Contacts of the helix formed by residues 832 - 849 (chain A) in PDB entry 1HU3
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 ASN 832 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A GLU* 3.4 19.5 + - - +
788A LEU* 4.4 14.6 - - - +
819A LEU 5.0 4.9 - - - +
820A LYS* 5.1 1.2 - - - -
821A VAL* 3.0 37.4 + - - +
822A PRO 5.2 0.2 - - - -
833A PHE* 1.3 70.4 + - - +
834A ARG 3.6 1.3 - - - -
835A LYS* 3.3 15.5 - - + +
836A LEU* 3.2 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 833 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A LEU* 3.7 28.3 - - + -
792A ILE* 3.5 28.7 - - + +
813A CYS* 3.8 23.3 - - + -
816A LEU* 3.5 39.9 - - + -
817A VAL* 3.3 32.3 - - + +
819A LEU 5.2 7.2 - - - +
832A ASN* 1.3 76.7 + - - +
834A ARG* 1.3 73.1 + - + +
835A LYS 3.0 1.3 - - - -
836A LEU* 2.8 16.3 + - - +
837A LEU* 2.9 35.7 + - + -
904A MSE 4.6 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 834 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A VAL* 4.2 30.3 - - + +
832A ASN 3.6 0.2 - - - -
833A PHE* 1.3 80.1 - - + +
835A LYS* 1.3 52.8 + - - +
837A LEU* 3.3 8.7 - - - +
838A LEU* 2.7 37.5 + - - +
902A LEU 5.4 1.4 + - - -
903A LYS* 3.9 20.4 + - - +
904A MSE 3.3 42.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 835 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A ASN* 3.3 20.5 + - + +
833A PHE 2.9 0.6 + - - -
834A ARG* 1.3 79.5 - - - +
836A LEU* 1.3 54.7 + - + +
838A LEU* 3.7 4.4 - - - +
839A ASN* 2.7 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 836 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A GLU* 4.7 25.8 - - + +
788A LEU* 3.3 40.8 - - + -
789A LYS* 4.4 17.9 - - + +
792A ILE* 3.9 16.9 - - + +
832A ASN* 3.4 14.8 - - + +
833A PHE 2.8 9.7 + - - +
835A LYS* 1.3 74.9 - - + +
837A LEU* 1.3 53.6 + - - +
839A ASN* 3.4 13.4 - - + +
840A ARG* 2.7 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 837 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A ILE* 4.6 8.0 - - + +
796A PHE* 3.4 30.7 - - + -
813A CYS* 4.3 11.0 - - - -
833A PHE* 2.9 35.3 + - + +
834A ARG* 3.3 8.7 - - - +
836A LEU* 1.3 74.8 - - - +
838A LEU* 1.3 56.3 + - - +
840A ARG* 2.9 5.7 + - - +
841A CYS* 2.7 40.5 + - - -
899A LEU* 3.6 27.8 - - + -
904A MSE 3.6 37.2 - - + +
905A LEU* 4.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 838 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A ARG 2.7 21.8 + - - +
835A LYS* 3.7 5.6 - - - +
837A LEU* 1.3 71.0 - - - +
839A ASN* 1.3 59.9 + - - +
841A CYS* 3.0 5.2 + - - +
842A GLN* 2.8 45.6 + - + +
905A LEU* 4.1 15.6 - - + +
906A THR* 5.9 8.1 - - + +
909A ILE* 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 839 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A LYS* 2.7 35.7 + - - +
836A LEU* 3.4 15.6 - - + +
838A LEU* 1.3 79.2 - - - +
840A ARG* 1.3 62.1 + - - +
842A GLN* 3.4 9.4 + - - +
843A LYS* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 840 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A LYS* 5.2 5.2 - - - +
792A ILE* 4.1 8.3 - - + -
793A ASP* 3.0 29.7 + - - +
796A PHE* 3.4 55.0 - - + +
797A GLU* 5.0 12.9 + - - +
800A ILE* 5.7 2.8 - - - +
836A LEU 2.7 21.0 + - - +
837A LEU 3.4 4.9 - - - +
839A ASN* 1.3 73.1 - - - +
