Contacts of the strand formed by residues 822 - 827 (chain A) in PDB entry 5KZX
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 822 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A GLU* 4.3 0.7 + - - -
748A GLU* 3.0 42.5 + - + -
749A ALA* 3.4 28.7 - - + -
818A LEU* 4.4 5.3 - - + +
819A ARG* 3.4 58.0 + - + +
820A ALA 3.8 6.5 - - - -
821A GLY* 1.3 84.9 - - - +
823A ILE* 1.3 66.6 + - - +
824A ILE* 4.9 2.0 - - + -
844A ALA 3.9 1.2 - - - +
846A ALA* 2.9 30.2 + - - +
853A ALA* 4.1 0.2 - - - -
854A ARG* 3.3 13.5 - - + -
855A GLY* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 823 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A HIS* 5.3 1.2 - - - -
822A TYR* 1.3 77.8 - - - +
824A ILE* 1.3 70.2 + - - +
825A PRO* 4.2 2.5 - - - +
843A LEU* 4.0 20.6 - - + -
844A ALA 3.3 10.1 - - - +
845A VAL* 3.8 27.1 - - + -
853A ALA* 3.7 26.9 - - + +
854A ARG 3.0 6.0 + - - +
855A GLY* 3.4 22.8 - - - +
856A GLU 4.1 3.6 + - - -
878A PHE* 3.7 47.1 - - + +
879A LEU 4.0 0.7 - - - +
880A ALA* 3.9 10.8 - - + +
885A ILE* 5.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 824 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A LEU* 4.1 9.2 - - + -
708A HIS* 3.4 44.4 - - + +
749A ALA* 4.5 11.4 - - + -
750A LEU* 4.8 6.5 - - + -
775A LEU* 6.2 2.5 - - + -
818A LEU* 3.5 37.2 - - + -
822A TYR* 4.9 1.1 - - + -
823A ILE* 1.3 84.3 - - - +
825A PRO* 1.4 75.3 - - - +
826A LEU* 3.8 17.4 + - + +
843A LEU* 3.5 2.8 - - - -
844A ALA* 2.9 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 825 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A ALA 4.5 0.9 - - - +
707A PRO* 4.1 4.2 - - + +
708A HIS* 3.6 47.9 + - - +
711A THR* 4.9 0.4 - - - +
823A ILE 4.2 3.6 - - - +
824A ILE* 1.4 87.7 - - - +
826A LEU* 1.3 62.1 + - - +
841A MET* 5.6 0.9 - - - -
842A ALA 3.5 7.0 - - - +
843A LEU* 4.1 12.3 - - + -
856A GLU 3.6 25.1 - - - +
857A LEU* 4.1 29.8 - - + -
878A PHE* 4.6 2.7 - - + -
943A MET* 5.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 826 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A ALA* 3.2 23.1 - - + +
705A LEU* 3.7 30.5 - - + -
707A PRO* 4.0 4.8 - - - +
775A LEU* 6.3 3.8 - - + -
778A VAL* 4.3 16.6 - - + -
780A ILE* 4.5 16.6 - - + -
824A ILE* 3.9 12.6 - - + +
825A PRO* 1.3 80.3 - - - +
827A GLN* 1.3 64.7 + - - +
841A MET* 3.2 11.3 - - - +
842A ALA* 2.8 44.4 + - + +
843A LEU 4.7 0.4 - - - -
844A ALA* 4.2 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 827 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A TYR* 3.7 8.8 + - - -
703A TYR 4.3 2.1 - - - +
704A ALA* 3.0 30.3 + - - +
707A PRO* 3.5 14.1 - - + -
826A LEU* 1.3 77.1 - - - +
828A GLY* 1.3 70.0 + - - +
836A SER* 3.1 23.1 + - - +
837A ARG* 3.0 25.6 + - - -
839A GLN 2.9 26.6 + - - +
840A PRO 3.7 5.4 - - - +
841A MET* 3.9 19.6 - - + +
842A ALA* 6.0 0.4 - - - -
859A TRP* 3.2 23.0 - - - -
899A LEU* 4.6 3.4 - - - +
----------------------------------------------------------
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