Contacts of the strand formed by residues 158 - 162 (chain C) in PDB entry 2Q5E
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 GLU 158 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C VAL* 4.3 12.6 - - - +
95C THR 5.3 0.3 + - - -
98C ASP* 3.7 38.6 - - + +
101C ARG* 4.0 8.5 - - + +
102C ILE 2.8 13.3 + - - +
103C CYS* 3.2 16.3 + - - +
104C VAL 2.8 27.9 + - - +
157C PHE* 1.3 69.1 - - - +
159C CYS* 1.3 62.1 + - - +
160C VAL* 3.8 11.6 + - + +
185C ALA* 5.8 1.9 - - - +
208C ARG* 2.7 46.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C VAL* 3.5 5.8 - - - -
106C ILE* 4.7 8.5 - - + -
153C MET* 3.6 46.2 - - - -
154C GLY* 3.9 7.0 - - - -
157C PHE* 3.7 12.3 + - - -
158C GLU* 1.3 74.9 - - - +
160C VAL* 1.3 64.5 + - - +
182C VAL* 3.6 34.6 + - + +
183C PHE* 3.6 20.1 - - + -
184C ARG 4.1 4.3 + - - -
185C ALA 4.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 3.9 28.3 - - + -
103C CYS* 3.8 21.5 - - - -
104C VAL 2.8 13.6 + - - +
105C VAL* 3.5 18.5 - - + -
106C ILE* 2.8 30.0 + - - +
158C GLU* 4.3 12.3 - - + +
159C CYS* 1.3 79.5 - - - +
161C LEU* 1.3 72.4 + - - +
183C PHE* 3.6 4.2 - - - -
185C ALA* 3.8 20.4 - - + +
187C LEU* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ILE 3.5 14.1 - - - +
107C ASP 4.3 0.7 - - - -
108C LEU* 3.9 34.8 - - + +
112C LEU* 5.2 1.1 - - + -
160C VAL* 1.3 73.8 - - - +
162C PHE* 1.3 60.3 + - - +
163C THR* 4.0 21.1 - - + -
170C ALA* 4.5 2.0 - - + -
174C THR* 3.5 23.6 - - + +
183C PHE* 3.4 33.1 - - + -
185C ALA 3.1 13.6 + - - +
186C ARG* 3.6 20.5 - - + -
187C LEU* 2.7 28.9 + - - +
188C PHE* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 4.2 12.1 - - + -
105C VAL* 3.8 39.7 - - + -
106C ILE 2.8 18.7 + - - +
107C ASP* 3.4 10.2 + - - -
160C VAL 3.3 1.0 + - - -
161C LEU* 1.3 73.4 - - - +
163C THR* 1.3 63.1 + - - +
187C LEU* 3.4 27.4 - - + -
188C PHE 4.1 1.1 - - - -
191C SER* 3.3 39.0 - - - -
192C CYS* 3.5 22.9 - - - -
201C LYS* 3.4 46.1 - - + +
202C ASP 4.8 2.7 - - - -
203C LEU* 5.2 1.8 - - + -
206C LEU* 4.4 6.3 - - + -
----------------------------------------------------------
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