Contacts of the helix formed by residues 857 - 883 (chain A) in PDB entry 5UAK
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 LYS 857 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A HIS* 1.3 76.2 + - - +
858A SER* 1.3 60.7 + - - +
859A LEU 3.2 0.4 - - - -
860A ILE* 2.9 37.2 + - + +
861A PHE* 3.4 24.2 - - + -
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Residues in contact with SER 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A HIS* 2.7 35.2 + - - -
857A LYS* 1.3 76.9 - - - +
859A LEU* 1.3 55.4 + - - +
861A PHE* 3.1 14.3 + - - +
862A VAL* 3.0 30.3 + - - +
939A HIS* 6.1 0.3 - - - -
940A THR* 3.6 14.1 - - - +
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Residues in contact with LEU 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A TYR* 5.8 2.7 - - + +
853A ILE* 3.5 43.7 - - + +
856A HIS* 3.9 18.1 - - + +
857A LYS 3.2 0.4 - - - -
858A SER* 1.3 81.0 + - - +
860A ILE* 1.3 61.4 + - - +
862A VAL* 3.4 17.4 - - + +
863A LEU* 3.2 24.6 - - + +
940A THR* 3.9 19.5 - - - +
941A LEU* 3.7 31.2 - - + -
944A VAL* 3.9 19.3 - - + -
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Residues in contact with ILE 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A ILE* 4.6 13.5 - - + +
854A THR* 5.1 15.3 - - + -
856A HIS 3.6 18.8 - - - +
857A LYS* 2.9 18.3 + - + +
859A LEU* 1.3 75.8 - - + +
861A PHE* 1.3 68.8 + - + +
863A LEU* 3.5 12.8 - - + +
864A ILE* 3.2 32.9 + - + +
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Residues in contact with PHE 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A LYS* 3.4 38.1 + - + -
858A SER* 3.1 11.5 + - - +
860A ILE* 1.3 84.3 - - + +
862A VAL* 1.3 58.0 + - - +
864A ILE* 3.4 7.8 + - + +
865A TRP* 2.8 30.8 + - - +
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Residues in contact with VAL 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A SER 3.0 15.2 + - - +
859A LEU* 3.4 20.6 - - + +
861A PHE* 1.3 77.2 - - - +
863A LEU* 1.3 62.9 + - + +
865A TRP* 3.4 17.1 + - + +
866A CYS* 2.8 27.6 + - + +
933A ARG 5.7 2.0 - - - +
934A GLY* 6.0 1.3 - - - -
936A PRO* 3.8 20.6 - - + -
937A LEU* 3.8 35.2 - - + +
940A THR* 3.8 19.7 - - + +
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Residues in contact with LEU 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A ILE* 3.8 29.8 - - + -
859A LEU* 3.2 28.0 - - + +
860A ILE* 3.5 15.3 - - + +
862A VAL* 1.3 80.9 - - + +
864A ILE* 1.3 74.7 + - + +
866A CYS* 3.4 7.3 + - - +
867A LEU* 2.9 48.0 + - + +
937A LEU* 5.3 8.5 - - + -
995A ILE* 6.4 1.6 - - + -
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Residues in contact with ILE 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A ILE* 3.2 27.8 + - + +
861A PHE* 3.6 8.5 - - + +
863A LEU* 1.3 85.4 - - + +
865A TRP* 1.3 55.9 + - - +
867A LEU* 3.2 12.6 + - + +
868A VAL* 2.8 38.6 + - + +
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Residues in contact with TRP 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A PHE 2.8 18.3 + - - +
862A VAL* 3.6 18.4 - - + +
864A ILE* 1.3 75.8 - - - +
866A CYS* 1.3 63.1 + - - +
868A VAL* 3.4 15.9 - - + +
869A ILE* 3.2 44.0 - - + +
932A PHE* 3.5 33.2 - + - -
933A ARG* 3.7 26.9 - - + -
936A PRO* 4.6 15.3 - - + -
