Contacts of the helix formed by residues 132 - 136 (chain E) in PDB entry 4ZXB
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 132 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E THR 3.9 1.0 + - - -
131E ILE* 1.3 71.0 - - - +
133E TRP* 1.3 62.5 + - - +
134E SER* 2.6 28.9 + - - -
135E ARG* 3.0 35.3 + - + +
136E ILE* 4.2 2.4 - - - +
172E THR* 2.7 21.8 + - + +
181E ARG* 3.5 28.0 + - + +
189E GLN* 2.9 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E LEU* 4.0 20.2 - - + -
104E LEU* 4.0 7.9 - - + -
109E LEU* 4.5 4.3 - - + -
112E ILE* 4.3 11.2 - - + -
117E VAL* 3.9 15.0 - - + -
119E ILE* 3.9 18.4 - - + -
128E LEU* 4.4 9.1 + - + +
131E ILE* 3.5 44.1 + - + +
132E ASP* 1.3 67.9 + - - +
134E SER* 1.4 55.4 + - - +
135E ARG 3.0 5.6 - - - -
136E ILE* 2.8 40.9 + - + +
137E LEU* 2.9 40.9 + - + +
140E VAL* 3.7 14.1 - - + -
143E ASN* 3.9 9.0 - - - +
145E ILE* 3.7 24.7 - - + +
183E TRP* 4.2 8.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E ASP* 2.6 27.9 + - - -
133E TRP* 1.4 76.8 - - - +
135E ARG* 1.3 72.2 + - - +
137E LEU 3.4 18.0 - - - +
138E ASP* 5.4 0.9 - - - -
140E VAL* 3.7 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E MET 3.4 11.4 - - - +
111E ASN* 5.6 0.9 + - - -
132E ASP* 3.0 25.9 + - + +
133E TRP 3.0 1.0 - - - -
134E SER* 1.3 89.5 + - - +
136E ILE* 1.3 58.5 + - + +
137E LEU 5.5 0.2 - - - -
172E THR* 3.5 32.5 - - + +
189E GLN* 3.6 23.8 - - - +
190E LYS 5.5 4.0 - - - +
191E VAL* 4.8 21.1 - - + +
194E THR* 6.0 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E LEU* 3.6 26.2 - - + +
110E MET* 3.5 8.5 - - - +
111E ASN* 3.5 17.8 + - - +
112E ILE* 2.9 61.1 + - + +
131E ILE* 4.1 4.7 - - + -
132E ASP 4.2 2.0 - - - +
133E TRP* 2.8 30.4 + - + +
135E ARG* 1.3 83.7 - - + +
137E LEU* 1.3 56.2 + - + +
183E TRP* 3.7 23.6 - - + -
189E GLN* 4.0 20.0 - - + +
----------------------------------------------------------
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