Contacts of the strand formed by residues 188 - 192 (chain B) in PDB entry 1D0N
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 CYS 188 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLN* 4.0 0.2 - - - -
165B VAL* 3.0 45.3 + - + +
187B ASP* 1.3 75.9 - - - +
189B PHE* 1.3 70.1 + - - +
199B GLN* 5.0 2.0 - - + -
200B TRP 3.1 5.6 - - - +
201B CYS* 2.0 46.7 - - - -
205B SER* 4.5 5.2 - - - -
209B GLU* 4.5 5.4 - - - +
210B ARG* 3.9 22.0 - - - -
213B ALA* 3.8 10.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
162B LEU* 4.0 22.7 - - + -
163B LEU 3.1 6.5 - - - +
164B GLN* 3.6 36.1 - - + -
165B VAL* 4.8 0.2 - - - -
176B VAL* 4.8 0.2 - - + -
182B SER* 3.2 30.7 - - - -
183B PHE* 3.5 39.9 - + + -
184B ASN* 3.8 33.9 - - - -
187B ASP* 3.9 18.4 - - + -
188B CYS* 1.3 78.6 - - - +
190B ILE* 1.3 65.3 + - - +
191B LEU 4.1 0.2 + - - -
198B TYR 3.7 0.7 - - - +
199B GLN* 3.6 2.3 - - - +
200B TRP* 2.6 42.3 + + - +
----------------------------------------------------------
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
----------------------------------------------------------
161B ARG 3.7 0.2 - - - +
162B LEU* 3.4 6.4 - - - +
163B LEU* 2.8 51.9 + - + +
165B VAL* 5.1 11.2 - - + -
173B ALA* 5.7 0.2 - - + -
189B PHE* 1.3 78.1 - - - +
191B LEU* 1.3 61.0 + - - +
192B ASP* 3.4 5.5 + - - +
197B ILE* 3.4 33.4 - - + -
198B TYR 3.4 5.6 - - - +
199B GLN* 4.4 9.0 - - + -
213B ALA 4.0 5.2 - - - +
216B VAL* 3.8 32.1 - - + -
217B SER* 3.3 25.6 - - - +
220B ILE* 4.4 11.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
161B ARG 3.5 16.2 - - - +
162B LEU* 4.0 18.3 - - + +
178B VAL* 4.4 18.6 - - + -
183B PHE* 6.1 0.2 - - + -
189B PHE 4.1 1.0 + - - -
190B ILE* 1.3 70.5 - - - +
192B ASP* 1.3 56.7 + - - +
193B LEU* 3.5 34.9 + - + -
197B ILE* 3.7 0.3 - - - -
198B TYR* 2.8 47.8 + - + +
243B MET* 3.6 44.2 - - + -
246B VAL* 4.3 11.2 - - + -
247B LEU* 4.5 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 3.2 10.4 - - - +
160B GLN* 3.4 2.1 - - - -
161B ARG* 2.6 81.3 + - + +
163B LEU* 5.1 3.1 - - + -
190B ILE* 3.4 10.3 + - + +
191B LEU* 1.3 69.1 - - - +
193B LEU* 1.3 63.7 + - - +
194B GLY 3.4 3.1 + - - -
196B ASN 4.5 1.1 - - - -
197B ILE* 3.8 10.9 - - - +
220B ILE* 3.9 7.5 - - - +
225B ARG* 2.9 36.1 + - - -
----------------------------------------------------------
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