Contacts of the strand formed by residues 163 - 166 (chain C) in PDB entry 4I5L
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 ILE 163 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU* 3.4 3.7 - - - -
159C VAL* 2.7 46.6 + - + +
162C GLN* 1.3 81.1 - - + +
164C PHE* 1.3 62.3 + - - +
165C CYS* 3.7 16.6 + - - -
235C THR* 4.5 11.7 - - + -
236C LEU* 3.6 34.5 - - + +
238C SER* 4.2 13.5 - - - -
276C MET* 5.9 0.7 - - - -
278C LEU* 3.9 32.5 - - + -
282C LEU* 4.3 24.9 - - + +
284C TYR* 5.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 4.8 2.0 - - + -
156C THR* 3.5 37.0 - - + -
157C ALA 3.5 11.7 - - - -
158C LEU* 4.3 6.1 - - + -
162C GLN 3.9 0.6 + - - -
163C ILE* 1.3 71.3 - - - +
165C CYS* 1.3 54.6 + - - +
166C LEU* 3.7 31.6 - - + -
170C LEU* 4.4 4.9 - - + -
177C LEU* 3.7 22.4 - - + -
180C ILE* 3.5 23.3 - - + -
198C LEU* 4.8 1.3 - - + -
228C PHE* 3.9 27.6 - + - -
234C LEU* 3.8 24.0 - - + -
236C LEU 3.0 10.2 + - - +
237C VAL* 3.4 11.5 - - + +
238C SER 2.7 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 4.4 11.0 - - - -
81C LEU* 4.1 28.0 - - + -
83C MET* 4.2 4.9 - - - -
114C LEU* 3.6 3.0 - - + +
156C THR* 3.3 4.7 - - - -
157C ALA* 2.7 43.5 + - + +
159C VAL* 3.8 27.4 - - - -
163C ILE* 4.1 6.5 - - - -
164C PHE* 1.3 76.5 - - - +
166C LEU* 1.3 62.2 + - - +
238C SER* 3.2 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C MET* 3.7 8.8 - - - +
114C LEU* 4.1 7.9 - - - -
155C LEU 4.0 3.8 - - - +
156C THR* 3.7 15.5 - - + -
164C PHE* 3.7 22.7 - - + +
165C CYS* 1.3 76.5 - - - +
167C HIS* 1.3 60.1 + - - +
169C GLY* 3.3 41.7 - - - +
170C LEU* 5.0 0.2 - - + -
198C LEU* 3.8 25.1 - - + +
237C VAL* 3.5 32.8 - - + -
238C SER 3.0 7.9 + - - +
239C ARG* 3.1 31.2 - - + +
----------------------------------------------------------
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