Contacts of the strand formed by residues 419 - 424 (chain F) in PDB entry 3FZ7
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 419 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381F LYS* 3.4 23.1 - - - +
382F LEU 4.6 0.9 + - - -
391F THR* 6.5 0.9 - - - -
392F LEU* 3.6 22.4 - - + +
393F TYR* 3.7 40.6 - - + -
408F ALA* 4.6 0.9 - - + -
409F PHE 3.5 12.3 - - - +
410F THR* 4.2 10.5 - - + -
417F ASP 3.6 7.5 + - - +
418F ILE* 1.3 74.5 - - - +
420F VAL* 1.3 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 420 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366F ILE* 3.7 30.1 - - + -
379F CYS* 3.9 14.1 - - - -
380F PHE 3.1 12.8 - - - +
381F LYS* 4.4 0.7 - - + -
392F LEU* 4.0 4.3 - - - -
407F PRO 3.9 0.2 - - - +
408F ALA* 3.2 6.4 - - - +
409F PHE* 2.8 73.7 + - + +
411F LEU* 3.7 25.8 - - + -
418F ILE* 3.9 5.2 - - + -
419F VAL* 1.3 76.9 - - - +
421F MET* 1.3 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 421 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378F VAL 3.8 0.7 - - - +
379F CYS* 3.3 6.2 - - - -
380F PHE* 2.9 65.7 + - + +
392F LEU* 3.7 36.4 - - + +
395F LEU* 3.9 22.9 - - + -
396F SER* 3.8 24.0 - - - +
399F LEU* 4.1 7.0 - - + -
406F VAL* 3.6 25.6 - - + +
407F PRO 3.4 13.5 - - - +
408F ALA* 5.0 0.9 - - + -
420F VAL* 1.3 76.1 - - - +
422F ARG* 1.3 59.0 + - - +
423F ILE* 4.9 0.7 - - + -
441F TYR* 4.4 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 422 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F LEU 3.9 0.7 - - - +
61F ALA* 2.8 34.2 + - - +
63F PHE* 3.7 12.6 - - - -
212F THR 2.8 26.9 + - - -
213F TYR* 3.6 17.0 - - - +
214F THR 4.4 8.5 - - - +
215F GLY* 4.8 0.9 - - - +
377F ALA* 4.8 5.4 - - + -
378F VAL 3.3 9.0 - - - +
379F CYS* 4.3 9.4 - - + -
406F VAL* 3.9 0.7 - - - +
407F PRO* 3.0 40.4 + - + +
409F PHE* 3.7 31.2 - - + -
420F VAL 4.2 0.2 - - - -
421F MET* 1.3 74.8 - - - +
423F ILE* 1.3 70.4 + - - +
424F MET* 4.1 15.1 - - - +
463F PHE 4.7 0.2 + - - -
464F LYS* 3.2 30.5 + - - +
466F THR 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 423 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F LEU* 3.8 26.9 - - + -
353F LEU* 4.1 20.0 - - + -
357F ILE* 3.5 32.3 - - + -
377F ALA* 3.2 8.1 - - - +
378F VAL* 2.8 44.3 + - + +
380F PHE* 4.5 10.5 - - + -
406F VAL* 3.6 25.4 - - + -
421F MET* 4.9 4.7 - - + -
422F ARG* 1.3 72.2 - - - +
424F MET* 1.3 67.2 + - - +
425F CYS* 3.8 5.2 + - - -
429F PHE* 4.8 0.4 - - + -
437F LEU* 4.4 11.9 - - + -
441F TYR* 5.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 424 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F LEU* 2.8 40.3 + - - +
61F ALA 4.1 10.1 - - - +
62F THR 3.5 20.0 - - - +
63F PHE* 3.6 43.1 - - + +
277F PHE* 3.3 39.0 - - + -
375F ILE* 3.8 14.4 - - - -
376F PRO 4.2 3.6 - - - +
377F ALA* 4.0 11.2 - - - -
422F ARG* 4.1 15.9 - - - +
423F ILE* 1.3 74.6 - - - +
425F CYS* 1.3 64.8 + - - +
426F ARG* 3.9 8.2 + - + +
429F PHE* 4.4 0.7 - - - +
----------------------------------------------------------
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