Contacts of the helix formed by residues 523 - 531 (chain A) in PDB entry 4KHW
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 SER 523 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ASP 3.4 3.7 + - - -
522A PHE* 1.3 76.2 - - - +
524A ASP* 1.3 60.3 + - - +
525A GLU* 3.7 14.5 + - - +
526A ILE* 3.0 36.1 + - - +
527A LYS* 2.8 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A PHE 5.2 0.2 - - - +
523A SER* 1.3 73.9 - - - +
525A GLU* 1.3 63.8 + - - +
527A LYS* 3.4 29.3 + - - +
528A GLU* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A SER* 3.7 14.5 + - - +
524A ASP* 1.3 85.5 + - - +
526A ILE* 1.3 64.6 + - + +
528A GLU* 3.2 7.9 + - - +
529A LYS* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LEU* 4.3 5.6 - - + -
516A VAL* 3.6 36.8 - - + -
517A ASP 5.9 0.2 - - - +
522A PHE* 3.8 24.5 - - + -
523A SER* 3.0 34.8 + - - +
525A GLU* 1.3 78.5 - - + +
527A LYS* 1.3 57.1 + - - +
529A LYS* 3.1 11.6 + - + +
530A ILE* 2.9 43.1 + - + +
541A MET* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A ILE* 3.7 35.6 - - + +
522A PHE* 3.7 29.5 + - + +
523A SER 2.8 16.9 + - - +
524A ASP* 3.4 29.7 + - - +
526A ILE* 1.3 72.2 - - - +
528A GLU* 1.3 61.7 + - - +
530A ILE* 3.4 16.0 + - - +
531A LYS* 3.4 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ASP 3.0 18.4 + - - +
525A GLU* 3.4 7.9 - - - +
527A LYS* 1.3 77.9 - - - +
529A LYS* 1.3 62.6 + - + +
531A LYS* 3.5 16.0 + - - +
532A LYS* 3.8 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LEU* 3.6 32.8 - - + -
525A GLU* 3.0 22.2 + - + +
526A ILE* 3.1 9.8 + - + +
528A GLU* 1.3 77.6 - - + +
530A ILE* 1.3 58.5 + - - +
532A LYS* 2.9 33.5 + - + +
533A LEU* 3.5 10.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A ILE* 4.4 12.6 - - + -
499A ILE* 4.3 8.5 - - + -
502A ALA* 3.6 25.3 - - + +
514A LEU* 3.7 14.1 - - + -
522A PHE* 3.5 40.4 - - + -
526A ILE* 2.9 25.3 + - + +
527A LYS* 3.6 7.6 - - - +
528A GLU 3.3 0.4 - - - -
529A LYS* 1.3 72.0 - - - +
531A LYS* 1.3 59.8 + - + +
532A LYS 3.0 10.2 + - - -
533A LEU* 3.1 22.0 + - - +
538A LEU* 3.6 18.5 - - + +
541A MET* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ALA* 4.6 14.6 - - + -
507A ASN* 2.5 11.4 + - - +
527A LYS 3.4 14.5 + - - +
528A GLU* 3.8 9.9 - - - +
529A LYS 3.3 1.0 - - - -
530A ILE* 1.3 75.8 - - + +
532A LYS* 1.3 53.5 + - + +
1006A CA 2.4 31.7 - - - -
----------------------------------------------------------
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