Contacts of the helix formed by residues 722 - 728 (chain A) in PDB entry 1KK8
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 ILE 722 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A ARG 4.2 10.7 + - - +
720A TYR* 2.9 2.4 - - - -
721A SER* 1.3 77.3 + - - +
723A LEU* 1.3 67.1 + - + +
724A ALA 3.1 6.1 - - - -
725A PRO* 3.2 17.7 - - + +
774A ARG* 4.0 26.9 - - + +
777A ARG* 3.6 12.6 - - + +
778A LEU* 3.8 47.6 - - + +
781A ILE* 3.9 18.1 - - + +
88C GLU* 4.2 17.3 - - + +
89C ALA* 4.2 9.2 - - - -
92C THR* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 723 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A TYR* 2.9 38.7 + - + +
722A ILE* 1.3 81.8 - - + +
724A ALA* 1.3 61.8 + - - +
725A PRO* 3.8 1.6 - - - -
742A ILE* 4.2 5.2 - - + -
746A LEU* 3.5 47.4 - - + +
770A LEU* 4.0 19.1 - - + +
773A MET* 3.8 15.7 - - + +
774A ARG* 3.7 30.7 - - + +
777A ARG* 4.0 19.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A TYR 4.2 0.6 + - - -
721A SER 3.3 6.2 + - - -
723A LEU* 1.3 81.8 - - - +
725A PRO* 1.3 67.7 - - - +
726A ASN 3.3 2.7 - - - -
727A ALA* 3.4 18.1 + - + +
728A ILE* 3.4 13.9 - - - +
741A LYS 4.6 1.3 - - - +
742A ILE* 4.0 31.4 - - + +
745A GLY* 4.5 12.6 - - - -
746A LEU 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A SER 3.3 7.1 - - - +
722A ILE* 3.2 29.2 - - + +
723A LEU 3.8 1.1 - - - -
724A ALA* 1.3 87.0 - - - +
726A ASN* 1.3 60.6 + - - +
727A ALA 3.2 4.5 + - - -
728A ILE* 3.6 22.3 + - + +
777A ARG* 5.7 3.6 - - - +
781A ILE* 4.7 3.1 - - + -
84C ALA* 3.7 22.9 - - - +
85C ASP* 3.5 28.3 - - - +
88C GLU* 3.7 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A ALA 3.3 1.2 - - - -
725A PRO* 1.3 76.9 - - - +
727A ALA* 1.3 58.3 + - - +
728A ILE 3.6 1.6 - - - -
79C GLU* 5.9 1.2 + - - -
82C THR* 2.8 33.9 + - - +
84C ALA* 4.0 10.3 - - - +
85C ASP* 3.3 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A ALA* 3.4 13.6 + - + +
725A PRO 3.2 1.4 - - - -
726A ASN* 1.3 80.2 - - - +
728A ILE* 1.3 61.8 + - - +
729A PRO* 3.8 5.7 - - - +
741A LYS* 3.6 35.1 - - + +
745A GLY* 5.5 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A SER* 3.3 49.6 - - - +
724A ALA 3.4 13.2 - - - +
725A PRO* 3.6 14.9 + - + +
726A ASN 3.6 1.5 - - - -
727A ALA* 1.3 80.9 - - - +
729A PRO* 1.3 76.7 - - + +
730A GLN* 4.1 0.8 + - + +
738A VAL* 4.4 27.4 - - + +
741A LYS* 5.6 1.8 - - + -
742A ILE* 4.5 6.7 - - + -
88C GLU* 4.4 11.4 - - - +
----------------------------------------------------------
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