Contacts of the strand formed by residues 354 - 359 (chain B) in PDB entry 5FI4
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 THR 354 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 3.7 12.9 - - + +
350B THR* 3.7 28.0 - - + +
351B ALA* 2.7 24.4 + - - +
352B ASP 3.5 0.4 + - - -
353B GLY* 1.4 73.6 - - - +
355B PHE* 1.3 58.8 + - - +
371B THR 3.9 0.5 - - - +
372B LEU* 3.6 0.5 - - - -
373B ARG* 2.8 32.8 + - - +
426B TYR* 3.1 32.4 - - + +
427B PRO 5.3 0.2 - - - -
428B VAL* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B TRP* 3.6 23.6 - + + -
347B LEU* 4.9 1.6 - - - -
353B GLY 3.5 13.0 - - - +
354B THR* 1.3 74.5 - - - +
356B LEU* 1.3 66.3 + - - +
357B VAL* 4.9 0.9 - - + -
370B LEU* 3.8 17.7 - - + -
371B THR 3.1 14.6 - - - +
372B LEU* 4.5 1.8 - - + -
405B ILE* 3.6 26.7 - - + -
409B ARG* 4.2 6.5 - - - -
424B LEU* 3.2 50.7 - - + -
426B TYR 3.0 10.0 + - - -
427B PRO* 3.5 37.4 - - + +
428B VAL* 3.0 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B TRP* 3.4 12.8 - - - +
335B TRP* 3.8 17.0 - - + +
338B ILE* 3.8 25.6 - - + -
343B VAL* 3.9 30.3 - - + -
346B LYS* 4.0 19.3 - - + -
347B LEU* 4.5 3.4 - - + -
355B PHE* 1.3 80.1 - - - +
357B VAL* 1.3 71.0 + - - +
358B ARG* 4.5 2.7 - - + -
369B THR 4.0 1.0 - - - +
370B LEU* 3.8 1.4 - - - +
371B THR* 3.1 28.5 + - - +
428B VAL* 3.7 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B TRP* 2.8 40.5 + - + +
334B TYR* 3.4 12.4 - - + -
335B TRP* 2.8 30.2 + - - +
355B PHE* 4.9 1.1 - - + -
356B LEU* 1.3 76.7 - - - +
358B ARG* 1.3 71.1 + - - +
368B TYR* 4.2 8.1 - - + -
369B THR 3.6 9.9 - - - +
370B LEU* 3.8 11.2 - - + -
383B ILE* 3.9 16.8 - - + -
401B VAL* 4.4 8.7 - - + -
405B ILE* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A GLU* 3.1 31.5 + - - -
334B TYR* 4.5 0.4 - - - -
335B TRP 3.4 7.4 - - - +
336B GLY 3.8 8.3 - - - +
338B ILE* 3.3 37.5 + - + -
339B SER* 5.0 0.2 - - - +
340B ARG* 3.8 15.0 - - - +
343B VAL* 3.4 28.5 - - + +
356B LEU* 4.5 2.5 - - + -
357B VAL* 1.3 74.3 - - - +
359B ASP* 1.3 80.8 + - - +
360B ALA* 4.3 0.4 - - - +
361B SER* 3.1 26.2 + - - +
368B TYR* 3.5 10.6 - - - +
369B THR* 3.0 43.1 + - + +
371B THR* 4.3 4.7 + - - +
380B LEU* 3.6 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B TYR* 2.7 27.6 + - - -
336B GLY* 3.1 23.7 + - - +
337B ASP* 4.1 12.0 + - - +
338B ILE 4.7 2.1 - - - +
358B ARG* 1.3 93.1 + - - +
360B ALA* 1.4 68.4 + - - +
361B SER* 4.4 0.5 - - - -
367B ASP 3.5 7.6 - - - +
368B TYR* 3.1 18.4 - - - -
369B THR 4.6 0.2 - - - -
----------------------------------------------------------
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