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Residues in contact with CYS 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862A VAL* 2.8 17.2 + - + +
863A LEU* 3.6 9.4 - - - +
865A TRP* 1.3 76.9 - - - +
867A LEU* 1.3 60.4 + - + +
869A ILE* 3.5 3.1 + - - +
870A PHE* 3.0 28.1 + - - +
929A MET* 3.7 42.6 - - + +
933A ARG 4.8 4.0 - - - +
934A GLY* 6.0 1.6 - - - -
937A LEU* 5.0 12.6 - - + -
995A ILE* 4.9 9.0 - - - -
999A LEU* 4.0 18.4 - - - -
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Residues in contact with LEU 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863A LEU* 2.9 37.9 + - + +
864A ILE* 3.7 13.9 - - + +
866A CYS* 1.3 78.8 - - + +
868A VAL* 1.3 58.1 + - - +
870A PHE* 3.3 5.6 + - + +
871A LEU* 2.8 47.9 + - + +
999A LEU* 4.6 19.7 - - + -
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Residues in contact with VAL 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A ILE* 2.8 24.5 + - + +
865A TRP* 3.4 30.5 - - + +
867A LEU* 1.3 72.2 - - - +
869A ILE* 1.3 57.7 + - + +
871A LEU* 3.5 8.5 + - + +
872A ALA* 2.8 35.2 + - + +
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Residues in contact with ILE 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A TRP* 3.2 43.3 - - + +
866A CYS* 3.5 4.3 + - - +
867A LEU 3.3 0.4 - - - -
868A VAL* 1.3 79.0 - - + +
870A PHE* 1.3 58.0 + - - +
872A ALA* 3.5 7.1 - - + +
873A GLU* 2.8 48.2 + - + +
929A MET* 5.0 6.3 - - + -
933A ARG* 3.7 52.3 - - + +
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Residues in contact with PHE 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A CYS* 3.0 20.1 + - - +
867A LEU* 3.5 9.6 - - + +
869A ILE* 1.3 77.2 - - - +
871A LEU* 1.3 76.2 + - + +
873A GLU* 4.2 4.7 - - - +
874A VAL* 3.2 34.3 + - + +
927A LEU* 3.8 28.7 - - + +
929A MET* 5.5 6.8 - - - -
999A LEU* 3.2 69.1 - - + -
1002A ILE* 3.9 9.2 - - + -
1003A GLY* 3.6 17.9 - - - -
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Residues in contact with LEU 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A LEU* 2.8 42.5 + - + +
868A VAL* 3.7 7.9 - - + +
870A PHE* 1.3 87.3 - - + +
872A ALA* 1.3 63.2 + - - +
874A VAL* 3.4 20.8 - - + +
875A ALA* 3.4 13.0 + - - +
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Residues in contact with ALA 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868A VAL* 2.8 23.7 + - + +
869A ILE* 3.2 11.0 + - + +
871A LEU* 1.3 74.9 - - - +
873A GLU* 1.3 63.7 + - + +
875A ALA* 3.7 5.6 - - - +
876A ALA* 3.3 18.7 + - - +
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Residues in contact with GLU 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869A ILE* 2.8 36.3 + - + +
870A PHE* 4.3 4.3 - - - +
872A ALA* 1.3 70.0 - - + +
874A VAL* 1.3 62.5 + - - +
875A ALA 3.2 2.2 - - - -
876A ALA* 2.9 23.8 + - - +
877A SER* 3.0 14.8 + - - -
919A TYR* 5.1 4.3 + - - -
926A LEU* 3.2 41.0 - - + +
927A LEU* 5.1 3.9 - - + +
928A ALA 5.0 1.7 + - - +
929A MET* 6.1 1.2 - - - +
933A ARG* 3.7 24.1 + - - -
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Residues in contact with VAL 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A PHE* 3.2 28.0 + - + +
871A LEU* 3.4 16.8 - - + +
873A GLU* 1.3 78.0 - - - +
875A ALA* 1.3 62.3 + - - +
877A SER* 3.5 19.1 - - - +
878A LEU* 3.6 13.4 - - + +
