Contacts of the strand formed by residues 406 - 412 (chain B) in PDB entry 1F1J
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 PHE 406 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 3.6 21.5 - - + -
368B GLY 3.2 20.9 - - - -
369B LYS 3.7 12.3 - - - -
370B CYS* 3.5 20.6 - - + -
401B PHE* 3.1 45.9 + + - +
402B ARG* 3.9 10.9 - - - +
404B LEU* 3.8 16.8 - - + -
405B GLY* 1.3 80.2 - - - +
407B ASP* 1.3 61.5 - - - +
408B VAL* 3.3 12.9 + - - +
436B CYS* 3.5 23.6 - - - -
438B ALA* 4.0 18.6 - - + -
480B LEU* 4.9 1.1 - - + -
601B PHE* 3.5 27.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LYS* 3.1 39.1 + - - +
368B GLY 2.9 12.4 + - - +
369B LYS* 3.1 46.0 + - - +
370B CYS 3.3 4.2 + - - -
405B GLY 4.4 4.5 - - - +
406B PHE* 1.3 73.5 - - - +
408B VAL* 1.3 59.8 + - - +
409B ILE* 4.0 1.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B CYS* 3.4 19.3 - - + +
372B ILE* 4.2 7.0 - - + -
398B PHE* 3.7 50.2 - - + +
401B PHE* 4.2 5.8 - - + -
402B ARG* 3.8 18.8 - - + +
406B PHE* 3.3 13.7 + - + +
407B ASP* 1.3 72.2 - - - +
409B ILE* 1.3 62.9 + - - +
410B VAL* 3.8 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LYS* 3.6 36.3 - - + -
370B CYS 3.4 3.7 + - - +
371B ILE* 3.6 8.3 - - + -
372B ILE* 2.9 26.0 + - - +
407B ASP* 4.0 1.8 - - + +
408B VAL* 1.3 78.3 - - - +
410B VAL* 1.3 66.8 + - - +
411B TYR* 3.3 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ILE* 3.4 18.2 - - + +
374B ASN* 4.4 9.0 - - + -
394B ALA* 4.6 10.8 - - + +
398B PHE* 4.1 17.7 - - + -
408B VAL* 3.8 20.2 - - + +
409B ILE* 1.3 81.1 - - - +
411B TYR* 1.3 70.3 + - - +
412B ASN* 3.3 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ILE* 3.7 35.7 - - + +
372B ILE 2.8 11.3 + - - +
373B ILE* 4.6 2.7 - - - -
374B ASN* 2.8 25.7 + - - +
409B ILE* 3.3 36.7 - - + +
410B VAL* 1.3 73.8 - - - +
412B ASN* 1.3 69.2 + - - +
414B CYS* 3.6 19.7 - - - -
418B LYS* 4.3 19.7 - - - -
422B LEU* 3.6 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ASN* 3.1 32.3 + - - +
394B ALA* 5.4 0.2 - - - +
410B VAL* 3.3 23.6 + - - +
411B TYR* 1.3 82.8 - - - +
413B ASP* 1.3 75.9 + - + +
414B CYS* 3.3 5.9 + - - -
----------------------------------------------------------
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