Contacts of the helix formed by residues 136 - 141 (chain D) in PDB entry 3REO
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 136 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 4.0 7.5 + - - +
132D LEU 3.3 12.6 + - - +
133D LEU* 3.2 18.6 + - - +
134D ALA 3.4 0.4 - - - -
135D THR* 1.3 80.3 - - - +
137D LYS* 1.3 69.3 + - - +
138D VAL* 2.8 28.4 + - - +
139D LEU* 3.0 19.0 + - + +
140D LEU* 3.1 11.3 + - - +
174D ARG* 2.8 43.3 + - - -
175D ILE* 4.6 8.1 - - + -
178D VAL* 4.3 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LYS* 4.7 8.3 - - - +
141B GLU* 2.4 41.3 + - - -
144B PHE* 3.6 46.3 - - + -
145B TYR* 6.2 0.9 - - - -
39D LYS* 4.5 2.0 - - - +
135D THR 3.6 1.8 + - - -
136D ASP* 1.3 76.9 + - - +
138D VAL* 1.3 67.9 + - + +
140D LEU* 3.1 11.4 + - - +
141D GLU* 3.4 23.3 + - + +
174D ARG* 5.4 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ASP* 2.8 9.4 + - - +
137D LYS* 1.3 82.5 - - + +
139D LEU* 1.3 61.1 + - + +
141D GLU* 3.8 0.4 - - - +
142D PRO* 3.3 15.9 - - - +
157D PHE* 4.5 8.3 - - + -
161D TYR* 2.8 37.1 + - + +
168D TYR* 3.9 36.3 - - + +
172D ASP* 4.2 5.4 - - - +
174D ARG* 3.5 22.4 - - - +
175D ILE* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D LEU* 3.3 52.0 - - + +
134D ALA* 4.3 4.7 - - - +
136D ASP* 3.0 8.4 + - + +
138D VAL* 1.3 81.1 - - + +
140D LEU* 1.3 64.9 + - - +
142D PRO* 3.6 3.6 - - - +
143D TRP* 3.4 8.1 - - - -
157D PHE* 4.2 15.5 - - + -
165D ILE* 4.1 16.6 - - + -
175D ILE* 4.8 14.1 - - + -
179D PHE* 5.4 1.6 - - + -
326D TYR* 3.0 43.5 + - + +
369D EUG 3.6 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA* 4.3 23.1 - - + -
36B MET* 5.7 3.4 - - + -
140B LEU* 6.1 10.3 - - + -
144B PHE* 3.5 25.4 - - + -
36D MET* 3.8 20.9 - - + -
134D ALA 4.1 13.2 - - - +
135D THR 3.3 24.9 - - - +
136D ASP 3.1 10.1 + - - +
137D LYS 3.1 6.6 + - - +
139D LEU* 1.3 79.5 - - - +
141D GLU* 1.3 64.2 + - - +
143D TRP* 3.2 33.7 + - + +
144D PHE* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LYS* 2.7 43.0 - - - +
137D LYS* 3.4 19.8 + - + +
138D VAL 3.8 0.2 - - - +
140D LEU* 1.3 74.4 - - - +
142D PRO* 1.3 70.7 - - + +
144D PHE* 3.0 23.7 + - - +
145D TYR* 3.5 30.8 + - - -
160D ALA* 4.5 3.7 - - + +
161D TYR* 3.4 28.5 - - + +
----------------------------------------------------------
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