927A LEU* 4.4 18.7 - - + +
1003A GLY* 4.3 12.6 - - - +
1006A ALA* 5.2 6.1 - - + -
1007A VAL* 3.5 26.2 - - + -
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Residues in contact with ALA 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871A LEU 3.4 14.3 + - - +
872A ALA* 3.7 6.3 - - - +
873A GLU 3.2 0.4 - - - -
874A VAL* 1.3 82.3 - - + +
876A ALA* 1.3 59.5 + - - +
877A SER 3.2 0.2 - - - -
878A LEU* 2.9 28.5 + - - +
879A VAL* 3.0 18.8 + - + +
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Residues in contact with ALA 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A ALA 3.3 10.7 + - - +
873A GLU* 2.9 14.3 + - - +
875A ALA* 1.3 79.2 - - - +
877A SER* 1.3 56.7 + - - +
879A VAL* 3.3 11.6 + - + +
880A VAL* 3.0 35.9 + - + +
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Residues in contact with SER 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A GLU 3.0 13.3 + - - -
874A VAL* 3.5 12.9 + - - -
876A ALA* 1.3 76.7 - - - +
878A LEU* 1.3 55.5 + - - +
880A VAL* 3.3 1.4 + - - +
881A LEU* 2.8 43.6 + - - +
920A VAL* 4.0 28.9 - - - +
926A LEU* 3.6 26.0 - - - +
1007A VAL* 4.7 9.7 - - - +
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Residues in contact with LEU 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874A VAL* 3.6 15.9 - - + +
875A ALA* 2.9 14.3 + - - +
877A SER* 1.3 79.8 - - - +
879A VAL* 1.3 53.9 + - + +
881A LEU* 3.6 6.2 - - + +
882A TRP* 2.8 39.6 + - + +
1007A VAL* 3.9 25.1 - - + +
1010A VAL* 3.8 40.6 - - + -
1011A LEU* 5.3 5.8 - - + -
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Residues in contact with VAL 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A ALA* 3.0 19.8 + - + +
876A ALA* 3.5 13.7 - - + +
877A SER 3.3 0.2 - - - -
878A LEU* 1.3 77.2 - - + +
880A VAL* 1.3 64.9 + - + +
882A TRP* 3.4 17.7 - - - +
883A LEU* 4.1 10.4 - - + +
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Residues in contact with VAL 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A ALA* 3.0 22.5 + - + +
877A SER* 3.3 5.8 + - - +
879A VAL* 1.3 80.4 - - + +
881A LEU* 1.3 68.5 + - + +
882A TRP 3.1 0.2 - - - -
883A LEU* 3.1 29.4 + - - +
916A PHE* 3.7 41.1 - - + -
920A VAL* 4.7 6.3 - - + -
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Residues in contact with LEU 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A SER* 2.8 27.3 + - - +
878A LEU* 3.6 7.2 - - + +
880A VAL* 1.3 81.2 - - + +
882A TRP* 1.3 63.9 + - - +
883A LEU 3.2 8.1 + - - +
917A TYR* 5.7 8.5 - - + -
920A VAL* 3.7 30.3 - - + -
1007A VAL* 5.7 5.8 - - + +
1011A LEU* 4.2 36.8 - - + +
1128A ARG* 5.1 8.3 + - - -
1131A ILE* 4.5 30.3 - - + -
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Residues in contact with TRP 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A LEU* 2.8 19.8 + - + +
879A VAL* 3.4 13.9 - - - +
881A LEU* 1.3 77.6 - - - +
883A LEU* 1.3 69.7 + - + +
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Residues in contact with LEU 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A VAL 4.1 12.8 - - - +
880A VAL 3.1 16.8 + - - +
881A LEU* 3.8 7.9 - - - +
882A TRP* 1.3 94.7 - - + +
917A TYR* 4.8 10.8 + - - -
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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