Contacts of the helix formed by residues 897 - 911 (chain A) in PDB entry 1DJL
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 ALA 897 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A LEU* 3.1 23.6 + - + +
895A ALA* 4.1 0.9 - - + -
896A LYS* 1.3 74.8 - - - +
898A GLN* 1.3 64.3 + - - +
899A TYR 3.2 2.9 - - - -
900A PRO* 3.3 18.9 - - + +
901A ILE* 3.2 14.4 + - - +
963A ILE* 5.2 0.2 - - + -
1026A ALA* 3.8 16.4 - - + +
1027A LYS* 3.8 29.4 - - - +
1030A CYS* 4.6 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 898 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A LEU* 3.8 15.1 - - + +
896A LYS* 2.8 34.4 - - - +
897A ALA* 1.3 71.0 + - - +
899A TYR* 1.3 75.0 + - + +
901A ILE* 2.9 26.8 - - - +
902A ALA* 2.9 15.4 + - - +
933A LEU* 3.3 55.9 - - + +
934A LEU* 4.7 5.2 - - + +
936A GLU* 3.5 22.6 + - - -
937A ALA* 3.5 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A LYS* 3.9 21.1 - - + -
898A GLN* 1.3 92.9 + - - +
900A PRO* 1.3 71.9 - - + +
902A ALA* 3.1 3.3 + - - +
903A ASP* 3.0 32.3 + - - +
936A GLU* 3.1 38.1 + - + +
937A ALA* 3.9 30.1 - - + -
1027A LYS* 6.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 900 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A LYS 4.5 3.4 - - - +
897A ALA* 3.3 23.6 - - - +
899A TYR* 1.3 94.3 - - + +
901A ILE* 1.3 54.4 + - - +
903A ASP* 3.3 3.0 + - - +
904A LEU* 2.9 29.2 + - - +
1027A LYS* 4.4 10.5 - - + +
1030A CYS* 3.7 18.4 - - + +
1031A ASP* 3.2 40.6 - - - +
1034A GLN* 3.8 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 901 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A ILE* 3.8 26.9 - - + -
892A LEU* 4.2 11.7 - - + -
897A ALA 3.2 12.8 - - - +
898A GLN* 2.9 29.6 - - - +
900A PRO* 1.3 78.2 - - - +
902A ALA* 1.3 61.0 + - - +
904A LEU* 3.9 23.8 - - + -
905A VAL* 2.9 36.2 + - + +
917A PHE* 4.1 15.5 - - + -
934A LEU* 4.6 2.9 - - + -
961A LEU* 4.9 2.9 - - + -
963A ILE* 3.7 28.3 - - + -
1030A CYS* 4.2 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 902 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A GLN 2.9 18.9 + - - +
899A TYR 3.4 5.2 - - - +
901A ILE* 1.3 75.6 - - - +
903A ASP* 1.3 66.5 + - - +
905A VAL* 3.2 5.5 + - - +
906A LYS* 3.0 23.1 + - - +
937A ALA* 3.5 26.5 - - + +
938A GLY 5.1 0.7 - - - -
939A VAL* 3.6 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 903 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A TYR* 3.0 17.9 + - - +
900A PRO* 3.5 4.1 - - - +
902A ALA* 1.3 78.6 - - - +
904A LEU* 1.3 63.2 + - - +
906A LYS* 3.0 18.9 + - - +
907A MET* 3.2 18.5 + - - +
937A ALA 5.4 0.9 - - - +
1034A GLN* 2.9 34.6 + - + +
1038A ARG* 4.3 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 904 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ILE* 4.7 7.4 - - + -
886A ILE* 5.9 0.2 - - + -
900A PRO 2.9 18.1 + - - +
901A ILE* 3.7 24.7 - - + +
903A ASP* 1.3 75.3 - - - +
905A VAL* 1.3 63.5 + - + +
907A MET* 3.2 11.3 + - + +
908A LEU* 3.0 41.7 + - + +
961A LEU* 4.8 6.5 - - + -
1030A CYS* 5.5 2.2 - - - +
1033A LEU* 4.2 24.7 - - + +
1034A GLN* 3.9 17.2 - - + +
1037A VAL* 3.6 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 905 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A ILE* 3.4 33.2 - - + -
901A ILE* 2.9 27.7 + - + +
902A ALA* 3.6 7.0 - - - +
904A LEU* 1.3 78.5 - - + +
906A LYS* 1.3 58.3 + - - +
908A LEU* 4.0 4.4 - - + +
909A THR* 2.7 39.5 + - - +
915A VAL* 3.9 20.2 - - + -
917A PHE* 3.7 13.7 - - + -
939A VAL* 5.3 1.8 - - + -
940A PRO* 5.9 0.7 - - + -
943A ILE* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 906 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902A ALA 3.0 12.6 + - - +
903A ASP* 3.0 12.5 + - - +
905A VAL* 1.3 78.8 - - - +
907A MET* 1.3 59.6 + - + +
909A THR* 3.4 5.5 + - - -
910A GLU* 2.9 58.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 907 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A ARG* 5.9 0.2 - - - +
903A ASP 3.6 5.6 - - - +
904A LEU* 3.2 14.7 + - - +
906A LYS* 1.3 76.7 - - + +
908A LEU* 1.3 59.8 + - - +
910A GLU* 3.2 13.5 + - - +
911A GLN* 2.9 38.0 + - + +
1034A GLN* 3.2 39.3 - - + +
1037A VAL* 3.8 22.2 - - + +
1038A ARG* 3.5 53.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 908 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ILE* 3.7 35.2 - - + -
879A ARG* 3.9 21.8 - - - +
884A ILE* 4.2 14.6 - - + -
904A LEU* 3.0 40.8 + - + +
905A VAL* 4.1 3.6 - - + +
907A MET* 1.3 75.9 - - - +
909A THR* 1.3 62.8 + - - +
911A GLN* 3.2 12.3 + - - +
913A LYS* 3.0 32.0 + - + +
915A VAL* 3.9 19.5 - - + -
961A LEU* 5.7 3.1 - - + -
1037A VAL* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 909 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905A VAL* 2.7 32.3 + - - +
906A LYS* 3.6 6.5 - - - -
908A LEU* 1.3 74.0 - - - +
910A GLU* 1.3 62.9 + - + +
911A GLN 3.0 1.6 - - - -
912A GLY* 2.8 22.5 + - - -
913A LYS 3.6 13.6 + - - +
915A VAL* 4.0 14.3 + - - +
943A ILE* 5.4 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 910 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A LYS* 2.9 49.3 + - + +
907A MET* 3.2 13.9 + - - +
909A THR* 1.3 78.2 - - + +
911A GLN* 1.3 66.0 + - - +
912A GLY 3.0 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 911 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A ARG* 3.4 41.8 - - - +
907A MET* 2.9 25.2 + - + +
908A LEU 3.4 9.2 - - - +
909A THR 3.0 0.8 - - - -
910A GLU* 1.3 82.7 + - - +
912A GLY* 1.3 60.1 + - - +
913A LYS* 3.4 6.5 + - + +
1040A SER 6.5 0.2 - - - -
----------------------------------------------------------
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