Contacts of the strand formed by residues 239 - 243 (chain C) in PDB entry 5EWL
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 VAL 239 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C TRP* 3.7 44.2 - - + -
162C HIS 4.0 8.2 + - - +
163C VAL* 3.5 26.1 - - + -
164C ILE* 2.8 34.5 + - - +
237C ALA* 3.6 1.4 - - - +
238C ARG* 1.4 78.3 - - + +
240C ILE* 1.3 61.3 + - - +
241C ILE* 4.6 7.6 - - + -
267C VAL* 3.5 29.6 - - + +
269C LEU* 4.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ILE* 3.4 22.2 - - + +
166C ILE* 3.4 32.8 - - + -
232C ALA* 5.6 1.1 - - + -
238C ARG 4.3 2.7 - - - +
239C VAL* 1.3 76.4 - - - +
241C ILE* 1.3 62.5 + - - +
242C LEU* 5.2 0.2 - - + -
261C MET* 4.4 11.4 - - + -
266C TYR* 3.6 33.7 - - + -
267C VAL 2.8 12.8 + - - +
268C TRP* 3.4 47.5 - - + +
269C LEU* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C TRP* 3.4 43.7 - - + -
155C MET* 4.0 19.3 - - - -
163C VAL* 3.8 34.8 - - + -
164C ILE 2.8 10.8 + - - +
165C LEU* 3.5 14.4 - - + -
166C ILE* 2.8 29.7 + - - +
180C LEU* 4.2 12.1 - - + -
239C VAL* 4.6 2.0 - - + -
240C ILE* 1.3 76.0 - - - +
242C LEU* 1.3 62.0 + - - +
269C LEU* 3.1 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C TRP* 4.1 9.0 - - - -
165C LEU* 5.4 0.2 - - - -
166C ILE* 3.3 35.0 - - + +
218C PHE* 4.4 1.3 - - + -
240C ILE* 5.2 0.2 - - + -
241C ILE* 1.3 75.8 - - - +
243C SER* 1.3 61.7 + - - +
244C ALA* 4.1 11.2 - - + -
249C ALA* 4.2 13.2 - - + -
252C VAL* 3.9 25.6 - - + -
253C TYR* 4.0 23.3 - - + +
268C TRP* 4.8 11.0 - - + -
269C LEU 3.0 7.7 + - - -
270C VAL* 3.5 32.2 - - + +
274C GLU* 3.2 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C TRP* 4.5 9.0 - - - -
165C LEU* 5.3 0.7 - - - -
166C ILE 2.9 8.7 + - - +
167C VAL* 3.3 24.3 - - - -
168C SER* 3.0 26.7 + - - -
172C GLU* 4.2 3.6 + - - +
173C GLY* 3.6 12.0 + - - -
176C ALA* 3.3 25.3 - - - +
242C LEU* 1.3 72.4 - - - +
244C ALA* 1.3 60.2 + - - +
273C ARG* 4.9 4.0 + - - -
274C GLU* 3.3 5.1 + - - -
----------------------------------------------------------
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