Contacts of the helix formed by residues 137 - 145 (chain D) in PDB entry 2WZJ
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 VAL 137 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLY 3.9 0.4 + - - -
136D GLU* 1.3 68.5 - - - +
138D PHE* 1.3 56.5 + - - +
140D TYR* 2.9 8.5 + - - +
141D LEU* 2.7 45.9 + - + +
147D MET* 4.4 10.1 - - + -
155D LYS* 5.4 0.7 - - + -
159D ILE* 5.8 0.2 - - + -
178D ALA* 3.8 11.0 - - + +
181D LEU* 2.7 42.1 + - + +
183D LEU* 3.9 15.0 - - + +
189D ILE* 3.7 20.6 - - + -
243D LEU* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D GLU* 3.9 12.8 - - - +
137D VAL* 1.3 75.1 - - - +
139D ASP* 1.3 93.4 + - - +
141D LEU* 3.0 18.0 + - + +
142D VAL* 3.0 36.5 + - + +
178D ALA* 2.9 36.5 + - + +
179D GLU* 3.8 29.6 - - + -
215D TYR* 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLY* 6.1 0.2 - - - -
136D GLU* 3.2 37.1 + - + +
137D VAL 3.4 0.4 - - - -
138D PHE* 1.3 96.3 - - - +
140D TYR* 1.3 56.9 + - - +
142D VAL* 3.6 8.5 + - - +
143D ALA* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D GLU 3.1 13.9 + - - +
137D VAL* 2.9 11.1 + - - +
139D ASP* 1.3 76.3 - - - +
141D LEU* 1.3 63.1 + - + +
143D ALA* 3.3 3.3 + - - -
144D HIS* 2.9 64.5 + + + +
145D GLY 5.4 1.3 - - - -
146D ARG 6.1 0.2 - - - -
147D MET* 3.7 37.7 - - + -
151D GLU* 3.0 23.3 + - - -
183D LEU* 4.0 18.2 - - + -
187D MET* 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D VAL* 2.7 35.3 + - + +
138D PHE* 3.6 6.1 - - + +
140D TYR* 1.3 73.2 - - + +
142D VAL* 1.3 59.5 + - + +
145D GLY* 2.8 48.1 + - - +
146D ARG* 4.3 3.1 - - - -
147D MET* 4.4 17.5 - - + -
178D ALA* 4.9 6.5 - - + -
242D THR* 3.6 42.6 - - - +
243D LEU* 4.1 19.5 - - + +
246D GLY* 4.8 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D PHE* 3.0 43.5 + - + +
139D ASP* 3.7 12.1 - - - +
141D LEU* 1.3 77.4 - - + +
143D ALA* 1.3 64.1 + - + +
145D GLY 4.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ASP 3.1 17.2 + - - +
140D TYR* 4.6 0.9 - - - -
142D VAL* 1.3 82.2 - - + +
144D HIS* 1.3 80.6 + - + +
145D GLY 3.6 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D TYR* 2.9 56.3 + + + +
143D ALA* 1.3 92.1 + - + +
145D GLY* 1.3 65.8 + - - +
146D ARG 3.8 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D TYR* 4.4 1.9 - - - +
141D LEU* 2.8 34.3 + - - +
142D VAL 4.5 1.8 + - - -
143D ALA 3.6 1.6 - - - -
144D HIS* 1.3 77.5 - - - +
146D ARG* 1.3 69.2 + - - +
147D MET* 5.2 0.3 - - - +
246D GLY* 4.8 3.1 - - - -
----------------------------------------------------------
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