Contacts of the helix formed by residues 832 - 849 (chain A) in PDB entry 5V4R
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 SER 832 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A GLU* 2.7 52.6 + - - +
824A ARG* 4.1 4.3 - - - -
827A LEU* 4.2 5.2 - - - -
828A GLY 4.0 1.2 + - - -
830A GLY* 3.5 2.2 - - - +
831A GLN* 1.3 76.2 - - - +
833A GLN* 1.3 63.6 + - - +
835A MET* 3.0 30.2 + - - +
836A ASN* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 833 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A GLU* 4.6 1.0 + - - -
830A GLY 4.8 7.9 + - - -
831A GLN 3.9 6.7 + - - +
832A SER* 1.3 70.4 - - - +
834A GLU* 1.3 66.1 + - - +
836A ASN* 3.0 39.6 + - - +
837A THR* 3.1 18.5 + - + +
905B TYR* 3.5 40.1 + - - +
908B GLY* 6.3 1.6 - - - -
910B LEU* 4.0 14.9 - - - +
940B LYS* 5.3 15.1 - - + +
941B PHE* 5.9 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 834 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A HIS* 3.0 34.1 + - - -
816A TYR* 3.7 1.9 - - - -
819A ARG* 3.4 33.6 + - + +
820A CYS* 3.4 26.2 - - - +
823A GLU* 3.5 27.7 + - - +
832A SER* 3.3 1.1 + - - +
833A GLN* 1.3 78.7 - - - +
835A MET* 1.3 61.4 + - - +
837A THR* 2.5 27.8 + - - +
838A LEU 3.3 3.1 + - - -
943B ARG* 5.5 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 835 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A CYS* 4.0 22.1 - - - +
821A LEU* 4.0 10.1 - - - -
824A ARG* 3.7 30.1 - - + -
830A GLY 6.4 0.2 - - - +
832A SER* 3.0 28.6 + - - +
833A GLN 3.2 0.2 - - - -
834A GLU* 1.3 74.8 - - - +
836A ASN* 1.3 64.1 + - - +
838A LEU* 3.0 24.9 + - + +
839A PHE* 3.1 45.7 + - + -
842A TRP* 3.9 14.8 - - + -
861A LEU* 3.8 23.8 - - + -
865A ASP* 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 836 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A GLY* 5.0 11.4 + - - -
832A SER 3.3 10.2 + - - +
833A GLN* 3.0 41.4 + - - +
835A MET* 1.3 79.1 - - - +
837A THR* 1.3 62.7 + - + +
839A PHE* 3.3 14.4 + - - -
840A ARG* 3.0 18.4 + - - +
865A ASP* 5.5 0.3 - - - +
872A TYR* 3.3 30.5 - - + +
908B GLY 5.6 3.8 + - - -
910B LEU* 3.6 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 837 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A HIS* 3.4 27.1 + - + +
799A SER* 4.5 5.6 - - - -
816A TYR* 2.6 25.5 + - - -
833A GLN* 3.1 16.1 + - + +
834A GLU* 2.5 23.1 + - - +
836A ASN* 1.3 75.5 - - + +
838A LEU* 1.3 55.4 + - - +
840A ARG* 3.3 10.8 + - - +
841A PHE* 2.8 25.6 + - - +
940B LYS* 5.9 5.4 - - + -
944B LEU* 4.7 21.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
813A TYR* 4.2 7.9 - - + -
816A TYR* 3.3 26.0 - - + +
817A ARG* 4.3 15.9 - - + +
820A CYS* 3.6 31.0 - - + -
821A LEU* 4.6 3.1 - - + -
834A GLU 3.3 0.2 + - - -
835A MET* 3.0 19.8 + - + +
837A THR* 1.3 78.5 + - - +
839A PHE* 1.3 60.8 + - - +
841A PHE* 3.2 8.2 + - + -
842A TRP* 2.9 77.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 839 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A MET* 3.1 41.8 + - + -
836A ASN* 3.5 20.9 - - - +
838A LEU* 1.3 74.5 - - - +
840A ARG* 1.3 63.8 + - - +
842A TRP* 3.5 12.4 + + - +
843A SER* 3.0 24.1 + - - -
858A PHE* 3.8 17.4 - + - -
861A LEU* 3.9 24.0 - - + -
862A ALA* 3.7 23.1 - - + -
865A ASP* 3.2 28.0 - - - -
872A TYR* 4.2 2.0 - + + -
873A GLY* 3.6 27.4 - - - -
876A CYS* 3.7 19.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
799A SER* 4.4 9.3 + - - -
800A HIS* 5.8 1.2 - - - +
803A LEU* 4.3 21.4 - - - +
836A ASN 3.0 10.2 + - - +
837A THR* 3.5 9.1 + - - +
839A PHE* 1.3 73.2 - - - +
841A PHE* 1.3 65.9 + - - +
843A SER* 3.3 3.5 + - - -
844A PHE* 3.2 54.1 + - + -
872A TYR* 3.5 22.9 - - - +
876A CYS* 3.9 9.1 - - - -
914B GLU* 5.0 4.6 + - - -
