Contacts of the helix formed by residues 896 - 910 (chain A) in PDB entry 4U6R
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 896 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A GLU* 2.9 21.9 + - - -
870A VAL* 3.9 2.9 - - - +
874A TRP* 3.1 25.3 + - - -
893A LYS* 3.6 22.9 - - - -
894A GLY 3.3 1.6 - - - -
895A GLY* 1.3 77.8 - - - +
897A VAL* 1.3 60.9 + - - +
898A ARG* 3.2 4.2 + - - +
899A ASP* 3.0 24.4 + - - +
900A LEU 3.5 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 897 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A LEU* 3.7 44.4 - - + +
863A GLU* 2.9 12.5 + - - +
866A GLY* 3.7 31.6 - - - +
869A VAL* 4.8 5.4 - - + -
870A VAL* 4.3 12.1 - - + -
896A SER* 1.3 71.8 - - - +
898A ARG* 1.3 67.8 - - - +
899A ASP 3.2 0.4 + - - -
900A LEU* 3.3 3.0 + - - +
901A LEU* 3.1 30.8 + - + +
940A LEU* 4.2 15.7 - - + -
943A HIS* 4.2 8.3 - - + +
944A THR* 4.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 898 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A ILE* 2.6 49.6 + - + +
850A GLU* 4.1 9.6 + - - -
852A GLU* 2.6 35.0 + - - +
854A LEU* 5.3 6.5 - - - +
859A VAL* 4.1 21.6 - - + +
862A LEU* 4.2 12.2 - - + +
863A GLU* 3.1 11.6 + - - +
896A SER* 3.5 7.2 - - - +
897A VAL* 1.3 78.3 - - - +
899A ASP* 1.3 67.8 + - - +
901A LEU* 3.2 5.3 + - - +
902A ARG* 2.8 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A TRP* 3.7 6.1 - - + -
891A THR 3.5 3.1 - - - +
892A TYR* 3.4 17.0 - - + -
893A LYS* 2.7 51.0 + - - +
896A SER* 3.0 15.1 + - - +
898A ARG* 1.3 90.4 + - - +
900A LEU* 1.3 58.9 + - - +
902A ARG* 3.5 29.1 + - - -
903A ALA* 2.8 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 900 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A VAL* 3.8 21.3 - - + -
874A TRP* 3.6 46.8 - - + +
878A ILE* 5.4 0.4 - - + -
896A SER 3.5 4.8 + - - +
897A VAL 3.3 8.1 + - - +
899A ASP* 1.3 74.7 - - - +
901A LEU* 1.3 59.8 + - - +
903A ALA* 3.4 2.4 + - + +
904A MET* 3.0 33.5 + - - +
933A PHE* 4.3 20.0 - - + -
937A PHE* 3.9 31.6 - - + -
940A LEU* 3.9 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 901 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A PHE* 3.6 41.2 - - + +
845A VAL* 4.0 26.0 - - + -
846A SER* 4.0 14.5 + - - -
849A ILE* 4.7 2.9 - - + -
862A LEU* 4.2 9.6 - - + -
897A VAL* 3.1 33.8 + - + +
898A ARG* 3.6 6.7 - - - +
900A LEU* 1.3 75.5 - - - +
902A ARG* 1.3 57.6 + - - +
904A MET* 3.3 10.5 + - - +
905A ARG* 2.9 28.1 + - - +
940A LEU* 4.1 19.7 - - + -
944A THR* 4.2 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 902 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A SER* 3.8 15.4 + - - +
850A GLU* 6.4 4.3 - - - +
891A THR* 3.4 52.3 + - - +
892A TYR* 3.6 16.3 - - - -
898A ARG* 2.8 25.0 + - + +
899A ASP* 3.5 27.7 + - - +
900A LEU 3.3 0.2 - - - -
901A LEU* 1.3 75.0 - - - +
903A ALA* 1.3 60.9 + - - +
905A ARG* 3.3 1.3 + - + +
906A ASN* 2.9 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 903 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A TRP* 3.9 19.3 - - + -
