Contacts of the helix formed by residues 288 - 296 (chain C) in PDB entry 5FLZ
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 288 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LYS* 1.3 75.9 - - - +
289C HIS* 1.4 66.0 + - + +
290C SER* 3.9 11.2 - - - -
291C SER* 3.3 28.7 - - - -
292C TYR* 3.0 27.5 + - - +
327C GLU* 3.4 18.8 - - - +
372C VAL* 3.6 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C CYS* 1.4 75.5 - - + +
290C SER* 1.4 84.0 + - - +
292C TYR* 3.2 13.2 + - - +
293C ASP* 3.0 30.3 + - - +
323C ILE* 5.1 9.2 - - + -
327C GLU* 3.3 25.9 + - + +
328C PRO 4.6 2.5 - - - -
331C ILE* 3.5 29.5 - - + +
332C SER* 3.0 55.6 + - - +
335C MET* 3.7 17.4 - - + +
372C VAL* 4.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 290 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C CYS* 3.5 9.8 - - - -
289C HIS* 1.4 95.2 + - - +
291C SER* 1.4 65.8 + - - +
293C ASP* 3.1 20.4 - - - +
294C VAL* 3.1 26.2 + - - +
335C MET* 3.8 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LYS* 4.1 12.9 - - - -
288C CYS* 3.3 32.5 + - - -
289C HIS 3.4 0.2 - - - -
290C SER* 1.4 78.6 - - - +
292C TYR* 1.4 62.1 + - - +
294C VAL* 3.5 6.0 + - - +
295C MET* 3.1 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C THR* 3.6 21.1 - - + -
287C LYS* 5.4 1.8 - - + -
288C CYS 3.0 18.8 + - - +
289C HIS* 3.2 11.2 + - - +
291C SER* 1.4 77.7 - - - +
293C ASP* 1.3 64.2 + - + +
295C MET* 3.4 13.7 + - - +
296C LEU* 3.2 50.5 + - + +
321C THR* 3.6 18.1 + - + -
322C ILE 4.0 5.2 - - - -
323C ILE* 4.3 20.0 - - + -
372C VAL* 4.6 7.9 - - + -
373C SER 4.4 5.6 - - - -
374C GLY* 3.3 36.3 - - - -
375C MET 3.0 30.1 + - - -
376C MET 3.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 293 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C HIS 3.0 10.9 + - - +
290C SER* 3.1 23.2 - - - +
292C TYR* 1.3 79.2 - - + +
294C VAL* 1.4 76.4 + - - +
295C MET 3.5 0.2 + - - -
296C LEU* 3.6 22.6 + - + +
297C ASP* 2.9 16.3 - - - +
319C TYR* 4.2 16.2 - - - +
321C THR* 5.7 1.3 - - - +
335C MET* 3.1 28.8 - - + +
339C GLN* 3.1 26.2 - - - +
344C PHE* 3.9 10.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C SER* 3.1 21.4 + - - +
291C SER* 3.9 6.5 - - - +
293C ASP* 1.4 83.8 + - - +
295C MET* 1.4 65.4 + - + +
297C ASP* 3.3 15.8 - - - +
298C LEU* 3.1 19.6 - - + +
344C PHE* 5.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C PHE 5.1 2.7 - - - +
273C THR* 3.4 35.4 - - - +
275C PHE* 6.4 1.8 - - + -
287C LYS* 3.8 30.1 - - + -
291C SER* 3.1 30.3 + - - +
292C TYR* 3.4 6.0 + - - +
294C VAL* 1.4 78.2 - - + +
296C LEU* 1.3 60.0 + - + +
298C LEU* 3.3 32.0 + - + +
301C PRO* 4.5 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C SER* 3.0 30.8 + - - +
272C PHE 3.5 33.7 - - - +
273C THR* 4.0 0.9 - - - +
292C TYR* 3.2 59.0 - - + +
293C ASP* 3.6 17.7 - - + +
294C VAL 3.3 0.6 - - - -
295C MET* 1.3 75.3 - - - +
297C ASP* 1.4 60.8 + - - +
298C LEU 3.3 1.3 - - - -
302C SER* 3.6 11.7 + - - +
312C ASN* 4.8 3.1 - - - +
319C TYR* 5.2 2.2 - - - +
321C THR* 4.4 5.2 - - - +
376C MET* 3.8 27.1 - - + +
----------------------------------------------------------
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