841A CYS* 1.3 63.2 + - - +
843A LYS* 3.1 24.5 - - - +
844A GLU* 3.8 25.4 + - - +
888A ARG* 5.6 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 841 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A PHE* 3.6 23.6 - - - -
837A LEU 2.7 19.2 + - - -
838A LEU* 3.4 9.9 - - - +
840A ARG* 1.3 68.3 - - - +
842A GLN* 1.3 58.9 + - - +
843A LYS 2.8 10.2 + - - -
844A GLU* 2.9 20.8 + - - +
845A PHE* 3.5 12.1 + - - -
896A ILE* 3.8 26.3 - - + +
899A LEU* 4.3 2.7 - - - -
905A LEU* 3.7 32.3 - - + -
909A ILE* 4.7 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 842 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A LEU* 2.8 28.0 + - + +
839A ASN* 3.8 8.5 + - - +
841A CYS* 1.3 72.0 - - - +
843A LYS* 1.3 53.5 + - - +
844A GLU 3.3 0.2 - - - -
845A PHE* 3.6 12.8 - - + -
846A GLU* 2.6 39.6 + - + +
908A ALA* 6.2 1.0 - - - +
909A ILE* 3.6 29.7 - - + +
912A ASP* 4.3 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 843 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A ASN 3.1 12.5 + - - +
840A ARG* 3.1 33.4 - - - +
841A CYS 2.8 1.0 + - - -
842A GLN* 1.3 78.3 - - - +
844A GLU* 1.3 55.8 + - - +
846A GLU* 3.7 4.1 - - - +
847A LYS* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 844 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A PHE* 5.3 2.9 - - + -
800A ILE* 4.6 6.3 - - + +
840A ARG* 3.9 28.4 + - - +
841A CYS* 2.9 7.4 + - - +
843A LYS* 1.3 79.2 - - - +
845A PHE* 1.3 53.4 + - - +
847A LYS* 3.5 5.8 + - - +
848A ASP* 2.7 35.8 + - - +
888A ARG* 2.7 46.6 + - - -
892A ASN* 3.4 41.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 845 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A CYS 3.8 9.9 - - - -
842A GLN* 3.6 8.7 - - + +
843A LYS 3.2 0.4 - - - -
844A GLU* 1.3 76.8 - - + +
846A GLU* 1.3 62.1 + - - +
847A LYS 2.9 4.5 - - - -
848A ASP* 3.0 19.3 + - + +
849A LYS* 3.1 14.6 + - - +
892A ASN* 4.0 8.7 - - - -
893A ILE* 4.7 10.3 - - + -
896A ILE* 3.2 31.9 - - + -
909A ILE* 3.1 46.9 - - + -
912A ASP* 4.3 16.2 - - + +
913A CYS* 3.7 25.4 - - - -
916A LYS* 5.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 846 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A GLN* 2.6 25.0 + - + +
843A LYS* 4.0 4.9 - - - +
845A PHE* 1.3 72.6 - - - +
847A LYS* 1.3 55.8 + - - +
849A LYS* 4.0 14.1 - - - +
850A ALA* 4.4 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 847 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A LYS 2.8 20.0 + - - +
844A GLU* 3.7 6.3 - - - +
846A GLU* 1.3 76.9 - - - +
848A ASP* 1.3 58.8 + - - +
849A LYS 3.1 5.8 - - - -
850A ALA* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 848 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A GLU 2.7 19.1 + - - +
845A PHE* 3.0 12.3 + - + +
847A LYS* 1.3 75.9 - - - +
849A LYS* 1.3 57.9 + - - +
850A ALA 3.1 10.4 + - - +
889A SER* 6.5 0.7 - - - -
916A LYS* 5.1 21.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 849 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A PHE 3.1 14.2 + - - +
846A GLU* 4.0 11.0 - - - +
847A LYS 3.1 0.2 - - - -
848A ASP* 1.3 78.3 - - - +
850A ALA* 1.3 56.0 - - - +
----------------------------------------------------------
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