Contacts of the helix formed by residues 158 - 161 (chain A) in PDB entry 3CEI
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 TRP 158 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.9 10.1 - - - -
69A GLN* 3.4 17.6 - - - +
119A SER* 3.5 22.4 - - - +
120A GLY 3.4 19.4 - - - +
121A TRP* 3.5 8.2 - + - +
140A ASN* 3.0 38.5 + - - -
156A ASP* 3.1 23.9 + - - +
157A VAL* 1.3 81.0 - - - +
159A GLU* 1.3 66.5 + - - +
160A HIS* 3.7 30.7 - + + +
161A ALA* 3.0 17.0 + - - +
162A TYR* 3.5 3.3 - - - -
117B PHE* 3.8 19.1 - + - -
118B GLY* 3.5 32.8 - - - -
159B GLU* 3.7 20.9 - - + +
170B ARG* 5.9 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLY 6.1 3.1 - - - +
119A SER* 5.1 2.8 + - - +
157A VAL 3.4 1.7 + - - +
158A TRP* 1.3 72.3 - - - +
160A HIS* 1.3 62.2 + - - +
161A ALA 2.9 1.6 + - - -
162A TYR* 3.0 28.9 + - + +
163A TYR* 3.0 36.8 + - + +
170A ARG* 5.5 3.1 - - - +
30B HIS* 3.7 10.6 - - - -
119B SER* 4.9 3.3 + - - +
158B TRP* 3.7 20.2 - - + -
159B GLU* 3.5 22.1 + - + +
160B HIS* 2.8 57.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 3.0 24.8 + + - +
30A HIS* 3.5 36.1 + + + +
34A TYR* 4.3 10.3 - - - -
73A HIS* 4.4 2.2 - + - -
156A ASP* 3.5 1.0 + - - -
158A TRP* 3.7 25.0 - + + +
159A GLU* 1.3 72.4 - - - +
161A ALA* 1.3 67.3 + - + +
162A TYR 3.2 0.6 + - - -
163A TYR 4.4 3.4 + - - +
164A ILE* 5.3 4.9 + - - +
500A FE 2.1 31.6 - - - -
159B GLU* 2.8 41.8 + - - +
163B TYR* 3.7 28.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.8 15.1 - - - +
22A ALA* 5.7 1.6 - - - +
26A HIS* 3.5 30.2 + - + +
76A TYR* 4.7 1.1 + - - +
156A ASP* 3.8 15.9 - - - +
158A TRP 3.0 13.8 + - - +
159A GLU 2.9 1.6 + - - -
160A HIS* 1.3 85.5 - - - +
162A TYR* 1.3 59.7 + - + +
173A TYR* 3.7 29.3 - - + +
----------------------------------------------------------
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