Contacts of the helix formed by residues 870 - 882 (chain A) in PDB entry 5MJ6
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 THR 870 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A MET* 4.5 15.5 - - - +
867A GLY 3.1 9.7 + - - -
868A ALA 3.1 1.3 - - - -
869A LYS* 1.3 81.0 - - - +
871A ASP* 1.3 59.1 + - + +
872A LYS* 3.3 24.7 - - + +
873A GLY 4.1 2.7 - - - -
874A TRP* 2.8 37.7 + - - +
905A LYS* 4.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 871 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A LYS 4.4 0.2 + - - -
870A THR* 1.3 75.6 - - + +
872A LYS* 1.3 65.0 + - - +
874A TRP* 3.6 0.7 - - - +
875A SER* 2.9 32.6 + - - +
902A ASP* 5.5 0.5 - - - +
905A LYS* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 872 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A MET* 3.3 39.2 - - + +
870A THR* 3.3 13.0 - - + +
871A ASP* 1.3 78.6 - - - +
873A GLY* 1.3 57.0 + - - +
875A SER* 4.0 4.5 - - - -
876A PHE* 3.1 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 873 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A PHE* 3.6 22.3 - - - -
847A MET* 4.2 3.6 - - - -
867A GLY 3.5 18.2 - - - -
870A THR* 3.3 7.4 + - - +
871A ASP 3.2 0.6 - - - -
872A LYS* 1.3 78.5 - - - +
874A TRP* 1.3 58.5 + - - +
876A PHE* 3.2 2.1 + - - +
877A LEU* 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 874 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A GLY 4.0 1.8 + - - -
868A ALA* 3.4 25.4 - - + +
870A THR 2.8 21.7 + - - +
871A ASP 3.6 3.4 - - - +
873A GLY* 1.3 68.3 - - - +
875A SER* 1.3 74.8 + - - +
877A LEU* 3.2 4.4 + - - +
878A LEU* 2.9 41.4 + - + +
897A LEU* 3.2 43.3 + - + +
900A SER* 3.7 16.4 - - - -
905A LYS* 3.4 48.7 - - + +
908A TRP* 4.0 27.1 - + - -
909A LEU* 4.3 17.9 - - + -
1143A BR 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 875 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A ASP* 2.9 19.1 + - - +
872A LYS* 4.0 5.2 - - - -
874A TRP* 1.3 86.9 - - - +
876A PHE* 1.3 63.6 + - - +
878A LEU* 3.4 5.6 + - - +
879A GLY* 3.1 19.4 + - - -
905A LYS* 5.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 876 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A PHE* 4.8 2.0 - + - -
846A TRP* 3.5 37.5 - + - -
847A MET* 3.6 55.2 - - + -
850A ASN* 4.0 15.9 - - + -
851A GLY 4.1 1.3 - - - -
872A LYS 3.1 20.7 + - - +
873A GLY 3.6 3.4 - - - +
874A TRP 3.2 0.2 - - - -
875A SER* 1.3 75.9 - - - +
877A LEU* 1.3 61.9 + - - +
879A GLY* 3.3 3.9 + - - -
880A LYS* 3.1 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 877 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A PHE* 4.0 9.2 - - + -
846A TRP* 4.0 17.9 - - + -
864A PHE* 3.6 43.1 - - + +
868A ALA* 3.5 35.2 - - + +
873A GLY 2.9 18.4 + - - +
874A TRP* 3.5 4.0 - - - +
876A PHE* 1.3 75.1 - - - +
878A LEU* 1.3 60.4 + - - +
880A LYS* 3.0 7.8 + - - +
881A TYR 2.9 24.4 + - - -
893A ILE* 3.7 24.7 - - + +
896A ALA* 4.3 7.4 - - + -
897A LEU* 3.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 878 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A TRP* 2.9 34.6 + - + +
875A SER* 3.6 10.1 - - - +
877A LEU* 1.3 74.4 - - - +
879A GLY* 1.3 62.7 + - - +
881A TYR* 3.1 5.0 + - + +
882A ILE* 3.1 42.0 + - + +
897A LEU* 4.1 15.5 - - + +
908A TRP* 3.8 25.8 - - + -
918A ASN* 5.5 0.7 - - + +
919A PHE* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 879 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A SER 3.1 14.1 + - - -
876A PHE* 3.6 5.2 - - - -
877A LEU 3.2 0.2 - - - -
878A LEU* 1.3 77.8 - - - +
880A LYS* 1.3 60.0 + - - +
882A ILE* 3.5 19.9 - - - +
883A SER* 3.1 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 880 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A TRP* 3.9 21.1 - - + -
850A ASN* 2.9 40.3 + - - -
851A GLY* 4.2 8.3 - - - -
876A PHE* 3.1 37.1 + - + +
877A LEU* 3.0 9.6 + - - +
879A GLY* 1.3 73.9 - - - +
881A TYR* 1.3 65.5 + - - +
883A SER* 3.0 4.7 + - - +
884A ILE* 2.9 51.6 + - + +
893A ILE* 3.8 15.9 - - + -
1G NAG 4.4 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 881 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A LEU 2.9 15.4 + - - +
878A LEU* 3.5 12.1 - - + +
880A LYS* 1.3 74.6 - - - +
882A ILE* 1.3 67.4 + - + +
883A SER 3.1 3.7 + - - -
884A ILE 4.5 0.5 + - - +
890A LYS* 3.3 82.3 + - + +
891A ASN* 5.2 0.4 - - - -
893A ILE* 3.9 17.6 - - + +
894A LEU* 3.8 17.3 - - + +
897A LEU* 4.7 2.9 - - + -
918A ASN 3.8 11.2 - - - -
919A PHE* 3.3 42.2 - + - +
920A ARG 5.0 0.9 + - - -
923A LYS* 3.9 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 882 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A LEU* 3.1 32.6 + - + +
879A GLY* 3.5 16.6 - - - +
881A TYR* 1.3 87.1 - - + +
883A SER* 1.3 60.0 + - - +
918A ASN* 3.8 34.5 - - + +
----------------------------------------------------------
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