Contacts of the helix formed by residues 650 - 665 (chain F) in PDB entry 5KHU
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 LYS 650 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649F GLU* 3.8 26.9 - - - +
651F PHE* 3.8 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 651 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650F LYS* 3.8 29.2 - - - +
652F SER* 3.8 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 652 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651F PHE* 3.8 26.5 - - - +
653F LEU* 3.8 29.6 - - - +
655F GLU* 4.4 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 653 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652F SER* 3.8 29.4 - - - +
654F ALA* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 654 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642F GLY* 3.6 31.6 - - - +
653F LEU* 3.8 28.9 - - - +
655F GLU* 3.8 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 655 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652F SER* 4.4 17.0 - - - +
654F ALA* 3.8 27.6 - - - +
656F MET* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 656 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655F GLU* 3.8 25.1 - - - +
657F HIS* 3.8 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 657 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656F MET* 3.8 29.6 - - - +
658F PHE* 3.8 26.9 - - - +
660F LYS* 4.5 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 658 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657F HIS* 3.8 25.6 - - - +
659F GLN* 3.7 29.8 - - - +
661F ALA* 4.5 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 659 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658F PHE* 3.7 28.9 - - - +
660F LYS* 3.8 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 660 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657F HIS* 4.5 14.6 - - - +
659F GLN* 3.8 24.2 - - - +
661F ALA* 3.8 29.2 - - - +
663F ASP* 4.4 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 661 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658F PHE* 4.5 16.8 - - - +
660F LYS* 3.8 28.0 - - - +
662F LEU* 3.8 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 662 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661F ALA* 3.8 29.6 - - - +
663F ASP* 3.8 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 663 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660F LYS* 4.4 19.5 - - - +
662F LEU* 3.8 26.2 - - - +
664F ILE* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 664 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663F ASP* 3.8 27.6 - - - +
665F ASN* 3.8 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 665 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664F ILE* 3.8 29.4 - - - +
666F PRO* 3.8 29.2 - - - -
----------------------------------------------------------
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