Contacts of the strand formed by residues 839 - 844 (chain A) in PDB entry 5J9H
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 VAL 839 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A PHE* 4.3 5.2 - - + -
817A ILE* 3.6 40.5 - - + +
819A LEU* 4.1 22.4 - - + -
822A GLU* 4.7 0.7 - - - +
834A LEU 4.0 0.5 - - - +
835A ILE* 3.6 1.7 - - - -
836A THR* 2.8 44.2 + - - +
838A SER* 1.3 85.8 - - - +
840A LYS* 1.3 68.5 + - - +
963A VAL* 4.1 16.2 - - + -
964A ILE 3.4 10.3 - - - +
965A VAL* 4.3 12.8 - - + -
971A PHE* 3.7 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 840 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A GLY* 3.8 13.5 - - - -
674A SER* 3.2 43.1 - - - +
676A ILE* 5.5 2.0 - - - -
833A CYS* 4.5 0.9 - - + -
834A LEU 3.3 9.4 - - - +
835A ILE* 4.6 3.1 - - + -
839A VAL* 1.3 74.2 - - - +
841A VAL* 1.3 65.8 + - - +
842A CYS* 3.7 28.7 - - - +
962A ASN* 3.5 24.8 + - - +
963A VAL* 3.4 4.9 - - - +
964A ILE* 3.1 50.6 + - + +
971A PHE* 4.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 841 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A LEU* 4.4 3.8 - - + -
717A LEU* 4.5 4.9 - - + -
815A VAL* 3.9 23.8 - - + -
817A ILE* 3.6 32.3 - - + -
828A VAL* 5.3 0.9 - - - +
832A ASP 4.4 0.2 - - - +
833A CYS* 3.1 2.9 - - - +
834A LEU* 2.8 39.9 + - + +
839A VAL* 4.2 0.4 - - + -
840A LYS* 1.3 80.3 - - - +
842A CYS* 1.3 63.2 + - - +
843A LEU* 4.4 12.9 + - + +
961A ILE* 4.4 11.4 - - + -
962A ASN 3.4 9.2 - - - +
963A VAL* 4.2 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 842 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A ASP 3.8 0.4 - - - -
833A CYS* 2.1 48.5 - - - -
840A LYS* 3.7 29.2 - - - +
841A VAL* 1.3 73.2 - - - +
843A LEU* 1.3 66.3 + - - +
844A ILE* 5.2 8.4 - - + +
960A HIS 3.6 1.0 - - - +
961A ILE* 3.5 6.8 - - - +
962A ASN* 3.0 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 843 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A LEU* 4.8 2.0 - - + -
720A GLN* 6.3 0.4 - - - +
813A ARG* 4.0 31.6 - - + +
815A VAL* 4.8 6.7 - - + -
828A VAL* 3.7 24.7 - - + +
829A ASP 3.7 18.4 - - - +
830A SER* 3.2 24.4 - - - +
831A ASN* 3.3 14.4 - - - -
832A ASP 3.1 12.6 + - - +
833A CYS* 5.5 0.2 - - - -
841A VAL* 4.5 14.4 - - + +
842A CYS* 1.3 82.0 - - - +
844A ILE* 1.3 65.3 + - - +
959A ASP* 5.7 4.9 - - + -
960A HIS 3.5 3.4 - - - +
961A ILE* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 844 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A SER 3.5 1.6 - - - -
831A ASN* 3.5 9.2 - - + +
842A CYS* 5.2 9.6 - - + +
843A LEU* 1.3 79.2 - - - +
845A GLY* 1.3 64.0 + - - +
846A THR 4.0 0.3 + - - -
959A ASP* 3.4 5.4 - - - +
960A HIS* 2.8 64.6 + - + +
962A ASN* 6.4 1.1 - - + -
----------------------------------------------------------
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