Contacts of the helix formed by residues 866 - 888 (chain A) in PDB entry 6PUO
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 ASP 866 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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862A LEU 3.7 8.0 + - - +
863A TYR* 3.1 17.4 + - - +
864A PHE 3.9 1.6 - - - +
865A SER* 1.3 81.4 - - - +
867A PHE* 1.3 64.0 + - - +
868A TRP* 4.6 2.2 - - + +
869A ASN* 3.7 15.0 - - + +
870A LYS* 3.1 24.1 + - - +
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Residues in contact with PHE 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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865A SER 3.7 2.0 + - - -
866A ASP* 1.3 71.5 - - - +
868A TRP* 1.3 112.2 + + + +
870A LYS* 3.1 8.4 + - + +
871A LEU* 2.9 56.2 + - + +
928A LYS* 3.3 41.5 - - + +
931A MET* 6.4 2.7 - - + -
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Residues in contact with TRP 868 (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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866A ASP* 4.6 2.4 - - + +
867A PHE* 1.3 107.2 - + + +
869A ASN* 1.3 60.7 + - - +
871A LEU* 3.3 9.7 + - + +
872A ASP* 2.9 27.9 + - - +
908A LEU 4.3 10.3 - - - -
909A ARG* 4.2 29.4 + - - +
911A MET* 3.9 12.3 - - + -
912A HIS* 3.4 67.0 - + + +
915A THR* 4.8 11.2 - - + +
924A ILE* 4.9 11.4 - - + -
928A LYS* 3.8 14.8 - - - +
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Residues in contact with ASN 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A GLU* 5.1 11.0 - - - +
863A TYR* 3.3 31.0 - - + +
864A PHE* 5.3 1.3 - - - -
866A ASP* 3.7 12.2 + - + +
867A PHE 3.2 0.8 - - - -
868A TRP* 1.3 78.2 - - - +
870A LYS* 1.3 56.7 + - - +
872A ASP* 3.3 7.2 + - - +
873A VAL* 3.0 36.7 + - + +
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Residues in contact with LYS 870 (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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864A PHE* 4.6 10.3 + - - +
866A ASP 3.1 19.6 + - - +
867A PHE* 3.1 8.5 + - - +
869A ASN* 1.3 77.2 - - - +
871A LEU* 1.3 60.8 + - + +
873A VAL* 3.3 11.9 - - + +
874A GLY* 2.9 24.6 + - - -
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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
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867A PHE* 2.9 53.7 + - + +
868A TRP* 3.7 13.9 - - + +
869A ASN 3.3 0.2 - - - -
870A LYS* 1.3 79.1 - - + +
872A ASP* 1.3 58.2 + - - +
874A GLY* 3.3 2.1 + - - -
875A ALA* 3.0 28.1 + - - +
905A LEU* 3.8 39.4 - - + +
908A LEU* 5.9 4.3 - - + -
909A ARG* 5.9 4.5 - - - -
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Residues in contact with ASP 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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839A LEU* 6.1 4.3 - - + -
843A GLU* 5.7 10.3 - - + +
868A TRP 2.9 18.3 + - - +
869A ASN* 3.5 9.0 - - - +
870A LYS 3.3 0.2 - - - -
871A LEU* 1.3 76.6 - - - +
873A VAL* 1.3 59.8 + - + +
875A ALA* 3.2 7.8 + - - +
876A ILE* 2.9 39.1 + - + +
906A PHE* 5.6 1.7 - - - -
909A ARG* 5.0 14.3 - - - +
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Residues in contact with VAL 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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843A GLU* 6.1 4.5 - - + -
869A ASN* 3.0 17.8 + - + +
870A LYS* 3.3 20.2 - - + +
872A ASP* 1.3 74.7 - - + +
874A GLY* 1.3 60.1 + - - +
876A ILE* 3.7 17.8 - - + +
877A LEU* 2.9 29.1 + - - +
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Residues in contact with GLY 874 (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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870A LYS 2.9 15.5 + - - -
871A LEU* 3.3 3.6 + - - -
872A ASP 3.2 0.2 - - - -
873A VAL* 1.3 78.7 - - - +
875A ALA* 1.3 56.6 + - - +
877A LEU* 3.3 6.4 + - - +
878A LEU* 2.9 28.9 + - - +
905A LEU* 3.9 10.0 - - - +
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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 3.0 13.4 + - - +
872A ASP* 3.6 10.1 - - - +
874A GLY* 1.3 73.3 - - - +
876A ILE* 1.3 60.6 + - - +
878A LEU* 4.5 0.2 - - - -
879A PHE* 2.9 27.7 + - - +
902A ASP* 3.2 14.5 - - - +
905A LEU* 3.6 20.0 - - + +
906A PHE* 3.6 35.6 - - + -
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Residues in contact with ILE 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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836A LEU* 5.4 8.1 - - + -
839A LEU* 5.7 4.9 - - + -
840A VAL* 3.7 34.1 - - + -
843A GLU* 5.7 8.5 - - + -
872A ASP* 2.9 28.4 + - + +
873A VAL* 3.7 21.5 - - + +
875A ALA* 1.3 76.7 - - + +
877A LEU* 1.3 57.3 + - - +
879A PHE* 3.3 6.4 + - - +
880A VAL* 3.0 33.6 + - + +
906A PHE* 5.3 3.6 - - + -
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Residues in contact with LEU 877 (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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873A VAL 2.9 17.2 + - - +
874A GLY* 3.7 6.5 - - - +
875A ALA 3.3 0.2 - - - -
876A ILE* 1.3 78.0 - - - +
