Contacts of the strand formed by residues 158 - 162 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E LEU* 5.0 2.8 - - - +
92E PRO* 4.7 5.0 - - - +
93E GLU 5.3 0.2 - - - +
94E VAL* 3.8 21.2 - - + +
95E THR* 5.1 0.9 + - - +
98E ASP* 3.7 30.6 - - + +
101E ARG* 4.1 7.4 - - - +
102E ILE 3.2 7.1 + - - +
103E CYS* 3.4 20.7 + - - +
104E VAL 2.9 27.4 + - - +
157E PHE* 1.3 74.9 - - - +
159E CYS* 1.4 56.5 + - - +
160E VAL* 3.6 7.9 + - + +
184E ARG* 4.1 14.6 - - + +
208E ARG* 2.8 44.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E VAL* 3.5 4.9 - - - -
106E ILE* 4.0 17.7 - - + -
150E LEU* 5.8 0.2 - - - -
153E MET* 3.6 43.5 - - - -
154E GLY* 4.4 0.7 - - - -
157E PHE* 3.6 8.9 + - - -
158E GLU* 1.4 71.1 - - - +
160E VAL* 1.3 65.7 + - - +
182E VAL* 3.4 33.3 + - + +
183E PHE* 3.8 7.4 - - + -
184E ARG* 3.3 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E LEU* 3.7 33.0 - - + -
103E CYS* 3.8 26.0 - - - -
104E VAL 2.5 11.6 + - - +
105E VAL* 3.6 15.5 - - + -
106E ILE* 2.9 32.6 + - - +
158E GLU* 3.9 10.1 - - + +
159E CYS* 1.3 80.8 - - - +
161E LEU* 1.3 72.8 + - - +
162E PHE 3.8 0.2 - - - -
183E PHE* 3.7 4.5 - - - -
184E ARG* 5.6 0.9 - - + -
185E ALA* 3.3 20.0 - - + +
187E LEU* 4.8 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E ILE 3.3 11.0 - - - +
107E ASP 4.6 1.1 - - - -
108E LEU* 4.1 35.2 - - + +
112E LEU* 4.8 1.8 - - + -
160E VAL* 1.3 78.1 - - - +
162E PHE* 1.3 55.5 + - - +
163E THR* 4.1 14.6 - - + -
174E THR* 3.4 22.9 - - + +
183E PHE* 3.6 32.8 - - + -
185E ALA 3.1 11.5 + - - +
186E ARG* 3.3 13.4 - - + -
187E LEU* 2.5 34.5 + - - +
188E PHE* 4.1 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 162 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E LEU* 5.1 2.0 - - + -
105E VAL* 3.4 31.4 - - + +
106E ILE 2.9 16.3 + - - +
107E ASP* 3.6 6.9 + - - +
160E VAL 3.8 0.6 + - - -
161E LEU* 1.3 72.7 - - - +
163E THR* 1.3 65.6 + - - +
187E LEU* 3.3 41.1 - - + -
188E PHE 4.3 1.8 - - - -
191E SER* 3.3 31.6 - - - -
192E CYS* 3.9 17.5 - - - -
201E LYS* 3.4 53.4 + - + +
202E ASP 4.5 8.3 - - - -
203E LEU* 5.1 2.7 - - + -
206E LEU* 4.0 16.8 - - + -
----------------------------------------------------------
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