Contacts of the helix formed by residues 870 - 885 (chain A) in PDB entry 4ZZ0
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 870 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A TYR* 3.4 4.6 - - - +
869A LYS* 1.3 88.9 - - - +
871A ARG* 1.3 64.0 + - - +
872A VAL* 3.1 14.2 + - - +
873A GLU* 3.0 42.5 + - - +
874A PHE* 3.3 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 871 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A ASN* 1.3 75.6 - - - +
872A VAL* 1.3 58.0 + - + +
874A PHE* 3.3 9.3 + - + +
875A ASP* 2.9 49.2 + - - +
897A ARG* 5.8 6.5 - - - +
898A ILE* 3.2 56.6 + - - +
899A LEU 4.8 1.6 + - - -
900A SER* 3.6 21.7 - - - +
1102A 3YE 4.3 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 872 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A ASN* 3.1 10.4 + - - +
871A ARG* 1.3 79.5 - - + +
873A GLU* 1.3 66.8 + - - +
875A ASP* 3.5 5.9 + - - +
876A SER* 3.0 29.2 + - - -
900A SER* 4.2 20.4 - - - +
902A PRO* 5.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 873 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A TYR* 3.7 25.3 - - + -
869A LYS* 4.6 11.2 - - + +
870A ASN* 3.0 35.6 + - - +
872A VAL* 1.3 81.8 - - - +
874A PHE* 1.3 65.6 + - - +
876A SER* 3.3 10.1 + - - -
877A ALA* 3.1 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 874 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A ILE* 6.5 0.2 - - + -
843A ASN* 3.9 17.0 - - + -
863A ILE* 3.2 40.4 - - + -
865A HIS* 3.5 34.3 - - + +
868A TYR* 3.9 17.8 - + + +
870A ASN 3.3 11.1 + - - +
871A ARG* 3.3 12.7 + - + +
873A GLU* 1.3 78.5 - - - +
875A ASP* 1.3 79.2 + - - +
877A ALA* 3.0 15.7 + - - +
878A ILE* 3.1 36.0 + - + +
895A PHE* 3.9 15.3 - + - -
897A ARG* 4.2 13.5 - - + -
898A ILE 5.9 1.1 - - - -
899A LEU* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 875 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A ARG* 2.9 21.6 + - - +
872A VAL* 3.8 4.3 - - - +
874A PHE* 1.3 92.8 - - - +
876A SER* 1.3 57.8 + - - +
878A ILE* 3.2 9.7 + - - +
879A ASP* 2.8 29.1 + - - +
898A ILE 4.8 0.5 - - - +
899A LEU* 3.6 21.5 - - - +
900A SER* 2.7 48.5 + - - +
903A PHE* 3.7 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 876 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A VAL* 3.0 21.0 + - - -
873A GLU* 3.5 13.9 - - - -
875A ASP* 1.3 76.5 - - - +
877A ALA* 1.3 57.3 + - - +
879A ASP* 3.3 7.5 + - - +
880A LEU* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 877 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A ILE* 3.7 12.1 - - + +
868A TYR* 3.3 39.7 - - + +
873A GLU 3.1 5.0 + - - +
874A PHE 3.0 10.6 + - - +
876A SER* 1.3 72.2 - - - +
878A ILE* 1.3 67.0 + - - +
880A LEU* 3.5 14.9 + - - +
881A VAL* 3.5 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 878 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A LEU* 4.2 18.4 - - + -
841A ILE* 4.2 13.9 - - + -
863A ILE* 3.7 18.6 - - + -
874A PHE* 3.1 48.8 + - + +
875A ASP* 3.2 13.7 + - - +
877A ALA* 1.3 76.4 - - - +
879A ASP* 1.3 63.2 + - - +
881A VAL* 3.0 15.8 + - - +
882A LEU* 3.0 21.0 + - + +
895A PHE* 4.1 15.5 - - + -
899A LEU* 4.6 6.3 - - + -
903A PHE* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 879 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A ASP 2.8 17.4 + - - +
876A SER* 3.6 9.0 - - - +
877A ALA 3.3 0.2 - - - -
878A ILE* 1.3 77.4 - - - +
880A LEU* 1.3 61.8 + - - +
882A LEU* 3.1 5.3 + - - +
883A GLU* 2.9 25.7 + - - +
903A PHE* 3.9 13.0 - - + -
906A LYS* 2.7 33.9 + - - +
907A TRP* 2.9 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 880 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A SER 3.0 16.9 + - - +
877A ALA* 3.7 9.6 - - - +
878A ILE 3.2 0.4 - - - -
879A ASP* 1.3 75.6 - - - +
881A VAL* 1.3 60.8 + - + +
883A GLU* 3.4 10.9 + - + +
884A GLU* 2.9 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 881 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A ILE* 4.0 10.3 - - + -
841A ILE* 3.8 20.9 - - + -
861A ARG* 4.1 18.6 - - + +
863A ILE* 4.0 15.3 - - + -
877A ALA 3.6 13.5 - - - +
878A ILE 3.0 7.8 + - - +
880A LEU* 1.3 76.1 - - + +
882A LEU* 1.3 65.9 + - - +
884A GLU* 3.2 14.0 + - - +
885A PHE* 3.1 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 882 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A ALA* 3.4 32.5 - - + -
813A LEU* 4.7 2.0 - - + -
839A ILE* 4.9 1.1 - - + -
841A ILE* 4.1 14.8 - - + -
878A ILE* 3.0 18.4 + - + +
879A ASP* 3.1 7.2 + - - +
881A VAL* 1.3 77.7 - - - +
883A GLU* 1.3 60.3 + - - +
886A SER 3.2 2.9 + - - -
887A ILE* 3.0 36.5 + - + +
890A VAL* 3.7 17.7 - - + -
903A PHE* 3.7 23.1 - - + -
907A TRP* 3.5 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 883 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A ASP* 2.9 22.7 + - - +
880A LEU* 3.7 10.8 - - + +
882A LEU* 1.3 75.2 - - - +
884A GLU* 1.3 66.7 + - - +
886A SER* 3.0 18.7 + - - +
887A ILE 5.1 0.2 - - - +
906A LYS* 3.1 34.1 + - - +
907A TRP* 4.3 10.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 884 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A ARG* 3.7 17.7 + - - -
880A LEU* 2.9 15.2 + - + +
881A VAL* 3.4 21.9 - - - +
883A GLU* 1.3 75.7 - - - +
885A PHE* 1.3 84.9 + - + +
886A SER* 3.6 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 885 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A ARG* 2.8 31.4 + - - +
838A ASP* 3.5 28.0 - - + -
839A ILE* 3.7 28.3 - - + -
859A PRO* 4.2 13.7 - - + -
861A ARG* 3.9 19.3 - - - -
881A VAL* 3.1 30.5 + - + +
883A GLU 3.1 0.2 - - - -
884A GLU* 1.3 104.1 - - + +
886A SER* 1.3 67.5 + - - +
887A ILE* 3.2 22.5 + - + +
----------------------------------------------------------
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