Contacts of the helix formed by residues 884 - 901 (chain A) in PDB entry 1HU3
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 884 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881A ALA* 3.6 25.1 - - + +
883A ASP* 1.3 80.2 - - - +
885A ALA* 1.3 62.0 + - - +
886A ARG 3.1 1.3 - - - -
887A ARG* 3.4 20.6 + - + +
888A ARG* 3.5 10.4 + - - +
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Residues in contact with ALA 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 4.3 1.8 + - - +
882A LYS* 4.3 29.8 - - + +
883A ASP 3.8 0.4 - - - +
884A LYS* 1.3 79.9 - - - +
886A ARG* 1.3 54.5 + - + +
887A ARG 3.3 0.2 - - - -
888A ARG* 3.3 9.8 + - - +
889A SER* 2.7 35.5 + - - -
916A LYS* 6.1 2.7 - - - +
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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
----------------------------------------------------------
882A LYS 4.4 9.1 + - - +
883A ASP* 3.7 39.2 + - - +
884A LYS 3.9 0.2 - - - +
885A ALA* 1.3 77.0 - - + +
887A ARG* 1.3 60.1 + - - +
889A SER* 3.0 8.1 + - - -
890A ILE* 2.8 37.2 + - + +
916A LYS* 5.4 4.0 - - - +
920A ASN* 3.5 43.4 - - + +
922A ASP* 4.2 22.3 - - - +
925A SER* 5.0 2.5 - - - +
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Residues in contact with ARG 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A ASP 4.9 1.1 + - - +
884A LYS* 3.4 17.2 + - + +
885A ALA 3.3 0.4 - - - -
886A ARG* 1.3 78.2 - - - +
888A ARG* 1.3 62.2 + - - +
890A ILE* 3.2 19.1 + - - +
891A GLY* 3.2 9.7 + - - -
924A GLU* 5.2 9.9 - - - +
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Residues in contact with ARG 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800A ILE* 3.7 36.7 - - + +
840A ARG* 5.6 0.8 - - - +
844A GLU* 2.7 44.0 + - - +
884A LYS 3.5 7.8 + - - +
885A ALA* 3.3 11.7 + - - +
886A ARG 3.3 0.2 - - - -
887A ARG* 1.3 79.9 - - - +
889A SER* 1.3 62.8 + - - +
891A GLY* 3.2 3.1 + - - +
892A ASN* 3.0 21.0 + - + +
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Residues in contact with SER 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A ALA 2.7 22.7 + - - -
886A ARG* 3.0 11.6 + - - -
888A ARG* 1.3 73.2 - - - +
890A ILE* 1.3 65.1 + - - +
892A ASN* 3.8 5.6 - - - +
893A ILE* 2.9 47.9 + - - +
916A LYS* 3.5 26.0 - - - +
920A ASN* 4.6 3.3 + - - -
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Residues in contact with ILE 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A ARG* 2.8 28.8 + - + +
887A ARG* 3.2 10.7 + - - +
889A SER* 1.3 82.2 - - - +
891A GLY* 1.3 63.2 + - - +
893A ILE* 3.4 5.1 + - - +
894A LYS* 3.0 23.9 + - + +
917A LEU* 4.0 19.1 - - + -
920A ASN* 5.1 1.6 - - - +
924A GLU* 4.4 23.3 - - + +
925A SER* 3.6 31.9 - - - +
928A CYS* 4.1 20.7 - - + -
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Residues in contact with GLY 891 (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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799A ALA 4.9 2.5 - - - +
800A ILE* 5.4 1.1 - - - -
803A PRO* 3.5 37.5 - - - +
887A ARG 3.2 6.5 + - - -
888A ARG* 3.2 7.8 + - - -
890A ILE* 1.3 81.2 - - - +
892A ASN* 1.3 60.9 + - - +
894A LYS* 3.2 7.2 + - - +
895A PHE* 3.1 21.1 + - - +
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Residues in contact with ASN 892 (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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796A PHE* 4.5 9.4 - - - -
800A ILE* 3.5 26.9 - - + +
844A GLU* 3.4 39.8 - - - +
845A PHE* 4.0 10.5 - - - -
888A ARG* 3.0 16.3 + - + +
889A SER* 3.8 7.2 - - - +
891A GLY* 1.3 74.1 - - - +
893A ILE* 1.3 59.1 + - - +
895A PHE* 3.0 9.1 + - - +
896A ILE* 2.8 60.1 + - - +
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Residues in contact with ILE 893 (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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845A PHE* 4.7 10.8 - - + -
889A SER* 2.9 34.2 + - - +
890A ILE* 3.8 4.3 - - - +
892A ASN* 1.3 77.1 - - + +
894A LYS* 1.3 56.0 + - - +
896A ILE* 3.7 7.6 - - - -
897A GLY* 2.8 27.7 + - - -
913A CYS* 3.8 34.8 - - + +
916A LYS* 4.1 15.9 - - + -
917A LEU* 3.8 29.8 - - + -
928A CYS* 4.3 15.9 - - - -
932A LEU* 4.5 11.7 - - + +
