Contacts of the helix formed by residues 181 - 196 (chain K) in PDB entry 6LTJ
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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156K GLY 3.3 11.7 - - - +
157K ASP 3.3 16.4 - - - +
158K GLY 3.7 2.2 - - - +
159K VAL 3.4 26.9 - - - +
160K THR* 3.8 7.9 - - + -
180K LEU* 1.3 78.3 - - - +
182K GLY* 1.3 57.3 + - - +
183K ARG 3.2 2.0 - - - -
184K ASP* 3.2 7.7 + - - +
185K LEU* 2.8 37.0 + - - +
261K LEU* 5.3 2.1 - - - +
303K THR* 4.6 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 182 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156K GLY 3.0 10.7 + - - -
157K ASP* 3.4 10.1 + - - -
181K ALA* 1.3 76.3 - - - +
183K ARG* 1.3 51.8 + - - +
185K LEU* 4.0 7.0 - - - +
186K THR* 2.3 39.1 + - - -
213K LYS* 4.6 1.6 - - - -
303K THR* 3.6 20.1 + - - -
306K TYR* 5.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157K ASP* 3.0 38.4 + - - +
158K GLY* 5.3 1.1 - - - -
182K GLY* 1.3 75.0 - - - +
184K ASP* 1.3 70.3 + - - +
186K THR* 3.2 6.7 + - - -
187K ASP* 2.4 67.3 + - - +
206K ARG* 4.5 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 184 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157K ASP 5.6 0.7 - - - -
158K GLY 5.1 5.0 - - - +
179K ASP* 3.6 8.5 - - - +
180K LEU* 3.3 28.3 - - + +
181K ALA* 3.2 11.4 + - - +
183K ARG* 1.3 88.8 + - - +
185K LEU* 1.3 60.9 + - - +
187K ASP* 3.2 12.2 + - - +
188K TYR* 3.0 26.7 + - - +
267K LEU* 4.3 16.0 - - + +
269K MET* 5.3 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180K LEU* 6.1 0.9 - - + +
181K ALA 2.8 21.3 + - - +
182K GLY* 4.0 5.2 - - - +
184K ASP* 1.3 72.5 - - - +
186K THR* 1.3 57.0 + - - +
188K TYR* 3.3 5.2 + - + +
189K LEU 2.9 19.4 + - - -
213K LYS* 2.8 26.9 + - - +
257K CYS* 3.3 30.5 - - - +
258K PRO* 4.1 12.3 - - + -
260K ALA* 4.1 14.1 - - + -
261K LEU* 3.8 32.8 - - + -
267K LEU* 4.6 7.1 - - + +
303K THR* 3.8 18.2 - - + -
306K TYR* 4.4 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157K ASP* 5.1 0.7 + - - -
182K GLY 2.3 27.0 + - - -
183K ARG* 3.2 9.5 + - - -
185K LEU* 1.3 74.0 - - - +
187K ASP* 1.3 59.2 + - - +
189K LEU* 3.1 4.3 + - - +
190K MET* 2.9 34.4 + - + +
206K ARG* 3.5 35.7 - - - +
209K VAL* 3.9 20.4 - - + -
210K ARG* 5.3 8.6 - - - +
213K LYS* 3.6 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183K ARG* 2.4 56.4 + - - +
184K ASP* 3.4 11.9 - - - +
186K THR* 1.3 77.0 - - - +
188K TYR* 1.3 57.5 + - - +
190K MET* 3.2 12.7 + - - +
191K LYS* 3.0 30.7 + - - +
206K ARG* 4.1 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 188 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184K ASP 3.0 13.3 + - - +
185K LEU* 3.7 8.1 - - + +
186K THR 3.3 0.2 - - - -
187K ASP* 1.3 73.4 - - - +
189K LEU* 1.3 60.0 + - - +
191K LYS* 3.3 19.6 + - + +
192K ILE* 2.9 47.9 + - + +
256K ARG 3.8 23.6 - - - -
