Contacts of the strand formed by residues 6064 - 6067 (chain F) in PDB entry 1HKN
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 TYR6064 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6025F ILE* 4.7 1.1 - - - -
6055F TYR* 3.7 41.3 - + + -
6056F ILE 3.6 3.6 - - - +
6057F LYS* 3.3 36.4 + - + -
6062F GLY 3.4 19.3 - - - -
6063F GLN* 1.3 73.7 - - - +
6065F LEU* 1.3 65.7 + - - +
6066F ALA 3.4 0.7 + - - -
6074F TYR 3.4 1.0 - - - +
6075F GLY* 3.5 2.1 - - - -
6076F SER* 2.6 45.6 + - - +
6077F GLN 4.7 3.1 - - - -
6078F THR 4.2 0.2 - - - -
6079F PRO* 3.5 47.8 - - + +
6083F CYS* 3.6 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU6065 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6023F LEU* 3.9 20.4 - - + -
6025F ILE* 4.1 14.1 - - + +
6031F VAL* 3.7 39.0 - - + -
6056F ILE* 2.7 53.6 + - + +
6064F TYR* 1.3 74.2 - - - +
6066F ALA* 1.3 64.9 + - - +
6073F LEU* 4.0 12.1 - - + -
6074F TYR 3.8 3.1 - - - -
6075F GLY* 4.9 0.2 - - - -
6083F CYS* 3.4 19.4 - - - +
6085F PHE* 3.5 20.3 - - + -
6109F VAL* 4.1 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA6066 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6064F TYR 4.0 1.1 - - - +
6065F LEU* 1.3 78.1 - - - +
6067F MET* 1.3 62.5 + - - +
6073F LEU* 3.2 8.5 - - - +
6074F TYR* 2.8 64.3 + - + +
6082F GLU 3.1 16.2 - - - +
6083F CYS* 3.7 14.6 - - - -
6085F PHE* 4.0 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET6067 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6066F ALA* 1.3 76.2 - - - +
6068F ASP* 1.3 64.6 + - - +
6071F GLY* 3.4 40.8 - - - +
6072F LEU 3.2 5.2 - - - +
6073F LEU* 4.0 20.0 - - + -
6074F TYR* 3.9 3.1 - - - -
6082F GLU* 3.0 27.1 + - - +
6085F PHE* 4.2 11.6 - - + -
6099F SER* 3.9 17.8 + - - +
6101F LYS* 4.5 5.9 - - - +
6102F HIS* 4.7 2.1 - - + -
6107F TRP* 3.7 28.3 - - + +
6108F PHE 3.1 33.2 - - - +
6109F VAL* 4.4 0.9 - - - +
6118F LYS 4.8 0.9 - - - +
6120F GLY* 3.8 7.2 - - - +
----------------------------------------------------------
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