Contacts of the strand formed by residues 190 - 197 (chain F) in PDB entry 1FZB
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 GLY 190 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F CYS* 3.5 23.0 - - - +
154F GLN* 2.5 35.0 + - - +
157F ALA* 3.8 6.5 - - - -
183F GLU 3.6 4.7 - - - -
184F ILE* 4.7 2.7 - - - -
188F GLY 3.6 0.8 + - - -
189F ASN* 1.3 70.5 - - - +
191F TRP* 1.3 63.5 + - - -
192F THR* 3.6 3.5 + - - +
387F ILE* 3.5 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 191 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F CYS* 3.5 0.8 - - - +
182F CYS* 3.4 4.7 - - - -
183F GLU* 2.7 71.8 + - + +
185F ASP* 4.3 8.2 + - + -
189F ASN* 4.2 19.5 - - + +
190F GLY* 1.3 70.7 - - - -
192F THR* 1.3 60.0 + - - +
193F VAL* 3.7 2.2 + - + -
245F ALA 4.4 2.7 - - - -
246F LEU 5.6 0.2 - - - -
247F ARG* 3.6 62.8 - - + +
385F LYS* 3.4 41.0 - - + +
386F ILE* 3.7 9.2 - - - -
387F ILE* 3.7 40.6 - - + -
392F LEU* 4.7 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 192 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F ASP* 4.1 16.2 - - + +
153F CYS* 2.9 41.9 - - + +
169F ILE* 4.7 3.1 - - - +
180F VAL* 4.9 5.0 - - - +
181F TYR 4.0 0.4 - - - -
190F GLY 4.1 3.8 - - - +
191F TRP* 1.3 70.3 - - - +
193F VAL* 1.3 64.2 + - - +
194F PHE* 3.8 2.6 + - - +
228F LEU* 5.5 1.7 - - - +
236F ILE* 4.1 20.0 - - + +
244F TYR* 5.0 2.0 - - + -
386F ILE* 2.9 53.8 + - + +
387F ILE* 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180F VAL* 5.2 1.2 - - - +
181F TYR* 3.4 41.3 + - + +
183F GLU* 4.3 18.2 - - + +
191F TRP 4.3 6.5 - - - +
192F THR* 1.3 73.1 + - - +
194F PHE* 1.3 62.4 + - - +
195F GLN 3.6 24.7 - - - +
196F LYS* 4.8 8.3 - - + +
226F PHE* 3.9 20.6 - - + -
228F LEU* 4.2 10.2 - - - +
383F THR* 4.5 7.4 - - - +
384F MET 3.8 9.6 - - - +
385F LYS* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 194 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192F THR 4.6 3.4 - - - +
193F VAL* 1.3 75.0 - - - +
195F GLN* 1.3 60.1 + - + +
226F PHE* 4.0 6.3 - - - -
227F TRP* 3.8 23.2 - + - -
228F LEU* 3.2 43.5 + - + -
233F ILE* 3.3 30.7 - - + -
246F LEU* 3.7 17.3 - - + -
265F PHE* 4.2 19.1 - + - -
335F TRP* 5.6 4.5 - + - -
384F MET* 2.9 50.3 + - + -
385F LYS* 4.5 0.9 - - - -
386F ILE* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F VAL* 3.6 9.1 - - - +
194F PHE* 1.3 81.4 - - + +
196F LYS* 1.3 66.1 + - - +
197F ARG* 3.3 7.3 - - - +
204F PHE* 3.7 12.9 - - - -
226F PHE* 3.6 9.7 - - - -
227F TRP* 3.1 22.9 - - + -
344F LEU* 3.3 9.6 - - - +
345F ASN* 2.8 25.6 + - - -
382F THR* 2.8 28.9 - - + +
383F THR* 3.4 2.3 - - - -
384F MET* 3.1 58.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181F TYR* 5.5 5.9 - - - -
183F GLU* 5.9 1.6 + - - -
193F VAL* 4.8 7.2 - - + +
195F GLN* 1.3 77.0 - - - +
197F ARG* 1.3 79.7 + - - +
198F LEU* 3.9 23.9 - - + +
222F GLY* 3.5 24.7 + - - +
224F THR 4.1 9.4 - - - +
225F GLU* 2.9 18.2 - - - +
226F PHE* 3.2 31.5 + - + +
381F LYS* 5.5 2.9 - - + -
382F THR 3.2 17.3 - - - +
383F THR* 3.3 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 197 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F GLN* 3.3 21.3 - - - +
196F LYS* 1.3 87.6 - - - +
198F LEU* 1.3 68.5 + - - +
202F VAL 4.5 3.8 + - - -
204F PHE* 3.6 40.6 - - - +
225F GLU* 3.6 12.9 + - - +
344F LEU 2.7 29.6 + - - +
345F ASN* 3.2 10.9 - - - +
346F GLY 2.9 29.1 + - - +
347F VAL* 4.8 0.2 - - - +
348F TYR* 4.0 25.9 - - + +
367F ILE* 3.6 19.4 - - + +
381F LYS* 3.4 3.6 - - - +
382F THR* 2.8 44.2 + - - +
----------------------------------------------------------
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