Contacts of the helix formed by residues 161 - 167 (chain C) in PDB entry 1EJI
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 SER 161 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LEU* 2.9 36.3 + - - -
150C THR* 4.8 1.6 - - - -
153C PHE* 3.3 13.8 + - - -
160C ILE* 1.3 82.2 - - - +
162C ALA* 1.3 64.2 + - - +
163C THR* 2.9 21.4 + - - -
164C SER* 3.1 23.0 + - - -
165C ILE* 3.2 9.4 - - - +
298D PRO 3.9 10.1 - - - -
299D GLY 4.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PHE* 4.0 14.8 - - + -
160C ILE 3.6 0.4 + - - -
161C SER* 1.3 72.9 - - - +
163C THR* 1.3 62.9 + - - +
165C ILE* 3.0 25.5 + - + +
166C PHE* 3.0 21.9 + - + +
129D THR* 5.8 0.7 - - + -
299D GLY 2.8 24.9 + - - +
300D LEU* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PHE* 4.7 4.8 - - - -
128C TYR* 3.5 30.2 - - + -
138C ILE* 4.3 15.9 - - + -
150C THR* 2.9 31.4 + - - +
151C HIS 4.4 2.2 - - - -
152C GLY* 3.8 14.8 - - - +
161C SER* 2.9 9.5 + - - -
162C ALA* 1.3 78.8 - - - +
164C SER* 1.3 57.7 + - - +
167C PHE* 3.0 42.7 + - + +
169C SER* 5.1 4.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C PHE 2.4 34.6 + - - -
154C MSE 3.5 18.9 - - - +
159C LYS* 2.8 31.9 + - - +
161C SER* 3.1 11.4 + - - -
163C THR* 1.3 78.4 - - - +
165C ILE* 1.3 52.4 + - - +
167C PHE 2.9 18.0 - - - +
169C SER* 3.3 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C HIS* 4.8 7.4 - - - -
159C LYS* 3.4 42.2 + - + +
160C ILE 3.9 7.2 - - - +
161C SER 3.2 16.1 + - - +
162C ALA* 3.0 17.8 + - + +
164C SER* 1.3 80.4 - - - +
166C PHE* 1.3 73.8 + - + +
167C PHE 4.4 0.3 - - - +
168C GLU* 5.4 0.2 - - - +
129D THR* 4.9 14.6 - - + -
134D PRO* 3.9 30.3 - - + +
299D GLY* 5.7 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PHE* 3.7 16.4 - + - -
134C PRO* 3.6 5.9 - - - +
135C HIS* 2.9 28.2 + - - -
162C ALA* 3.0 18.2 + - + +
165C ILE* 1.3 86.5 - - + +
167C PHE* 1.3 73.2 + - + +
125D PHE* 3.9 12.6 - + - -
129D THR* 3.4 39.7 - - + -
134D PRO* 3.5 31.2 - - + -
166D PHE* 3.7 45.8 - + + -
167D PHE* 4.0 15.9 - + - -
300D LEU* 4.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PHE* 3.8 24.0 - + - -
128C TYR* 3.5 45.3 - + + -
129C THR* 3.8 4.5 - - - -
132C VAL* 3.6 11.0 - - + -
133C GLU* 3.4 36.8 - - - -
134C PRO* 4.0 2.9 - - + -
135C HIS 4.0 2.7 - - - +
136C GLY 3.5 7.0 - - - +
138C ILE* 3.8 15.3 - - + -
163C THR* 3.0 27.3 + - + +
164C SER* 2.9 24.9 - - - +
165C ILE 4.2 0.3 - - - -
166C PHE* 1.3 85.2 - - + +
168C GLU* 1.3 72.8 + - - +
169C SER* 5.8 0.2 - - - -
166D PHE* 4.0 18.4 - + - -
----------------------------------------------------------
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