Contacts of the helix formed by residues 183 - 193 (chain B) in PDB entry 3OTB
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 LEU 183 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLY 4.2 8.5 - - - +
182B THR* 1.3 80.4 - - - +
184B ALA* 1.3 69.4 + - - +
185B ALA* 4.3 7.4 - - + +
186B ASP* 3.0 30.5 - - + +
187B LYS* 3.3 15.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
152B HIS* 6.1 3.1 - - + -
156B LEU* 4.3 20.6 - - + +
183B LEU* 1.3 79.3 - - - +
185B ALA* 1.3 61.1 + - - +
186B ASP 3.2 0.2 + - - -
187B LYS* 3.4 2.9 + - - +
188B ASN* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 4.3 5.5 - - + +
184B ALA* 1.3 79.8 - - - +
186B ASP* 1.3 62.4 + - - +
187B LYS 3.5 0.2 - - - -
188B ASN* 3.9 8.0 - - - +
189B GLU* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ARG* 4.7 7.8 + - - -
181B GLY 4.8 0.7 - - - +
182B THR* 3.3 24.9 - - - +
183B LEU* 3.0 42.8 + - - +
184B ALA 3.1 0.6 - - - -
185B ALA* 1.3 80.8 - - - +
187B LYS* 1.3 61.3 + - - +
189B GLU* 3.7 4.3 - - - +
190B ILE* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 3.9 32.7 - - + +
157B TYR* 3.9 29.8 - - - +
160B VAL* 4.1 16.9 - - + +
179B LEU* 3.7 15.6 + - + -
182B THR* 2.8 46.9 + - - +
183B LEU 3.3 9.7 + - - +
184B ALA* 4.1 4.0 - - - +
186B ASP* 1.3 72.7 - - - +
188B ASN* 1.3 64.8 + - - +
189B GLU 2.9 4.3 - - - -
190B ILE* 2.9 21.9 + - - +
191B LEU* 3.1 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 4.4 12.6 - - + +
184B ALA 3.1 17.1 + - - +
185B ALA* 4.0 9.0 - - - +
187B LYS* 1.3 78.0 - - - +
189B GLU* 1.3 60.4 + - - +
191B LEU* 3.6 8.1 - - - +
192B PHE* 3.4 22.3 + - - +
197B ILE 4.8 0.2 - - - +
198B ASN* 5.8 0.9 - - - -
199B TYR* 4.0 33.2 + - - +
200B ASN* 4.1 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ALA 3.0 19.4 + - - +
186B ASP* 3.7 4.9 - - - +
187B LYS 2.9 0.8 - - - -
188B ASN* 1.3 77.8 - - - +
190B ILE* 1.3 63.3 + - - +
191B LEU 2.8 6.8 + - - -
192B PHE* 3.2 17.3 + - - +
193B SER* 2.9 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B VAL* 2.9 30.3 - - + -
164B LEU* 4.6 8.3 - - + -
178B ARG* 3.4 44.9 - - + +
179B LEU* 4.1 20.0 - - + -
182B THR* 4.9 2.5 - - + -
186B ASP 3.1 11.9 + - - +
187B LYS* 2.9 7.9 + - - +
189B GLU* 1.3 77.4 - - - +
191B LEU* 1.3 55.9 + - - +
193B SER* 5.5 0.4 - - - -
194B GLU* 2.7 40.3 - - + +
195B PHE* 3.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 4.9 4.0 - - + -
159B THR* 3.9 22.7 - - + +
160B VAL* 4.0 25.1 - - + -
163B ALA* 4.6 0.7 - - + -
187B LYS 3.1 11.0 + - - +
188B ASN* 3.6 11.0 - - - +
189B GLU 2.8 1.2 + - - -
190B ILE* 1.3 75.5 - - - +
192B PHE* 1.3 62.7 + - - +
193B SER 3.1 1.3 - - - -
195B PHE* 2.9 33.0 + - + -
196B ASN 3.0 5.7 + - - -
197B ILE* 3.3 41.1 + - + +
199B TYR* 3.6 45.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ASN* 3.4 15.6 + - - +
189B GLU* 3.2 17.4 + - - +
191B LEU* 1.3 79.6 - - - +
193B SER* 1.3 67.2 + - - +
196B ASN* 3.2 30.9 + - - +
197B ILE 3.0 15.8 + - - +
198B ASN* 4.4 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU* 2.9 38.1 + - - -
190B ILE* 5.5 0.4 - - - -
192B PHE* 1.3 83.8 - - - +
194B GLU* 1.3 63.4 + - - +
195B PHE 3.6 1.1 - - - -
196B ASN 4.5 0.7 - - - -
----------------------------------------------------------
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