Contacts of the strand formed by residues 809 - 813 (chain B) in PDB entry 5KJH
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 TYR 809 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B VAL* 3.5 15.4 - - - +
301B PRO* 2.7 51.4 + - + -
302B PRO 3.5 14.8 - - - -
303B TYR* 3.6 12.3 - + + -
307B HIS* 6.1 0.2 - + - -
799B LEU* 3.8 27.4 - - + -
800B GLY 3.4 14.8 - - - +
802B SER* 4.0 0.9 - - - -
807B CYS 3.3 6.6 + - - +
808B GLY* 1.3 71.7 - - - -
810B GLY* 1.3 53.7 + - - +
855B TYR* 6.0 1.1 - - - -
878B TYR* 3.7 36.8 - + + +
880B ASN* 2.9 25.8 + - - +
2561B PHE* 4.0 13.5 - + - -
2566B LYS* 3.4 24.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 810 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B LEU* 3.7 6.8 - - - +
800B GLY 3.0 30.7 + - - +
802B SER* 3.8 5.2 - - - +
809B TYR* 1.3 72.5 - - - +
811B LEU* 1.3 59.5 + - - -
812B PHE* 4.0 5.2 - - - -
878B TYR* 3.3 15.5 - - - -
880B ASN* 3.5 11.9 - - - -
913B GLU* 3.6 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 811 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B VAL* 3.9 18.8 - - + -
798B VAL 3.6 22.9 - - - +
799B LEU* 4.1 6.7 - - + +
810B GLY* 1.3 73.1 - - - +
812B PHE* 1.3 55.3 + - - +
824B ILE* 4.2 9.6 - - + -
875B LEU* 3.3 49.4 - - + +
876B SER* 4.1 1.3 - - - +
878B TYR* 3.6 4.6 + - + -
879B ILE* 3.6 37.2 - - + +
913B GLU* 3.5 5.9 + - - +
914B LEU* 2.7 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 812 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B VAL* 3.3 5.0 - - - +
798B VAL* 2.7 57.9 + - + +
800B GLY* 3.7 22.9 - - - -
801B LYS 3.3 28.0 - - - -
803B GLN* 4.3 5.6 - - - -
810B GLY 3.8 15.5 - - - -
811B LEU* 1.3 75.9 - - - +
813B ALA* 1.3 62.9 + - - +
911B GLY* 3.4 24.2 - - - +
912B GLU 3.4 4.7 - - - +
913B GLU* 3.5 37.2 - - + -
914B LEU* 4.4 3.8 - - - -
2554B PRO* 5.4 0.2 - - + -
2556B THR* 4.4 5.2 - - + -
2558B GLN* 3.7 22.0 - - + -
2560B LEU* 4.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 813 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B ALA 4.0 4.0 - - - -
797B VAL* 4.6 5.6 - - - -
812B PHE* 1.3 72.9 - - - +
814B ALA* 1.3 58.9 - - - +
815B GLU 3.5 16.6 - - - +
817B ILE* 3.9 11.9 - - + -
908B ILE* 3.9 15.5 - - + -
909B LYS 3.8 13.5 - - - +
911B GLY* 2.8 23.4 + - - -
912B GLU 2.9 16.9 + - - +
914B LEU* 4.1 6.2 - - + +
2554B PRO* 3.6 6.6 - - - +
----------------------------------------------------------
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