Contacts of the helix formed by residues 227 - 235 (chain F) in PDB entry 1ZUM
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 THR 227 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F GLU* 5.2 7.2 + - - +
54F GLY 4.0 4.2 + - - -
55F ASP* 3.5 37.2 - - - +
56F LYS* 5.4 0.3 - - - +
224F PHE* 3.0 26.9 + - + +
225F GLY 3.0 0.6 - - - -
226F PRO* 1.3 86.6 - - + +
228F ALA* 1.3 66.5 + - - -
229F GLY 3.4 0.9 - - - -
230F ALA* 3.4 1.4 + - - +
231F ALA* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F GLY 3.6 24.6 + - - +
55F ASP* 4.5 2.4 - - - +
59F VAL* 3.6 15.8 - - + +
192F LYS* 3.8 21.5 - - + -
221F VAL* 4.6 5.2 - - + -
223F GLY* 4.4 3.4 - - - -
224F PHE 3.0 12.7 + - - +
227F THR* 1.3 79.5 + - - +
229F GLY* 1.3 62.5 + - - +
231F ALA* 3.3 3.9 + - - +
232F ILE* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F ILE* 3.6 25.8 - - - +
192F LYS* 3.9 16.6 - - - +
224F PHE 3.3 3.6 + - - -
225F GLY* 3.2 13.0 + - - -
228F ALA* 1.3 78.7 - - - +
230F ALA* 1.3 61.3 + - - +
232F ILE* 3.2 6.4 + - - +
233F ALA* 3.1 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225F GLY 2.9 7.7 + - - +
226F PRO* 3.3 29.2 - - + +
227F THR 3.9 0.4 - - - +
228F ALA 3.4 0.4 - - - -
229F GLY* 1.3 75.0 - - - +
231F ALA* 1.3 64.6 + - - +
233F ALA* 3.2 8.1 + - - +
234F SER* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F LYS* 3.7 40.2 - - + +
59F VAL* 4.0 13.0 - - + +
227F THR 2.9 19.4 + - - +
228F ALA 3.5 4.9 - - - +
229F GLY 3.2 0.2 - - - -
230F ALA* 1.3 77.0 - - - +
232F ILE* 1.3 60.9 + - - +
234F SER* 3.5 7.1 + - - -
235F HIS* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F VAL* 3.7 23.3 - - + -
63F VAL* 5.8 0.4 - - + -
163F GLY* 3.6 31.6 - - - -
164F GLN 4.6 0.4 - - - +
165F ILE* 4.6 7.6 - - + -
190F VAL* 3.8 27.6 - - + +
191F MET 4.5 0.2 - - - -
192F LYS* 3.6 34.5 - - + +
221F VAL* 5.5 1.8 - - + -
228F ALA 3.1 13.7 + - - +
229F GLY 3.2 6.9 + - - +
231F ALA* 1.3 76.8 - - - +
233F ALA* 1.3 60.0 + - - +
234F SER 3.3 0.3 + - - -
235F HIS* 3.4 9.2 + - - +
238F VAL* 3.9 10.5 - - + +
241F VAL* 4.5 7.6 - - + -
263F LYS* 3.0 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F ILE* 5.1 3.1 - - + -
229F GLY 3.1 12.2 + - - +
230F ALA* 3.7 10.3 - - - +
232F ILE* 1.3 77.4 - - - +
234F SER* 1.3 57.9 + - - +
241F VAL* 4.2 24.1 - - + +
263F LYS* 3.0 24.8 + - - +
265F VAL* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 234 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F LYS* 6.1 1.2 - - - -
230F ALA 2.9 17.6 + - - -
231F ALA* 3.5 10.2 + - - -
233F ALA* 1.3 77.2 - - - +
235F HIS* 1.3 65.4 + - - +
236F GLU* 3.3 8.5 + - - +
263F LYS* 4.6 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 235 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F LYS* 5.8 1.6 - - + -
59F VAL* 4.5 5.6 - - + -
60F ASP* 3.0 36.4 + - + -
63F VAL* 3.6 37.8 - - + +
64F LYS* 6.3 0.7 - - + -
231F ALA 3.0 16.4 + - - +
232F ILE* 3.4 3.3 + - - +
234F SER* 1.3 74.6 - - - +
236F GLU* 1.3 69.3 + - + +
237F ASP* 2.9 36.6 + - + -
238F VAL* 3.4 19.3 + - + -
263F LYS* 2.8 28.6 + - - -
----------------------------------------------------------
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