Contacts of the helix formed by residues 125 - 132 (chain F) in PDB entry 2ZSU
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 GLY 125 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F ASP* 3.1 11.0 + - - -
124F GLY* 1.3 77.6 - - - +
126F ILE* 1.3 61.7 + - - +
127F LEU 3.5 0.2 - - - -
128F GLU* 3.9 12.2 + - - +
129F LYS* 3.7 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ILE* 4.0 13.9 - - + -
92F ARG* 3.9 28.3 - - + +
95F LEU* 3.7 26.9 - - + -
123F ASP* 2.9 22.6 + - + +
124F GLY 4.4 3.6 - - - +
125F GLY* 1.3 76.4 - - - +
127F LEU* 1.3 68.0 + - - +
129F LYS* 3.2 5.9 + - - +
130F MET* 3.0 38.2 + - - +
135F HIS* 3.9 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F GLY 3.5 25.8 - - - +
87F ASP 3.7 14.6 - - - +
88F GLY* 3.8 16.4 - - - -
91F ILE* 5.3 3.1 - - + -
105F MET* 4.0 21.3 - - + -
113F ILE* 3.7 30.4 - - + +
116F SER* 3.8 2.0 - - - -
117F ALA* 3.8 21.3 - - + +
123F ASP* 2.9 24.6 + - + +
126F ILE* 1.3 77.4 - - - +
128F GLU* 1.3 58.6 + - - +
130F MET* 3.1 8.8 + - - +
131F LEU* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ALA* 3.5 27.6 - - + +
123F ASP* 4.4 0.4 + - - -
125F GLY* 3.9 14.4 + - - +
126F ILE 3.3 0.4 - - - -
127F LEU* 1.3 76.9 - - - +
129F LYS* 1.3 59.6 + - + +
131F LEU* 3.0 19.5 + - - +
132F SER* 2.9 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F GLY 3.7 15.4 + - - +
126F ILE* 3.2 8.6 + - - +
128F GLU* 1.3 81.1 - - + +
130F MET* 1.4 57.6 + - - +
132F SER* 3.5 8.5 - - - +
133F ASP 2.9 7.3 + - - -
134F LYS* 2.7 46.8 + - + +
135F HIS* 3.5 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ILE* 3.3 33.2 - - + -
105F MET* 3.9 20.6 - - + +
126F ILE* 3.0 27.1 + - + +
127F LEU* 3.1 11.0 + - - +
129F LYS* 1.4 75.8 - - - +
131F LEU* 1.3 61.1 - - - +
133F ASP* 3.8 13.9 + - - +
135F HIS* 4.0 10.8 - - + -
138F GLY* 3.4 15.0 - - - +
139F LYS 3.2 20.9 - - - +
140F LEU* 3.1 60.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F LYS* 4.3 23.3 - - + +
113F ILE* 3.9 23.3 - - + -
114F GLU* 4.7 14.6 - - + -
117F ALA* 4.7 4.9 - - + -
127F LEU 2.9 19.4 + - - +
128F GLU* 3.0 31.6 + - - +
130F MET* 1.3 80.3 - - - +
132F SER* 1.3 58.5 + - - +
133F ASP* 3.3 5.3 + - - +
140F LEU* 3.5 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 132 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F GLU* 2.9 17.6 + - - -
129F LYS* 3.4 12.5 + - - +
131F LEU* 1.3 75.9 - - - +
133F ASP* 1.3 67.6 + - - +
134F LYS* 3.3 33.2 + - - +
----------------------------------------------------------
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