Contacts of the strand formed by residues 189 - 195 (chain F) in PDB entry 5LK5
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 189 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F LYS* 4.0 6.3 - - - +
186F ILE 3.1 32.4 + - - +
187F ASP* 3.9 5.2 - - - -
188F ASN* 1.3 80.4 - - - +
190F GLN* 1.3 70.6 + - - +
191F VAL* 3.4 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 190 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F GLU* 3.0 34.5 + - + +
184F VAL 3.6 5.4 - - - -
185F LYS* 3.9 8.5 - - - +
189F SER* 1.3 79.0 + - - +
191F VAL* 1.3 65.6 + - - +
192F GLU* 3.8 16.1 + - - +
193F SER* 3.0 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F ILE* 3.9 19.8 - - + +
162F ARG 5.8 0.2 - - - +
184F VAL* 2.8 35.9 + - + +
186F ILE* 3.9 30.7 - - + +
189F SER* 3.7 9.9 - - - +
190F GLN* 1.3 80.0 - - - +
192F GLU* 1.3 69.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F LYS* 3.0 40.5 + - + +
160F ASP 4.9 4.7 - - - +
161F ILE* 3.8 38.2 - - + +
182F TYR* 3.8 15.0 - - + +
183F GLU* 3.4 3.5 - - - +
184F VAL* 2.8 36.0 + - + +
190F GLN* 3.8 4.5 - - - +
191F VAL* 1.3 87.3 - - + +
193F SER* 1.3 81.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F LYS* 2.9 21.5 + - - -
182F TYR* 3.4 22.4 - - - -
183F GLU* 4.3 5.2 - - - -
190F GLN* 3.0 26.6 + - - -
192F GLU* 1.3 84.0 + - - +
194F GLY* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 194 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F LYS* 4.5 0.9 - - - -
181F THR* 3.3 10.0 - - - +
182F TYR* 2.9 37.6 + - - +
193F SER* 1.3 79.2 - - - +
195F SER* 1.3 61.9 + - - -
199F ASP* 3.7 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F ASP 5.3 0.6 + - - -
180F ASN 3.3 6.5 - - - -
181F THR* 3.9 14.6 - - - +
182F TYR* 3.8 4.7 - - - -
194F GLY* 1.3 74.1 + - - -
196F LEU* 1.3 66.4 + - - +
197F GLU* 3.3 17.0 - - - -
198F ASP* 3.1 25.6 + - - +
199F ASP* 3.0 25.9 + - - +
----------------------------------------------------------
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