in PDB entry 2OZL
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 GLY 168 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 3.7 34.5 + - - +
167C ASP* 1.3 78.1 + - - +
169C ALA* 1.3 60.9 + - - +
170C ALA 3.3 0.7 + - - -
171C ASN* 3.5 16.4 + - - +
199C GLY* 4.3 7.2 - - - -
207C ALA* 5.9 4.7 - - - -
1330C TPP 2.7 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C VAL* 3.4 29.6 - - + -
139C GLY 4.2 8.7 - - - +
141C GLN* 5.0 1.6 - - - +
165C TYR* 4.1 12.1 - - + -
166C GLY 3.1 17.7 + - - +
168C GLY* 1.3 71.3 - - - +
170C ALA* 1.3 56.2 + - - +
171C ASN 3.0 5.8 - - - -
172C GLN* 2.9 24.9 + - - +
175C ILE* 3.0 15.6 - - + +
1330C TPP 2.9 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C TYR* 3.9 21.5 - - + -
166C GLY 3.1 10.6 + - - +
167C ASP 3.2 15.9 - - - +
168C GLY 3.1 0.6 - - - -
169C ALA* 1.3 77.0 - - - +
171C ASN* 1.3 57.9 + - - +
172C GLN 3.3 1.6 + - - +
175C ILE* 4.0 5.0 - - - +
176C PHE* 3.3 26.3 - - - -
179C TYR* 5.4 1.7 + - - +
193C CYS* 4.6 0.2 - - - -
213C TYR* 3.5 28.7 - - + -
216C ARG* 4.1 7.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLU* 3.6 10.2 - - - +
180A ASN* 3.5 22.0 + - + +
56B PRO* 4.0 9.1 - - + +
57B ILE 4.1 3.8 - - - +
58B SER* 2.9 27.3 + - - +
167C ASP 4.3 7.2 + - - -
168C GLY 3.5 13.2 + - - +
169C ALA 2.9 2.0 + - - -
170C ALA* 1.3 76.9 - - - +
172C GLN* 1.3 61.8 + - - +
173C GLY 3.6 2.3 + - - -
176C PHE* 4.6 3.3 - - - -
207C ALA* 3.2 31.3 + - - +
208C ALA* 4.0 5.8 - - - +
213C TYR* 5.3 0.2 + - - -
216C ARG* 3.1 34.8 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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