Contacts of the helix formed by residues 181 - 196 (chain F) in PDB entry 3LUE
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 ALA 181 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F SER* 4.2 9.0 - - - +
156F GLY 3.3 14.6 - - - +
157F ASP 3.5 17.7 - - - +
158F GLY 3.9 0.9 - - - -
159F VAL 3.6 23.3 - - - +
160F THR* 4.1 1.8 - - - +
180F LEU* 1.3 78.6 - - - +
182F GLY* 1.4 54.7 + - - +
183F ARG 3.3 1.6 - - - -
184F ASP* 2.9 35.7 + - - +
185F LEU* 3.5 5.3 + - - +
261F LEU* 5.1 0.7 - - - -
303F THR* 3.9 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 182 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F GLY 2.9 6.4 + - - -
157F ASP* 3.8 8.0 + - - -
181F ALA* 1.4 71.9 - - - +
183F ARG* 1.3 55.8 + - - +
185F LEU* 3.2 6.5 + - - +
186F THR* 3.0 31.1 + - - -
213F LYS* 3.2 14.6 + - - -
303F THR* 2.8 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F GLU* 1.1 184.5 + - + +
73F HIS* 2.7 45.8 + - + +
75F ILE 3.5 0.4 + - - -
77F THR* 2.1 37.5 - - - +
157F ASP* 3.2 14.4 + - - +
181F ALA 3.0 2.6 + - - -
182F GLY* 1.3 70.1 - - - +
184F ASP* 1.3 68.5 + - - +
186F THR* 3.3 6.1 + - - +
187F ASP* 3.0 33.7 + - - +
206F ARG* 5.0 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 184 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F HIS* 3.4 29.5 + - - -
157F ASP 4.3 0.9 - - - +
179F ASP 4.0 5.9 - - - +
180F LEU* 3.6 31.5 - - + -
181F ALA* 2.9 24.1 + - - +
183F ARG* 1.3 76.3 - - - +
185F LEU* 1.3 57.0 + - - +
187F ASP* 3.6 7.0 - - - +
188F TYR* 3.1 28.8 + - - +
267F LEU* 4.1 9.9 - - + +
269F MET* 4.0 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180F LEU* 3.9 25.6 - - + -
181F ALA 3.5 2.4 + - - +
182F GLY* 3.2 9.8 + - - +
183F ARG 3.1 0.2 - - - -
184F ASP* 1.3 79.0 - - - +
186F THR* 1.3 63.0 + - - +
188F TYR* 4.1 3.1 - - + +
189F LEU* 3.2 9.0 + - - +
213F LYS* 3.6 4.9 - - + +
257F CYS* 3.2 36.7 - - - +
258F PRO* 4.2 3.4 - - + -
260F ALA* 4.0 21.8 - - + -
261F LEU* 3.9 19.7 - - + -
267F LEU* 4.9 0.7 - - + -
303F THR* 3.9 12.8 - - + -
306F TYR* 3.1 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F GLY 3.0 9.9 + - - -
183F ARG* 3.3 6.9 + - - -
185F LEU* 1.3 73.5 - - - +
187F ASP* 1.3 62.6 + - - +
189F LEU* 3.4 5.7 + - - +
190F MET* 3.2 22.5 + - - +
206F ARG* 3.7 22.7 - - - +
209F VAL* 3.4 26.7 - - + +
210F ARG* 3.9 21.8 - - + +
213F LYS* 2.6 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F GLU* 4.8 8.0 - - - +
183F ARG* 3.0 23.9 + - - +
184F ASP* 3.6 6.9 - - - +
186F THR* 1.3 75.4 - - - +
188F TYR* 1.3 63.1 - - - +
190F MET* 3.7 15.6 + - - +
191F LYS* 3.4 20.6 + - - +
206F ARG* 3.1 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 188 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F ASP 3.1 15.9 + - - +
185F LEU* 4.2 3.8 - - - +
187F ASP* 1.3 77.3 - - - +
189F LEU* 1.3 65.4 + - - +
191F LYS* 3.6 21.4 + - - +
192F ILE* 3.1 52.4 + - + +
256F ARG* 3.3 30.8 + - - +
