Contacts of the helix formed by residues 181 - 196 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I SER* 4.2 8.3 - - - +
156I GLY 3.3 13.7 - - - +
157I ASP 3.5 17.3 - - - +
158I GLY 3.9 0.6 - - - -
159I VAL 3.6 24.0 - - - +
160I THR* 4.1 1.8 - - - +
180I LEU* 1.3 78.2 - - - +
182I GLY* 1.4 55.2 + - - +
183I ARG 3.3 2.0 - - - -
184I ASP* 2.9 35.8 + - - +
185I LEU* 3.5 6.3 + - - +
261I LEU* 5.1 0.7 - - - -
303I THR* 3.9 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 182 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156I GLY 2.9 6.2 + - - -
157I ASP* 4.3 7.6 - - - -
181I ALA* 1.4 71.5 - - - +
183I ARG* 1.3 55.6 + - - +
185I LEU* 3.2 6.5 + - - +
186I THR* 3.0 30.7 + - - -
213I LYS* 3.2 15.4 + - - -
303I THR* 2.8 29.2 + - - +
306I TYR* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I GLU* 1.1 182.4 + - + +
73I HIS* 2.7 44.4 + - - +
75I ILE 3.5 0.2 + - - -
77I THR* 2.1 38.9 - - - +
157I ASP* 3.2 14.4 + - - +
181I ALA 3.0 2.4 + - - -
182I GLY* 1.3 69.6 - - - +
184I ASP* 1.3 67.6 + - - +
186I THR* 3.3 5.8 + - - +
187I ASP* 3.0 34.2 + - - +
206I ARG* 5.0 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 184 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I HIS* 3.4 29.5 + - - -
157I ASP 4.3 1.0 - - - +
179I ASP 4.0 5.9 - - - +
180I LEU* 3.6 31.6 - - + -
181I ALA 2.9 23.8 + - - +
183I ARG* 1.3 75.0 - - - +
185I LEU* 1.3 56.3 + - - +
187I ASP* 3.6 6.5 - - - +
188I TYR* 3.1 28.4 + - - +
267I LEU* 4.1 10.8 - - + +
269I MET* 4.0 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180I LEU* 3.9 25.4 - - + -
181I ALA 3.5 2.9 + - - +
182I GLY* 3.2 8.5 + - - +
183I ARG 3.1 0.2 - - - -
184I ASP* 1.3 79.8 - - - +
186I THR* 1.3 62.8 + - - +
188I TYR* 4.1 3.5 - - + +
189I LEU* 3.2 9.7 + - - +
213I LYS* 3.6 4.7 - - + -
257I CYS* 3.2 37.5 - - - +
258I PRO* 4.2 3.4 - - + -
260I ALA* 4.0 21.5 - - + -
261I LEU* 3.9 20.9 - - + -
267I LEU* 4.9 1.1 - - + -
303I THR* 3.9 11.4 - - + -
306I TYR* 3.1 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182I GLY 3.0 9.8 + - - -
183I ARG* 3.8 6.9 - - - -
185I LEU* 1.3 73.4 - - - +
187I ASP* 1.3 62.4 + - - +
189I LEU* 3.4 5.7 + - - +
190I MET* 3.2 22.3 + - - +
206I ARG* 3.7 23.1 - - - +
207I GLU* 5.4 0.2 - - - +
209I VAL* 3.4 26.7 - - + +
210I ARG* 3.9 22.3 - - + +
213I LYS* 2.6 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I GLU* 4.8 8.3 - - - +
183I ARG* 3.0 23.6 + - - +
184I ASP* 3.6 6.7 - - - +
186I THR* 1.3 75.6 - - - +
188I TYR* 1.3 62.8 + - - +
190I MET* 3.7 15.0 + - - +
191I LYS* 3.4 21.0 + - - +
206I ARG* 3.1 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 188 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I ASP 3.1 15.9 + - - +
185I LEU* 3.6 4.5 + - - +
186I THR 3.4 0.2 - - - -
187I ASP* 1.3 76.9 - - - +
189I LEU* 1.3 65.4 + - - +
191I LYS* 3.8 21.4 - - - +
192I ILE* 3.1 51.1 + - + +
256I ARG* 3.3 31.1 + - - +
