Contacts of the helix formed by residues 158 - 166 (chain A) in PDB entry 1LDJ
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 GLU 158 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.6 1.2 + - - -
134A ASN* 3.6 16.3 + - - +
140A LEU* 6.5 0.9 - - - -
141A ASN* 3.3 29.1 + - + +
145A VAL* 4.3 9.3 - - + +
157A TYR* 1.3 88.0 - - - +
159A ILE* 1.3 59.5 + - - +
160A TYR* 5.9 0.7 - - - -
161A SER* 2.6 34.0 + - - +
162A LEU* 3.4 10.0 + - - +
219A PHE* 4.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 5.1 5.2 - - + -
92A LEU* 4.5 14.1 - - + -
96A LEU* 3.9 20.4 - - + -
130A SER 5.2 0.2 - - - +
133A LEU* 3.9 37.0 - - + -
134A ASN* 3.4 13.0 - - - +
137A CYS* 3.6 24.0 - - + -
140A LEU* 6.0 3.7 - - + +
141A ASN* 3.0 32.7 - - - +
158A GLU* 1.3 70.6 - - - +
160A TYR* 1.3 57.5 + - - +
161A SER 3.1 1.1 - - - -
162A LEU* 2.6 31.6 + - + +
163A ALA* 2.6 17.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG* 3.0 25.3 + - + -
130A SER* 3.9 29.4 - - - -
131A LYS* 4.2 13.2 - - + -
134A ASN* 2.7 40.7 - - + +
158A GLU* 5.3 1.1 - - - +
159A ILE* 1.3 73.4 - - - +
161A SER* 1.3 59.6 - - - +
163A ALA* 2.7 31.9 + - - +
164A LEU* 3.0 34.9 + - + +
210A GLU* 2.6 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 4.1 4.0 - - - -
158A GLU* 2.6 45.8 + - - +
160A TYR* 1.3 83.3 - - - +
162A LEU* 1.3 57.1 + - - +
164A LEU* 2.7 33.3 + - - +
165A VAL* 2.9 20.7 + - - +
214A ASN* 5.4 10.1 - - - -
219A PHE* 5.2 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 2.8 45.3 - - + +
93A LYS* 3.7 32.5 - - + +
96A LEU* 3.3 32.8 - - + -
157A TYR* 5.2 3.8 - - + -
158A GLU 3.5 4.5 - - - +
159A ILE* 2.6 18.6 + - + +
161A SER* 1.3 77.5 + - - +
163A ALA* 1.3 51.9 + - - +
165A VAL* 4.3 13.5 - - + -
166A THR* 2.5 55.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 4.6 8.3 - - + -
126A TYR* 2.3 30.8 + - + +
130A SER* 3.2 39.3 - - - +
133A LEU* 5.7 0.2 - - + -
159A ILE* 2.6 14.3 + - + +
160A TYR* 2.7 20.5 + - + +
162A LEU* 1.3 75.1 - - - +
164A LEU* 1.3 54.0 + - - +
166A THR* 3.3 3.4 - - - -
167A TRP 3.1 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TRP* 3.2 39.0 - - + -
126A TYR* 5.3 3.4 - - + -
127A ARG* 6.2 0.7 - - - -
160A TYR* 3.0 51.1 + - + +
161A SER* 2.7 16.8 + - - +
163A ALA* 1.3 67.9 - - - +
165A VAL* 1.3 58.1 + - + +
166A THR 3.1 1.1 - - - -
167A TRP* 2.5 26.0 + - - +
168A ARG* 2.9 10.7 + - - +
210A GLU* 3.5 18.4 - - - +
211A LEU* 3.5 15.3 - - + +
213A LEU* 5.8 0.9 - - - -
214A ASN* 4.5 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS* 6.2 2.7 - - - -
161A SER* 2.9 18.1 + - - +
162A LEU* 3.8 16.8 - - + +
164A LEU* 1.3 74.5 - - - +
166A THR* 1.3 61.4 + - - +
168A ARG* 2.9 65.5 + - - +
169A ASP* 3.6 3.3 + - - +
213A LEU* 4.8 3.3 - - + +
214A ASN* 3.6 31.4 - - + +
215A GLU* 3.7 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS* 4.7 3.5 + - - +
96A LEU* 3.4 31.2 - - + +
97A LYS* 3.8 12.3 + - + +
100A LEU* 2.8 35.9 - - + +
126A TYR* 3.8 1.3 - - - +
162A LEU* 2.5 43.9 + - - +
163A ALA 3.3 6.5 - - - -
165A VAL* 1.3 77.6 - - - +
167A TRP* 1.3 56.0 + - - +
169A ASP* 3.4 24.7 - - - +
----------------------------------------------------------
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