Contacts of the helix formed by residues 144 - 152 (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 ASP 144 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F VAL* 4.2 0.4 - - - -
108F ILE* 4.2 22.5 - - + +
143F GLY* 1.3 72.1 - - - -
145F GLY* 1.3 64.6 + - - +
146F VAL* 2.6 38.5 + - - +
147F LYS* 3.2 24.8 + - + +
148F PHE* 3.1 23.6 + - - +
171F MET* 5.0 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F ILE* 4.1 35.7 - - - +
106F VAL* 4.2 14.5 + - - -
108F ILE* 5.2 2.2 - - - +
143F GLY 3.5 3.8 + - - -
144F ASP* 1.3 76.8 + - - +
146F VAL* 1.3 59.3 + - - -
148F PHE* 3.5 3.5 + - - +
149F ILE* 3.3 22.0 + - - +
171F MET* 5.9 2.3 - - - +
172F LEU* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F ASP* 2.6 14.9 + - - +
145F GLY* 1.3 69.4 - - - -
147F LYS* 1.3 62.1 + - - +
149F ILE* 2.8 27.6 - - + +
150F GLU* 3.2 21.5 - - + +
171F MET* 4.1 35.4 - - + +
172F LEU* 4.1 10.1 - - + +
177F PHE* 3.9 32.3 - - + -
180F ASN* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F ASP* 3.2 26.2 + - + +
146F VAL* 1.3 79.1 - - - +
148F PHE* 1.3 63.1 + - - +
150F GLU* 3.1 36.8 + - + +
151F GLU* 3.3 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F LEU* 3.9 20.6 - - + -
83F ILE* 6.2 0.4 - - + -
104F ILE* 4.0 17.0 - - + -
106F VAL* 3.9 24.2 - - + -
141F ILE* 3.8 28.5 - - + -
144F ASP 3.1 18.2 + - - +
145F GLY* 3.7 6.3 - - - +
146F VAL 3.3 0.2 - - - -
147F LYS* 1.3 78.3 - - - +
149F ILE* 1.3 59.2 + - - +
150F GLU 3.3 0.2 + - - -
151F GLU* 3.3 2.3 + - - -
152F ASN* 2.9 75.7 + - + +
155F PHE* 3.6 25.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F LEU* 3.9 24.5 - - + -
83F ILE* 4.8 4.5 - - + -
145F GLY 3.3 7.2 + - - +
146F VAL* 2.8 25.4 - - - +
148F PHE* 1.3 81.0 - - + +
150F GLU* 1.3 51.9 + - + +
151F GLU 3.4 0.2 - - - -
152F ASN 3.6 5.6 - - - +
155F PHE* 5.3 0.4 - - + -
158F ILE* 4.0 13.5 - - + -
177F PHE* 3.5 32.8 - - + -
180F ASN* 3.7 10.7 - - + +
181F ALA* 3.8 22.4 - - + +
183F ARG* 2.4 28.8 + - - -
184F ALA* 3.4 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146F VAL* 3.2 31.9 - - + +
147F LYS* 3.5 32.9 - - + +
148F PHE 3.1 1.0 - - - -
149F ILE* 1.3 77.4 - - + +
151F GLU* 1.3 63.8 + - + +
176F GLU* 4.0 14.1 - - - +
180F ASN* 3.5 26.4 + - - +
183F ARG* 3.1 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F LYS* 3.3 41.6 + - - +
148F PHE* 3.3 3.7 + - - +
150F GLU* 1.3 85.8 - - + +
152F ASN* 1.3 70.8 + - - +
153F SER* 5.4 0.3 + - - -
183F ARG* 4.6 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 152 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ARG* 6.0 0.8 + - - +
148F PHE* 2.9 75.3 + - + +
149F ILE* 3.6 6.8 - - - +
151F GLU* 1.3 86.1 + - - +
153F SER* 1.3 57.5 + - - +
155F PHE* 4.1 6.8 - - + -
183F ARG* 2.6 24.5 + - - -
184F ALA* 3.6 7.8 - - - +
----------------------------------------------------------
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