257I CYS* 4.2 18.8 - - - -
260I ALA* 4.4 4.7 - - + -
266I PHE* 3.3 43.7 + + + +
267I LEU* 3.4 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I LEU 3.2 18.1 + - - +
186I THR* 3.5 3.4 - - - +
188I TYR* 1.3 77.5 - - - +
190I MET* 1.3 50.0 + - - +
192I ILE* 3.2 16.2 + - + +
193I LEU* 2.8 48.4 + - + +
209I VAL* 3.2 38.4 - - + +
212I ILE* 4.1 13.2 - - + -
213I LYS* 3.6 20.9 - - + +
217I CYS* 4.5 9.4 - - - -
250I ILE* 5.3 3.4 - - + -
253I GLU* 4.6 12.6 - - + +
257I CYS* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 190 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I THR 3.2 6.8 + - - +
187I ASP* 3.7 29.2 - - - +
188I TYR 3.4 0.2 - - - -
189I LEU* 1.3 78.4 - - - +
191I LYS* 1.3 51.9 + - - +
193I LEU* 3.4 4.8 + - - +
194I THR* 2.8 43.6 + - - +
200I PHE* 4.3 20.0 - - + +
206I ARG* 3.7 44.9 - - + +
209I VAL* 3.8 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I ASP 3.4 13.9 + - - +
188I TYR* 3.8 31.0 - - - +
189I LEU 3.3 0.6 - - - -
190I MET* 1.3 75.4 - - - +
192I ILE* 1.3 71.9 + - - +
194I THR* 3.8 8.4 - - + -
195I GLU* 2.9 50.1 + - + +
173J HIS 5.9 1.3 - - - -
175J ILE 6.1 0.9 - - - -
176J LEU* 5.2 14.4 - - + -
284J LYS* 5.1 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I TYR* 3.1 57.7 + - + +
189I LEU* 3.3 19.3 - - + +
191I LYS* 1.3 79.5 - - - +
193I LEU* 1.3 61.4 + - - +
195I GLU* 3.2 25.8 + - - +
196I ARG* 3.3 11.8 + - - +
253I GLU* 3.9 44.9 - - + +
256I ARG* 3.8 33.0 + - + +
257I CYS* 4.3 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I LEU* 2.8 31.4 + - + +
190I MET 3.6 4.9 - - - +
192I ILE* 1.3 75.8 - - - +
194I THR* 1.3 55.2 + - - +
196I ARG* 3.1 13.0 + - - +
198I TYR* 2.7 45.8 + - + +
200I PHE* 3.8 26.9 - - + -
209I VAL* 4.6 2.7 - - + -
212I ILE* 3.9 20.9 - - + -
248I ILE* 4.5 5.8 - - + -
250I ILE* 3.9 26.9 - - + -
253I GLU* 3.9 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I MET* 2.8 26.7 + - - +
191I LYS* 4.0 7.9 - - + +
193I LEU* 1.3 67.6 - - - +
195I GLU* 1.3 65.5 + - + +
196I ARG 3.1 1.6 - - - -
197I GLY* 3.0 14.8 + - - -
198I TYR 3.5 23.6 + - - +
200I PHE* 3.8 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191I LYS* 2.9 49.0 + - + +
192I ILE* 3.2 25.0 + - - +
194I THR* 1.3 73.8 - - + +
196I ARG* 1.3 57.9 + - - +
197I GLY 2.8 11.1 + - - -
256I ARG* 5.4 3.0 + - - +
110J LEU* 6.4 3.4 - - + -
113J LYS* 3.5 11.6 + - - +
175J ILE 5.5 2.8 - - - +
177J ARG* 5.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 196 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I ILE 3.3 9.4 + - - +
193I LEU 3.1 13.4 + - - +
195I GLU* 1.3 73.1 - - - +
197I GLY* 1.3 61.9 + - - +
198I TYR* 3.4 25.3 + - + -
237I GLU* 2.9 31.9 + - - -
249I THR* 3.0 34.9 + - - +
251I GLY* 4.1 1.0 - - - +
252I ASN 5.2 0.6 - - - +
253I GLU* 3.2 33.8 + - - +
113J LYS* 3.1 31.4 + - - +
----------------------------------------------------------
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