Contacts of the helix formed by residues 184 - 193 (chain B) in PDB entry 3ORH
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 ASP 184 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B MET* 3.6 2.8 - - - +
182B TYR* 4.0 3.4 - - - +
183B SER* 1.4 82.6 + - - +
185B ILE* 1.3 57.7 + - - +
186B THR* 3.1 23.0 + - - -
187B ILE* 3.1 32.1 + - + +
188B MET* 3.0 25.8 + - - +
225B PHE* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TRP* 5.7 4.0 - - + -
178B MET* 3.6 22.3 - - + +
183B SER 4.2 0.4 + - - -
184B ASP* 1.3 69.9 + - - +
186B THR* 1.4 62.7 + - - +
188B MET* 3.5 5.3 + - + +
189B PHE* 3.0 26.5 + - - +
211B VAL* 3.8 25.8 - - + -
223B TYR* 3.4 26.0 - - - +
225B PHE* 4.0 15.4 - - + -
227B GLN* 3.4 34.9 + - + +
228B MET 3.9 0.7 - - - -
229B ILE* 3.8 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP* 3.1 9.8 + - - -
185B ILE* 1.4 74.9 - - - +
187B ILE* 1.4 62.5 + - + +
189B PHE* 3.4 2.9 + - - +
190B GLU* 2.9 32.8 + - + +
209B THR* 4.7 16.2 - - + +
211B VAL* 3.6 23.4 - - - +
229B ILE* 3.9 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TYR* 3.9 16.2 - - + -
184B ASP* 3.1 33.6 + - + +
186B THR* 1.4 75.8 - - + +
188B MET* 1.4 64.8 + - - +
190B GLU* 3.2 7.4 + - + +
191B GLU* 2.9 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TRP* 3.9 34.5 - - - -
177B LEU* 3.9 15.0 - - + -
178B MET* 3.7 24.7 - - + +
182B TYR* 3.6 38.1 - - + -
184B ASP 3.0 7.5 + - - +
185B ILE* 3.6 12.3 - - - +
186B THR 3.4 0.2 - - - -
187B ILE* 1.4 74.8 - - - +
189B PHE* 1.4 59.7 + - - +
192B THR* 2.8 51.6 + - - +
193B GLN* 4.6 0.9 - - - -
229B ILE* 6.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B TYR* 3.6 24.9 - + - -
174B TRP* 4.2 6.7 - + - -
185B ILE 3.0 14.5 + - - +
186B THR* 3.6 7.4 - - + +
187B ILE 3.3 0.2 - - - -
188B MET* 1.4 77.5 - - - +
190B GLU* 1.3 60.7 + - - +
193B GLN* 2.9 47.5 + - + +
194B VAL* 3.3 27.5 + - + -
197B LEU* 4.1 8.1 - - + -
204B ARG* 6.2 0.4 - - - -
207B ILE* 4.2 15.5 - - + -
209B THR* 5.0 12.3 - - + -
229B ILE* 3.9 32.8 - - + -
231B PRO* 3.6 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B THR* 2.9 22.7 + - + +
187B ILE* 3.2 10.1 + - + +
189B PHE* 1.3 79.8 - - - +
191B GLU* 1.3 63.5 + - + +
194B VAL* 3.4 34.7 - - - +
195B PRO* 3.6 6.9 - - - +
204B ARG* 2.9 43.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TYR* 2.8 43.5 + - + +
187B ILE* 2.9 29.6 + - + +
190B GLU* 1.3 80.3 - - + +
192B THR* 1.3 60.3 + - - +
195B PRO* 3.8 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PHE* 3.3 22.2 - - - -
177B LEU* 4.1 16.0 - - + +
181B LYS* 6.2 0.7 - - + -
182B TYR* 3.6 32.1 - - + +
188B MET* 2.8 31.5 + - - +
191B GLU* 1.3 77.8 - - - +
193B GLN* 1.3 78.2 + - - +
195B PRO* 4.4 3.6 - - - +
196B ALA* 5.2 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B HIS 5.0 2.8 + - - -
148B GLN* 3.0 22.2 + - - +
149B PHE* 3.3 14.6 - - - -
168B TYR* 2.9 30.8 + - - +
173B SER* 5.1 1.0 + - - -
174B TRP* 3.2 25.4 - - + +
177B LEU* 5.0 2.6 - - - +
188B MET* 4.8 0.2 - - - -
189B PHE* 2.9 43.7 + - + +
192B THR* 1.3 108.8 + - - +
194B VAL* 1.4 64.5 + - - +
195B PRO* 3.4 2.5 - - - -
196B ALA* 3.3 8.3 + - - +
197B LEU* 3.2 22.9 + - - +
----------------------------------------------------------
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