Contacts of the helix formed by residues 179 - 187 (chain B) in PDB entry 1LUA
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 179 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B THR 3.4 0.6 - - - -
178B ALA* 1.3 80.3 - - - +
180B ASP* 1.3 66.8 + - - +
181B ALA* 4.0 11.3 - - - +
182B SER* 3.0 24.0 + - - -
183B ARG* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 1.3 73.5 - - + +
181B ALA* 1.3 65.0 + - - +
183B ARG* 2.9 30.3 + - - +
184B ALA* 2.8 25.3 + - - +
203B LEU 5.8 0.4 - - - -
205B PRO* 5.6 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 3.3 13.2 + - - +
180B ASP* 1.3 78.6 - - - +
182B SER* 1.3 57.4 + - - +
184B ALA* 3.4 7.1 + - - +
185B GLU* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLU 3.3 22.0 + - - -
177B THR* 3.3 14.4 - - - +
178B ALA 4.2 2.0 + - - -
179B ASP* 3.0 25.5 + - - -
181B ALA* 1.3 75.0 - - - +
183B ARG* 1.3 57.5 + - - +
185B GLU* 3.3 8.2 + - - +
186B ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.6 29.5 - - + +
152B ARG* 4.9 1.0 - - - +
177B THR* 3.9 34.6 + - - +
178B ALA 4.4 3.2 + - - -
179B ASP* 3.0 18.4 + - - +
180B ASP* 2.9 37.3 + - - +
182B SER* 1.3 74.7 - - - +
184B ALA* 1.3 65.9 + - - +
186B ALA* 3.1 14.1 + - - +
187B VAL* 3.4 17.2 + - - +
202B GLU 4.0 18.0 + - - -
203B LEU* 3.3 43.2 + - - +
204B LEU* 5.3 0.7 - - - -
1456B NAP 4.2 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASP 2.8 17.8 + - - +
181B ALA* 3.7 8.1 - - - +
183B ARG* 1.3 73.0 - - - +
185B GLU* 1.3 61.3 + - - +
187B VAL* 3.1 24.5 - - - +
188B LYS* 3.8 13.5 - - - +
204B LEU* 5.0 1.1 - - - +
208B ALA* 4.0 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ALA 2.9 18.2 + - - +
182B SER* 3.3 10.5 - - - +
184B ALA* 1.3 78.3 - - - +
186B ALA* 1.3 62.4 + - - +
187B VAL 3.2 0.7 + - - -
188B LYS* 3.2 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LYS* 3.7 19.4 + - - -
124B VAL* 3.7 11.3 - - + +
126B LEU* 4.8 4.7 - - + -
148B VAL* 6.0 1.7 - - + +
150B CYS* 4.4 14.6 - - - -
175B ALA* 5.9 2.5 - - + -
177B THR* 3.9 19.7 - - + -
182B SER 2.9 13.6 + - - +
183B ARG* 3.1 10.0 + - - +
185B GLU* 1.3 75.9 - - - +
187B VAL* 1.3 60.5 + - - +
188B LYS 3.5 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 4.4 8.1 - - + -
126B LEU* 4.1 9.2 - - + -
183B ARG 3.4 9.6 + - - +
184B ALA* 3.1 21.1 - - - +
186B ALA* 1.3 76.3 - - - +
188B LYS* 1.3 65.9 + - + +
189B GLY 3.4 0.3 + - - -
190B ALA* 3.2 22.8 + - - +
193B VAL* 4.0 31.0 - - + -
204B LEU* 4.0 17.7 - - + -
208B ALA 3.5 23.6 - - - +
212B GLU* 4.0 1.5 - - + +
215B ILE* 4.0 16.2 - - + +
----------------------------------------------------------
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