878A LEU* 1.3 57.2 + - - +
880A VAL* 3.3 12.6 - - + +
881A ALA* 3.0 28.4 + - - +
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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 GLY 2.9 17.6 + - - +
875A ALA* 3.9 3.6 - - - +
877A LEU* 1.3 76.7 - - - +
879A PHE* 1.3 57.5 + - - +
881A ALA* 3.4 7.1 + - + +
882A GLY* 2.9 23.0 + - - -
898A ILE* 3.7 31.8 - - + +
899A LEU* 5.5 0.2 - - - +
901A LEU* 4.0 13.9 - - + +
902A ASP* 3.6 37.3 - - + +
905A LEU* 5.0 9.4 - - + -
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Residues in contact with PHE 879 (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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813A PHE* 4.3 24.0 - + - -
832A ILE* 5.1 7.9 - - + -
833A TYR* 4.8 17.9 - - + -
836A LEU* 3.6 38.1 - - + -
875A ALA 2.9 15.1 + - - +
876A ILE* 3.7 5.2 - - - +
878A LEU* 1.3 77.9 - - - +
880A VAL* 1.3 62.8 + - + +
882A GLY* 3.3 1.5 + - - -
883A LEU* 2.9 56.8 + - + +
899A LEU* 5.1 14.4 - - + -
902A ASP* 3.2 24.8 + - - +
906A PHE* 5.0 0.4 - + - -
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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
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876A ILE* 3.0 20.7 + - + +
877A LEU* 3.3 20.4 - - + +
879A PHE* 1.3 80.2 - - + +
881A ALA* 1.3 59.7 + - + +
883A LEU* 4.2 9.4 - - + +
884A THR* 3.4 23.0 + - - +
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Residues in contact with ALA 881 (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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877A LEU 3.0 18.3 + - - +
878A LEU* 3.7 11.0 - - + +
880A VAL* 1.3 78.7 - - + +
882A GLY* 1.3 58.3 + - - +
884A THR* 3.3 10.9 - - - +
885A CYS* 3.0 28.0 + - - +
898A ILE* 4.7 5.2 - - + -
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Residues in contact with GLY 882 (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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878A LEU 2.9 13.0 + - - -
881A ALA* 1.3 76.9 - - - +
883A LEU* 1.3 58.1 + - - +
885A CYS* 3.4 6.9 + - - +
886A ARG* 2.9 27.9 + - - +
895A GLY* 4.3 2.4 - - - -
898A ILE* 3.7 23.1 - - - +
899A LEU* 3.7 20.9 - - - +
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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
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833A TYR* 5.3 10.5 - - + -
879A PHE* 2.9 46.4 + - + +
880A VAL* 4.2 9.6 - - + +
881A ALA 3.3 0.2 - - - -
882A GLY* 1.3 78.5 - - - +
884A THR* 1.3 61.5 + - - +
886A ARG* 3.1 6.4 + - - +
887A LEU* 3.0 50.3 + - + +
899A LEU* 4.3 2.4 - - - +
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Residues in contact with THR 884 (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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880A VAL 3.4 14.8 + - - +
881A ALA* 3.3 17.5 - - - +
883A LEU* 1.3 81.8 - - - +
885A CYS* 1.3 62.6 + - - +
887A LEU* 4.0 7.8 - - - +
888A ILE* 3.8 23.7 + - - +
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Residues in contact with CYS 885 (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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881A ALA 3.0 18.3 + - - +
882A GLY* 3.7 8.1 - - - +
883A LEU 3.2 0.4 - - - -
884A THR* 1.3 79.8 - - + +
886A ARG* 1.3 60.0 + - - +
888A ILE* 3.3 3.0 + - - +
891A THR* 2.3 48.4 + - - +
894A PRO* 3.7 15.3 - - - -
895A GLY* 3.3 28.3 - - - -
898A ILE* 5.6 3.8 - - + -
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Residues in contact with ARG 886 (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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820A ASP 5.8 0.6 + - - -
821A PHE* 3.7 34.0 - - + -
822A GLN* 2.5 32.2 + - - +
823A PRO* 3.7 19.8 + - + +
824A VAL 3.0 14.8 + - - -
825A PRO* 3.5 26.7 - - - +
826A SER* 4.0 5.1 - - - +
829A GLU* 4.7 13.3 - - - +
882A GLY 2.9 16.8 + - - +
883A LEU* 3.1 7.6 + - - +
885A CYS* 1.3 77.4 - - - +
887A LEU* 1.3 84.2 + - - +
888A ILE 3.3 9.5 - - - +
889A PRO* 4.3 2.9 - - - +
891A THR 4.6 5.2 - - - -
892A LEU* 5.4 5.9 - - + +
895A GLY* 4.6 4.9 - - - -
899A LEU* 5.5 4.3 - - + -
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Residues in contact with LEU 887 (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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823A PRO 5.9 2.7 - - - +
825A PRO* 6.2 4.0 - - + -
883A LEU* 3.0 44.4 + - + +
884A THR* 3.9 8.9 + - - +
885A CYS 3.4 0.6 - - - -
886A ARG* 1.3 100.9 - - - +
888A ILE* 1.3 65.9 + - + +
889A PRO* 3.4 9.2 - - - +
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Residues in contact with ILE 888 (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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884A THR* 3.8 15.4 + - - +
885A CYS* 3.3 6.0 + - - +
886A ARG 3.2 5.1 - - - +
887A LEU* 1.3 79.3 - - + +
889A PRO* 1.3 72.3 - - + +
890A ALA* 3.9 13.0 - - + +
891A THR* 3.0 39.4 + - + +
892A LEU 4.3 0.2 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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