886A LEU* 4.1 15.3 - - + -
892A TYR* 3.5 25.3 - - + -
899A ASP 2.8 20.9 + - - +
900A LEU* 3.7 6.7 - - + +
902A ARG* 1.3 72.0 - - - +
904A MET* 1.3 62.4 + - + +
906A ASN* 4.0 0.5 - - - +
907A LYS* 3.1 31.5 + - + +
933A PHE* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 904 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A LEU* 4.8 10.1 - - + -
842A PHE* 3.4 45.3 - - + -
900A LEU* 3.0 18.6 + - + +
901A LEU* 3.5 13.7 - - - +
903A ALA* 1.3 77.2 - - - +
905A ARG* 1.3 62.8 + - - +
908A LYS* 3.0 21.7 + - - +
929A PHE* 3.4 12.0 - - + -
930A VAL* 5.3 1.6 - - + -
933A PHE* 3.7 57.4 - - + -
940A LEU* 3.9 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 905 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A PHE 5.5 0.2 - - - +
843A GLN* 3.7 47.7 + - + +
846A SER* 3.3 33.7 - - - +
847A ASP* 2.9 28.3 + - - +
901A LEU 2.9 12.0 + - - +
902A ARG* 3.6 4.3 - - + +
904A MET* 1.3 75.8 - - - +
906A ASN* 1.3 67.6 + - - +
908A LYS* 3.4 8.0 + - - +
909A HIS* 3.0 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 906 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A TYR* 3.0 26.1 + - - +
902A ARG* 2.9 36.6 + - - +
903A ALA 4.0 1.6 - - - +
905A ARG* 1.3 87.0 - - - +
907A LYS* 1.3 65.9 + - - +
909A HIS* 3.1 7.1 + - - +
910A HIS* 2.9 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 907 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A LEU* 4.0 24.5 - - + -
885A ASP* 2.9 29.6 + - - +
886A LEU* 3.6 16.8 - - + -
889A PHE* 4.0 17.1 - - - -
892A TYR* 4.7 2.2 + - - -
903A ALA* 3.1 22.8 + - + +
904A MET* 4.0 3.4 - - - +
906A ASN* 1.3 84.2 + - - +
908A LYS* 1.3 61.4 + - - +
910A HIS* 4.6 4.4 - - - +
911A TYR* 3.2 27.2 + - - +
914A LEU* 3.5 31.4 - - + +
918A VAL* 4.8 0.4 - - + -
922A LEU* 4.1 8.3 - - + -
929A PHE* 4.0 16.2 - - + -
933A PHE* 5.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 908 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A LEU* 3.7 35.7 - - + -
840A GLN* 4.8 8.9 + - - -
843A GLN* 2.8 36.3 + - + +
904A MET 3.0 18.5 + - - +
905A ARG* 3.6 8.2 - - - +
907A LYS* 1.3 78.3 - - - +
909A HIS* 1.3 62.5 - - - +
911A TYR* 3.5 16.3 - - - +
925A LEU* 4.0 21.9 - - + +
926A PRO* 6.1 0.2 - - - -
929A PHE* 3.6 13.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 909 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905A ARG* 3.0 46.0 + - - +
906A ASN* 3.5 9.2 + - - +
908A LYS* 1.3 77.4 - - - +
910A HIS* 1.3 90.6 + + - +
911A TYR 3.3 1.8 + - - -
913A GLU* 4.7 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 910 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A ASN* 2.9 37.4 + - + +
907A LYS* 3.9 5.4 - - - +
909A HIS* 1.3 107.7 + + + +
911A TYR* 1.3 64.4 + - - +
912A ARG 3.4 1.6 - - - -
913A GLU* 3.0 44.8 + - + +
914A LEU* 3.2 24.0 + - + +
----------------------------------------------------------
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