Contacts of the strand formed by residues 190 - 196 (chain B) in PDB entry 2OSL
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 VAL 190 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LYS 4.0 0.2 - - - +
149B VAL* 3.6 4.7 - - - +
150B ASP* 2.8 50.2 + - - +
151B ASN* 5.4 4.7 - - - +
189B LYS* 1.3 78.7 - - + +
191B TYR* 1.3 67.4 + - - +
192B ALA* 4.1 4.7 - - + +
207B SER* 4.5 17.0 - - - +
208B PHE 4.0 6.7 - - - +
209B ASN* 4.1 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 3.5 8.9 - - + +
131B VAL* 4.6 11.9 - - + -
147B TRP* 5.7 2.5 - + + -
148B LYS 3.7 1.6 - - - -
149B VAL* 3.6 31.0 - - + -
178B LEU* 4.9 2.9 - - + -
180B LEU* 3.8 16.1 - - + +
184B ASP 3.8 1.7 + - - -
185B TYR* 2.6 55.6 + + - -
188B HIS* 3.3 40.1 - - + +
189B LYS 3.5 10.5 - - - -
190B VAL* 1.3 72.4 - - - +
192B ALA* 1.3 60.3 + - - +
207B SER* 3.1 18.0 - - - -
208B PHE* 3.1 45.5 + + + +
210B ARG* 4.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 4.2 2.7 - - - -
147B TRP* 3.3 10.9 - - - -
148B LYS* 2.7 57.6 + - + +
151B ASN* 6.1 0.9 - - - +
190B VAL* 4.1 5.3 - - + -
191B TYR* 1.3 74.8 - - - +
193B CYS* 1.3 62.5 + - - +
194B GLU* 4.2 0.4 - - + -
205B THR* 4.0 12.3 - - - +
206B LYS 3.9 0.4 - - - -
207B SER* 3.6 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL* 5.0 1.3 - - - +
116B ILE* 3.9 11.2 - - + -
133B CYS* 2.0 51.8 - - + -
145B VAL* 3.6 20.9 - - - -
146B GLN 3.9 3.6 - - - -
147B TRP* 4.1 5.6 - - + -
192B ALA* 1.3 76.7 - - - +
194B GLU* 1.3 58.5 + - - +
195B VAL* 3.9 8.8 + - - +
204B VAL 3.8 1.0 - - - +
205B THR* 3.4 4.3 - - - -
206B LYS* 3.1 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LYS 3.5 1.2 - - - +
145B VAL* 3.4 4.2 - - - -
146B GLN* 2.9 54.0 + - + +
148B LYS* 3.5 23.4 - - + +
192B ALA* 4.2 0.6 - - + +
193B CYS* 1.3 73.4 - - - +
195B VAL* 1.3 62.3 + - - +
196B THR* 5.6 3.3 - - - +
203B PRO* 3.6 26.2 - - + +
204B VAL 3.6 9.4 - - - +
205B THR* 4.0 17.2 - - + +
107L ARG* 4.0 14.2 + - - -
108L THR* 3.4 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PRO* 4.3 7.0 - - + -
114B VAL* 4.5 16.6 - - + -
135B LEU* 3.6 49.6 - - + -
144B LYS 3.3 4.9 - - - +
145B VAL* 4.1 8.7 - - + -
193B CYS* 4.1 12.3 - - - -
194B GLU* 1.3 77.6 - - - +
196B THR* 1.3 72.8 + - - +
197B HIS* 4.7 0.9 - - + -
200B LEU* 4.2 16.0 - - + +
203B PRO* 3.3 3.2 - - - +
204B VAL* 2.8 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA* 3.7 3.1 - - - -
144B LYS* 3.0 66.4 + - - +
194B GLU* 5.4 4.3 - - - +
195B VAL* 1.3 75.1 - - - +
197B HIS* 1.3 63.8 + - - +
203B PRO* 3.4 36.6 - - + -
15L PRO* 5.6 4.5 - - + -
----------------------------------------------------------
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