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Residues in contact with LYS 894 (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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803A PRO* 3.6 19.7 - - + +
804A SER* 4.1 16.4 - - - +
806A SER* 3.4 20.0 - - - +
807A VAL* 5.8 5.0 - - - +
890A ILE* 3.0 16.1 + - + +
891A GLY* 3.4 11.0 - - - +
892A ASN 3.2 0.2 - - - -
893A ILE* 1.3 77.0 - - - +
895A PHE* 1.3 57.8 + - - +
897A GLY* 3.8 1.4 - - - -
898A GLU* 3.1 36.4 + - - +
928A CYS* 5.3 4.9 - - - -
932A LEU* 6.1 1.3 - - - -
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Residues in contact with PHE 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A VAL* 4.0 21.3 - - + -
796A PHE* 3.6 46.0 - + - -
799A ALA* 3.7 24.2 - - + +
800A ILE* 5.5 1.6 - - + -
806A SER* 3.7 28.5 - - - -
809A TYR* 3.7 20.0 - - + -
810A ALA* 3.8 15.7 - - + -
813A CYS* 4.3 5.8 - - - -
891A GLY 3.1 8.8 + - - +
892A ASN* 3.0 14.2 + - - +
894A LYS* 1.3 77.6 - - - +
896A ILE* 1.3 61.3 + - - +
898A GLU* 2.8 20.1 + - - +
899A LEU* 2.8 29.8 + - + +
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Residues in contact with ILE 896 (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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796A PHE* 5.1 3.6 - - + -
841A CYS* 3.8 24.2 - - + -
845A PHE* 3.2 27.4 - - + -
892A ASN* 2.8 51.9 + - - +
893A ILE* 3.8 5.8 - - - +
895A PHE* 1.3 74.9 - - + +
897A GLY* 1.3 58.0 + - - +
899A LEU* 3.3 2.6 + - - -
900A PHE* 2.9 24.8 + - - +
905A LEU* 3.4 23.1 - - + +
909A ILE* 4.4 9.4 - - + -
910A MSE 4.3 7.6 - - - -
913A CYS* 4.0 17.7 - - - -
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Residues in contact with GLY 897 (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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893A ILE 2.8 18.1 + - - -
894A LYS* 3.8 2.0 - - - -
896A ILE* 1.3 74.2 - - - +
898A GLU* 1.3 64.1 + - - +
900A PHE* 3.4 2.1 + - - +
901A LYS* 3.1 35.4 + - - +
910A MSE 3.7 24.3 - - - +
932A LEU* 4.5 7.9 - - - -
936A ILE* 5.4 0.2 - - - +
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Residues in contact with GLU 898 (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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806A SER* 3.5 31.6 + - - +
807A VAL* 3.5 33.9 - - + +
810A ALA* 3.8 7.4 - - + -
894A LYS* 3.1 23.7 + - - +
895A PHE* 2.8 13.1 + - - +
897A GLY* 1.3 76.0 - - - +
899A LEU* 1.3 63.3 + - - +
901A LYS* 3.3 43.8 + - - +
902A LEU* 3.6 17.1 + - + +
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Residues in contact with LEU 899 (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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796A PHE* 4.1 5.6 - - + -
810A ALA* 3.8 13.2 - - - -
813A CYS* 3.6 22.7 - - + -
837A LEU* 3.6 32.8 - - + -
841A CYS* 4.3 2.5 - - - -
895A PHE* 2.8 38.9 + - + +
896A ILE* 3.6 2.5 - - - +
898A GLU* 1.3 77.5 - - - +
900A PHE* 1.3 62.6 + - - +
902A LEU* 3.0 14.9 + - - +
904A MSE 3.4 40.7 + - + +
905A LEU* 3.5 25.8 - - + -
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Residues in contact with PHE 900 (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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896A ILE 2.9 10.8 + - - +
897A GLY 3.8 3.4 - - - +
898A GLU 3.3 0.2 - - - -
899A LEU* 1.3 76.6 - - - +
901A LYS* 1.3 62.5 + - - +
902A LEU 3.1 0.4 - - - -
903A LYS* 3.2 13.3 + - - -
905A LEU* 3.5 30.2 - - + +
906A THR 3.9 4.7 - - - -
907A GLU* 3.6 34.3 - - + -
910A MSE 3.3 53.4 - - + -
936A ILE* 3.9 31.0 - - + -
939A ASP* 4.7 15.0 - - + -
940A LEU* 4.1 7.9 - - + -
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Residues in contact with LYS 901 (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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897A GLY 3.1 19.6 + - - +
898A GLU* 3.5 39.3 + - - +
899A LEU 3.1 1.2 - - - -
900A PHE* 1.3 78.2 - - - +
902A LEU* 1.3 65.9 + - + +
903A LYS 3.4 1.6 - - - -
932A LEU* 6.4 1.8 - - - -
935A THR* 3.7 32.2 + - + +
936A ILE* 4.1 17.9 - - + -
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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
------------------------------------------------------------
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