257K CYS* 4.5 6.5 - - - -
260K ALA* 4.4 10.5 - - + -
266K PHE* 2.7 49.1 + + - -
267K LEU* 3.2 47.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K LEU 2.9 5.7 + - - -
186K THR* 3.3 9.6 - - - +
188K TYR* 1.3 74.9 - - - +
190K MET* 1.3 61.5 + - - +
192K ILE* 3.4 7.1 - - + +
193K LEU* 2.9 56.6 + - + +
209K VAL* 4.1 22.2 - - + +
212K ILE* 4.3 18.2 - - + -
213K LYS* 3.4 45.3 - - + +
217K CYS* 5.9 3.4 - - + -
253K GLU* 4.9 2.9 - - + +
257K CYS* 3.7 24.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 190 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186K THR* 2.9 24.8 + - + +
187K ASP* 3.2 15.7 + - - +
189K LEU* 1.3 77.7 - - - +
191K LYS* 1.3 51.6 + - + +
193K LEU 3.3 1.7 + - - -
194K THR* 2.8 41.8 + - + +
200K PHE* 3.5 44.4 - - + -
206K ARG* 4.1 26.9 - - + +
209K VAL* 3.7 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187K ASP* 3.0 16.5 + - - +
188K TYR* 3.7 26.7 - - + +
190K MET* 1.3 76.0 - - + +
192K ILE* 1.3 58.5 + - - +
194K THR* 2.3 36.1 + - - +
195K GLU* 3.2 9.8 + - - +
267K LEU 5.5 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188K TYR* 2.9 43.4 + - + +
189K LEU* 3.4 20.9 - - + +
191K LYS* 1.3 76.0 - - - +
193K LEU* 1.3 72.8 + - + +
195K GLU* 3.2 28.5 - - - +
196K ARG* 3.2 21.3 - - - +
253K GLU* 3.8 8.5 - - + +
256K ARG* 3.6 46.7 - - + +
257K CYS* 5.1 2.2 - - + -
266K PHE* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189K LEU* 2.9 40.1 + - + +
190K MET* 3.5 0.4 - - - -
192K ILE* 1.3 79.7 - - - +
194K THR* 1.3 61.3 - - - +
195K GLU 3.3 1.3 - - - -
196K ARG* 3.7 10.0 + - + +
197K GLY 4.2 0.5 + - - -
198K TYR 3.0 18.1 + - - +
200K PHE* 3.5 28.5 - - + -
209K VAL* 6.2 1.6 - - + -
212K ILE* 6.0 9.6 - - + -
248K ILE* 4.9 6.5 - - + -
250K ILE* 3.7 38.6 - - + -
253K GLU* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190K MET* 2.8 21.8 + - + +
191K LYS* 2.3 32.9 + - - +
193K LEU* 1.3 76.9 - - - +
195K GLU* 1.3 64.2 + - - +
197K GLY* 4.0 6.8 + - - -
198K TYR 4.3 7.5 - - - +
199K SER* 5.3 8.6 - - - +
200K PHE* 4.6 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191K LYS 3.2 6.6 + - - +
192K ILE* 3.2 48.7 - - - +
193K LEU 3.3 0.4 - - - -
194K THR* 1.3 85.2 + - - +
196K ARG* 1.3 67.9 + - - +
197K GLY* 3.0 8.5 + - - -
256K ARG* 3.5 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 196 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192K ILE 3.2 21.3 - - - +
193K LEU* 3.7 8.9 + - - +
194K THR 3.4 1.0 - - - -
195K GLU* 1.3 81.8 - - - +
197K GLY* 1.3 56.6 + - - +
198K TYR 3.8 2.0 - - - +
237K GLU* 4.4 10.1 + - - -
248K ILE* 6.2 0.2 - - - -
250K ILE* 3.7 24.1 - - + +
251K GLY* 3.6 23.8 - - - +
252K ASN* 3.4 17.5 + - - +
253K GLU* 2.7 33.8 + - - +
256K ARG* 4.1 7.1 - - - +
----------------------------------------------------------
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