Contacts of the strand formed by residues 179 - 181 (chain E) in PDB entry 2WNU
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 GLN 179 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D GLN* 4.7 1.3 - - - +
148E SER* 3.3 4.7 - - - -
149E SER* 2.8 63.8 + - - +
151E GLY 3.0 9.1 + - - -
153E LEU* 4.3 4.2 - - - +
172E ASP* 2.8 52.7 + - - +
173E TYR 3.4 8.1 - - - +
174E ALA* 3.6 19.5 - - + +
177E THR* 5.7 0.7 - - + -
178E PHE* 1.3 74.5 - - - +
180E VAL* 1.3 62.0 + - - +
181E THR* 4.9 5.8 - - - +
165F CYS 3.7 8.5 - - - +
166F GLY* 4.6 2.7 - - - -
173F GLN* 5.9 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D VAL 5.6 1.2 - - - +
146E HIS* 4.3 1.8 - - + -
147E ALA 3.3 11.4 - - - +
148E SER* 4.6 2.9 - - - +
172E ASP* 4.6 3.3 - - - +
179E GLN* 1.3 77.7 - - - +
181E THR* 1.3 71.7 + - - +
146F HIS* 6.0 0.2 - - + -
164F PHE* 3.9 23.6 - - + -
165F CYS 3.7 19.5 - - - +
166F GLY* 4.2 3.3 - - - +
174F VAL 4.3 10.3 - - - +
175F ASN* 3.9 36.6 - - - +
176F SER* 3.4 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D VAL* 3.8 12.0 - - - +
145E TYR* 4.6 9.8 + - + +
146E HIS* 3.1 7.4 - - - +
147E ALA* 2.8 50.1 + - + +
149E SER* 6.0 0.2 - - - -
153E LEU* 4.2 14.8 - - + +
170E PHE* 6.0 1.3 - - + +
172E ASP* 2.6 43.8 + - + +
179E GLN* 4.9 5.4 - - - +
180E VAL* 1.3 73.9 - - - +
182E THR* 1.3 69.1 + - - +
176F SER* 4.4 2.7 - - - -
----------------------------------------------------------
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