941B PHE* 6.3 1.3 - - - -
944B LEU* 3.3 55.5 + - - +
945B GLU* 5.8 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 841 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A SER* 4.0 20.0 - - - -
802A LEU* 3.4 32.1 - - + -
803A LEU* 3.7 28.7 - - + -
808A PHE* 4.1 10.3 - + - -
813A TYR* 3.6 22.2 - + - -
816A TYR* 4.3 3.8 - + - +
837A THR 2.8 21.1 + - - +
838A LEU* 3.2 15.5 + - + +
840A ARG* 1.3 74.3 - - - +
842A TRP* 1.3 70.2 + + - +
844A PHE* 3.2 2.4 + - - +
845A PHE* 2.7 77.8 + + + +
854A MET* 4.6 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 842 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A TYR* 2.9 26.9 + - - -
817A ARG* 5.0 1.3 - - + -
821A LEU* 4.9 0.9 - - + -
835A MET* 3.9 19.3 - - + -
838A LEU* 2.9 49.1 + - + +
839A PHE* 3.8 9.6 - + - +
841A PHE* 1.3 87.0 - + - +
843A SER* 1.3 63.5 + - - +
845A PHE* 4.5 2.0 - - - +
846A LEU* 3.1 31.9 + - + +
854A MET* 3.5 32.5 - - + +
857A GLU* 3.7 23.3 - - + -
858A PHE* 3.5 53.6 - + + -
861A LEU* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 843 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A PHE 3.0 18.3 + - - -
840A ARG* 3.6 7.4 - - - -
841A PHE 3.2 0.2 - - - -
842A TRP* 1.3 77.5 - - - +
844A PHE* 1.3 56.4 + - - +
847A ARG* 2.7 49.9 + - - +
858A PHE* 3.9 10.7 - - - -
876A CYS* 2.8 34.3 + - - -
879A ARG* 4.0 5.1 + - - +
880A TYR* 3.6 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 844 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A LEU* 4.1 20.4 - - + -
840A ARG* 3.2 54.4 + - + +
841A PHE 3.2 3.1 + - - +
843A SER* 1.3 80.6 - - - +
845A PHE* 1.3 65.6 + - - +
846A LEU 3.3 0.4 - - - -
847A ARG* 3.1 54.1 + - - +
848A ASP* 4.0 6.9 + - - +
879A ARG* 6.2 3.6 - - - -
1001A MGT 6.1 0.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
802A LEU 4.0 8.1 - - - -
803A LEU* 3.8 10.9 - - + +
804A LYS 6.0 0.4 - - - -
808A PHE* 3.5 50.7 - + + -
841A PHE* 2.7 53.3 + + + +
842A TRP* 4.4 1.1 - - - +
844A PHE* 1.3 73.8 - - - +
846A LEU* 1.3 57.1 + - - +
847A ARG 3.2 0.7 + - - -
848A ASP* 3.3 4.0 + - - +
849A HIS* 3.0 73.6 + + + +
851A ASN* 6.3 0.4 - - + -
854A MET* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 846 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A TRP* 3.1 21.6 + - + +
845A PHE* 1.3 74.6 - - - +
847A ARG* 1.3 65.8 + - - +
848A ASP 3.5 0.2 + - - -
849A HIS 3.9 7.9 - - - +
850A PHE* 3.6 24.0 + - + +
851A ASN 3.6 36.3 - - - +
854A MET* 4.1 23.8 - - + -
855A TYR* 3.8 26.7 - - + +
858A PHE* 3.5 33.0 - - + -
880A TYR* 3.5 22.1 + - + -
890A ARG* 5.0 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 847 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A SER* 2.7 41.9 + - - +
844A PHE* 3.1 46.4 + - - +
846A LEU* 1.3 79.2 - - - +
848A ASP* 1.3 66.9 + - - +
850A PHE 5.3 0.2 + - - -
879A ARG* 3.9 21.2 + - - +
880A TYR* 4.0 11.8 - - + +
883A TYR* 3.4 41.7 - - - +
884A GLY* 3.9 25.6 - - - +
887A LYS* 4.6 15.1 - - + +
888A LYS* 5.4 4.9 - - - +
890A ARG* 5.2 6.6 + - - -
----------------------------------------------------------
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 PHE 4.0 6.5 + - - +
845A PHE* 3.3 3.6 + - - +
847A ARG* 1.3 83.8 - - - +
849A HIS* 1.3 87.1 + - + +
850A PHE 3.9 2.1 + - - -
887A LYS* 5.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 849 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A LYS 5.5 2.6 + - - -
805A GLU* 4.9 14.5 + - - -
845A PHE* 3.0 63.9 + + + +
846A LEU* 3.9 6.9 - - - +
848A ASP* 1.3 98.3 + - + +
850A PHE* 1.3 66.1 + - - +
851A ASN* 3.5 4.0 + - - +
----------------------------------------------------------
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