Contacts of the helix formed by residues 227 - 235 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E GLU* 5.1 4.7 + - - +
54E GLY 4.0 4.1 + - - -
55E ASP* 3.4 36.5 - - - +
56E LYS* 5.6 0.2 - - - +
224E PHE* 3.3 31.1 + - + +
225E GLY 3.0 0.8 + - - -
226E PRO* 1.3 84.1 - - + +
228E ALA* 1.3 64.6 + - - -
229E GLY 3.4 0.7 - - - -
230E ALA* 3.4 1.6 + - - +
231E ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E GLY 3.5 25.5 + - - +
55E ASP* 4.6 1.8 - - - +
59E VAL* 3.6 17.8 - - + +
192E LYS* 4.0 17.5 - - + -
221E VAL* 4.3 7.0 - - + -
223E GLY* 4.5 2.5 - - - -
224E PHE 3.0 13.4 + - - +
227E THR* 1.3 78.6 + - - +
229E GLY* 1.3 64.1 + - - +
231E ALA* 3.2 3.4 + - - +
232E ILE* 3.1 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E ILE* 3.7 28.6 - - - +
192E LYS* 4.1 14.0 - - - +
224E PHE 3.3 4.4 + - - -
225E GLY* 3.3 14.0 + - - -
228E ALA* 1.3 78.2 - - - +
230E ALA* 1.3 61.9 + - - +
232E ILE* 3.3 3.0 + - - +
233E ALA* 3.2 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E GLY 3.0 7.7 + - - +
226E PRO* 3.4 26.7 - - + +
227E THR 3.4 1.3 + - - +
228E ALA 3.3 0.2 - - - -
229E GLY* 1.3 75.5 - - - +
231E ALA* 1.3 55.5 + - - +
233E ALA* 3.3 5.6 + - - +
234E SER* 2.8 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E LYS* 3.9 31.2 - - + +
59E VAL* 3.8 22.0 - - + +
227E THR 2.9 18.1 + - - +
228E ALA* 3.4 6.1 - - - +
230E ALA* 1.3 77.6 - - - +
232E ILE* 1.3 57.2 + - - +
234E SER* 3.9 3.4 - - - -
235E HIS* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E VAL* 3.6 24.9 - - + -
163E GLY* 3.5 32.3 - - - -
164E GLN 5.0 0.2 - - - +
165E ILE* 4.9 7.0 - - + -
190E VAL* 3.8 27.8 - - + +
191E MET 4.5 1.1 - - - +
192E LYS* 3.6 33.7 - - + +
221E VAL* 5.3 2.0 - - + -
228E ALA 3.1 12.7 + - - +
229E GLY* 3.7 6.3 - - - +
230E ALA 3.3 0.4 - - - -
231E ALA* 1.3 76.8 - - - +
233E ALA* 1.3 63.3 + - - +
234E SER 3.2 0.9 + - - -
235E HIS* 3.3 15.3 + - - +
238E VAL* 3.7 20.3 - - + +
241E VAL* 4.7 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E ILE* 5.1 3.4 - - + -
229E GLY 3.2 13.6 + - - +
230E ALA* 3.8 7.4 - - - +
232E ILE* 1.3 79.8 - - - +
234E SER* 1.3 58.8 + - - +
241E VAL* 4.2 25.9 - - + +
263E LYS* 3.2 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 234 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E ALA* 2.8 25.4 + - - +
231E ALA* 4.2 4.3 - - - -
233E ALA* 1.3 75.8 - - - +
235E HIS* 1.3 67.6 + - - +
236E GLU* 3.2 10.9 + - - +
263E LYS* 4.0 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 235 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E LYS* 5.9 3.4 - - + -
59E VAL* 4.6 4.0 - - + -
60E ASP* 2.7 37.0 + - + -
63E VAL* 3.5 36.5 - - + +
64E LYS* 6.3 1.3 - - + -
231E ALA* 3.0 18.9 + - + +
232E ILE* 3.3 10.0 + - - +
234E SER* 1.3 75.8 - - - +
236E GLU* 1.3 65.4 + - + +
237E ASP* 2.9 35.6 + - + +
238E VAL* 3.4 15.3 + - + -
263E LYS* 3.0 20.3 + - - -
----------------------------------------------------------
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