Contacts of the helix formed by residues 182 - 195 (chain B) in PDB entry 3LSG
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 SER 182 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER* 3.5 0.2 - - - -
181B LEU* 1.3 75.3 - - - +
183B SER* 1.3 58.3 + - - +
184B GLY 3.6 3.5 + - - -
185B TYR* 3.2 22.4 + - - +
186B LEU* 2.9 25.8 + - - +
222C TYR* 3.5 34.6 - - - +
226C GLU* 5.8 3.8 - - - -
233C VAL* 5.9 2.7 - - - -
184D GLY* 3.8 16.0 + - - -
188D ILE* 5.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLU* 4.0 37.3 + - - +
172B LEU* 4.4 9.4 - - - +
173B SER* 5.2 2.0 - - - -
176B SER* 3.3 20.0 + - - -
182B SER* 1.3 72.4 - - - +
184B GLY* 1.3 58.9 + - - +
186B LEU* 4.3 2.0 - - - -
187B SER* 2.8 37.1 + - - -
222C TYR* 4.8 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLU 5.3 2.7 - - - -
182B SER* 3.1 6.1 + - - -
183B SER* 1.3 84.1 + - - +
185B TYR* 1.3 61.0 + - - +
187B SER* 3.9 5.5 - - - -
188B ILE* 3.8 12.0 - - - +
182D SER* 3.7 21.8 + - - -
184D GLY* 4.3 5.8 - - - -
185D TYR* 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 3.9 28.3 - - + -
182B SER* 3.2 17.9 + - - +
184B GLY* 1.3 75.1 - - - +
186B LEU* 1.3 62.4 + - - +
188B ILE* 3.3 3.3 + - - -
189B MSE 2.9 64.0 + - + +
184D GLY 3.6 12.3 - - - +
185D TYR* 3.5 41.0 - + - +
188D ILE* 3.4 43.2 - - + +
189D MSE 4.9 2.0 - - + -
192D LYS* 5.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 4.7 2.7 - - + -
172B LEU* 3.5 22.7 - - + -
175B LEU* 3.6 26.7 - - + -
176B SER* 3.4 27.6 - - - +
179B LEU* 3.6 17.3 - - + -
181B LEU* 4.3 7.0 - - + -
182B SER 2.9 17.1 + - - +
183B SER* 4.1 1.6 - - - +
185B TYR* 1.3 78.1 - - - +
187B SER* 1.3 68.3 + - - +
189B MSE 3.6 29.8 - - + +
190B PHE* 2.7 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLU 3.2 20.1 + - - -
232A ASP* 3.3 36.1 - - - +
233A VAL* 4.8 3.1 - - - -
234A ASN* 4.9 0.7 + - - -
172B LEU* 3.4 12.8 - - - +
183B SER 2.8 25.9 + - - -
184B GLY* 3.9 7.2 - - - -
186B LEU* 1.3 76.4 - - - +
188B ILE* 1.3 69.4 + - - +
190B PHE* 3.9 4.2 - - - +
191B LYS* 3.4 19.8 + - - +
197B PRO* 5.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL* 4.0 20.6 - - + -
234A ASN* 3.8 22.9 - - - +
184B GLY 3.8 14.6 - - - +
185B TYR 3.3 1.0 + - - -
186B LEU 3.2 0.2 - - - -
187B SER* 1.3 77.4 - - - +
189B MSE 1.3 66.8 + - - +
191B LYS* 3.3 6.3 + - + +
192B LYS* 3.1 23.2 + - + +
181D LEU* 4.7 12.3 - - + -
182D SER* 5.3 3.4 - - - +
185D TYR* 3.5 38.1 - - + -
212E LEU* 5.8 1.8 - - + -
216E THR* 3.8 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ALA* 6.0 2.5 - - + -
157B ILE* 3.7 26.5 - - + -
179B LEU* 4.9 0.2 - - + -
181B LEU* 3.3 35.0 - - + -
185B TYR* 2.9 44.5 + - + +
186B LEU* 3.6 15.0 - - + +
188B ILE* 1.3 77.3 - - - +
190B PHE* 1.3 68.6 + - - +
192B LYS* 3.4 11.0 + - + +
193B ASN* 3.0 49.4 + - - +
185D TYR* 4.4 4.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 3.8 24.0 - - + -
161B ILE* 3.8 11.7 - - + -
172B LEU* 5.8 0.2 - - + -
175B LEU* 4.6 4.5 - - + -
186B LEU* 2.7 30.3 + - + +
187B SER* 3.9 4.0 - - - +
189B MSE 1.3 79.4 - - - +
191B LYS* 1.3 58.3 + - - +
193B ASN 3.0 1.4 + - - -
194B PHE* 2.8 71.7 + + + -
196B ILE 3.4 13.7 - - - -
198B PHE* 3.3 49.4 - + + +
201B TYR* 3.6 29.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ASN* 3.7 35.4 + - + +
187B SER 3.4 11.1 + - - +
188B ILE* 3.3 8.3 + - + +
190B PHE* 1.3 78.6 - - - +
192B LYS* 1.3 58.1 + - - +
195B GLY* 2.7 47.0 + - - -
196B ILE* 3.6 29.6 - - - +
197B PRO* 3.9 12.1 - - + -
212E LEU* 6.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 3.1 14.5 + - + +
189B MSE 3.5 13.7 - - + +
191B LYS* 1.3 78.7 - - - +
193B ASN* 1.3 82.2 + - - +
195B GLY* 4.3 2.1 + - - -
185D TYR* 6.0 0.2 - - - +
192D LYS* 6.2 2.2 - - - +
216E THR* 3.5 23.6 - - - +
217E THR* 4.2 26.7 - - + +
218E GLU* 4.2 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B SER* 4.2 14.4 + - - -
153B ALA* 5.3 5.0 - - - +
154B LYS* 3.4 32.5 + - + +
157B ILE* 5.5 0.9 - - - +
189B MSE 3.0 46.9 + - - +
190B PHE* 3.0 5.0 + - - +
192B LYS* 1.3 98.3 - - - +
194B PHE* 1.3 76.2 + - + +
195B GLY 3.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LYS* 3.4 53.6 + - + +
157B ILE* 4.0 19.1 - - + -
158B GLN* 3.5 24.7 - - + -
190B PHE* 2.8 64.1 + + + +
193B ASN* 1.3 82.2 - - + +
195B GLY* 1.3 58.5 + - - +
196B ILE* 3.1 16.7 + - + +
201B TYR* 3.6 32.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LYS* 2.7 38.4 + - - -
192B LYS 4.3 1.9 + - - -
193B ASN 3.6 1.6 - - - -
194B PHE* 1.3 70.6 - - - +
196B ILE* 1.3 64.8 + - - +
----------------------------------------------------------
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