257F CYS* 4.2 18.6 - - - -
260F ALA* 4.4 4.7 - - + -
266F PHE* 3.3 43.0 + + + +
267F LEU* 3.4 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F LEU 3.2 18.5 + - - +
186F THR 3.5 3.1 - - - +
187F ASP 3.3 0.2 - - - -
188F TYR* 1.3 78.2 - - - +
190F MET* 1.3 50.7 + - - +
192F ILE* 3.2 16.2 + - + +
193F LEU* 2.8 48.1 + - + +
209F VAL* 3.2 38.8 - - + +
212F ILE* 4.1 13.9 - - + -
213F LYS* 3.6 21.1 - - + +
217F CYS* 4.5 9.9 - - - -
250F ILE* 5.3 2.0 - - + -
253F GLU* 4.6 13.7 - - + +
257F CYS* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 190 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186F THR 3.2 5.8 + - - +
187F ASP* 3.7 28.7 - - - +
189F LEU* 1.3 78.8 - - - +
191F LYS* 1.3 51.8 + - - +
193F LEU* 3.4 4.3 + - - +
194F THR* 2.8 43.2 + - - +
200F PHE* 4.3 20.1 - - + +
206F ARG* 3.7 44.6 - - + +
209F VAL* 3.8 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187F ASP 3.4 14.1 + - - +
188F TYR* 3.8 30.6 - - - +
189F LEU 3.3 0.6 - - - -
190F MET* 1.3 74.5 - - - +
192F ILE* 1.3 72.4 + - - +
194F THR* 3.8 8.4 - - + -
195F GLU* 2.9 52.2 + - + +
173G HIS 5.9 1.8 - - - -
175G ILE 6.1 0.7 - - - -
176G LEU* 5.2 13.9 - - + -
284G LYS* 5.1 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F TYR* 3.1 59.0 + - + +
189F LEU* 3.3 19.7 - - + +
191F LYS* 1.3 78.0 - - - +
193F LEU* 1.3 61.9 + - + +
195F GLU* 3.2 26.4 + - - +
196F ARG* 3.3 12.0 + - - +
253F GLU* 3.9 44.7 - - + +
256F ARG* 3.8 33.0 + - + +
257F CYS* 4.3 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189F LEU* 2.8 30.3 + - + +
190F MET 3.6 4.9 - - - +
192F ILE* 1.3 74.7 - - - +
194F THR* 1.3 55.0 + - - +
196F ARG* 3.1 13.2 + - - +
198F TYR* 2.7 47.6 - - + +
200F PHE* 3.8 27.6 - - + -
209F VAL* 4.6 2.7 - - + -
212F ILE* 3.9 21.8 - - + -
248F ILE* 4.5 5.6 - - + -
250F ILE* 3.9 25.4 - - + -
253F GLU* 3.9 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190F MET* 2.8 26.6 + - - +
191F LYS* 4.0 8.5 - - + +
193F LEU* 1.3 66.7 - - - +
195F GLU* 1.3 66.0 + - + +
196F ARG 3.1 1.8 - - - -
197F GLY* 3.0 15.0 + - - -
198F TYR 3.5 24.4 + - - +
200F PHE* 3.8 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191F LYS* 2.9 48.7 + - + +
192F ILE* 3.2 24.7 + - - +
194F THR* 1.3 74.0 - - + +
196F ARG* 1.3 57.5 + - - +
197F GLY 2.8 11.7 + - - -
256F ARG* 5.4 3.2 + - - +
110G LEU* 6.4 3.1 - - + -
113G LYS* 3.5 11.1 + - - +
175G ILE 5.5 2.8 - - - +
177G ARG* 5.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 196 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192F ILE 3.3 9.8 + - - +
193F LEU 3.1 13.4 + - - +
195F GLU* 1.3 73.5 - - - +
197F GLY* 1.3 62.5 + - - +
198F TYR* 3.4 23.9 + - + -
237F GLU* 2.9 32.9 + - - -
249F THR* 3.0 34.6 + - - +
251F GLY* 4.1 1.0 - - - +
252F ASN 5.2 0.4 - - - +
253F GLU* 3.2 33.2 + - - +
113G LYS* 3.1 31.7 + - - +
----------------------------------------------------------
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