Contacts of the helix formed by residues 784 - 802 (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 THR 784 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747A GLU* 5.6 0.5 + - - -
782A VAL* 3.5 1.1 - - - +
783A ASP* 1.3 83.8 + - - +
785A GLU* 1.3 58.4 + - - +
786A GLU* 2.8 31.0 - - + +
787A ARG* 3.1 35.7 + - + +
788A LEU* 2.9 23.7 + - - +
821A VAL* 3.0 13.1 - - - +
822A PRO* 5.1 1.8 - - - -
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Residues in contact with GLU 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A THR* 1.3 72.3 - - - +
786A GLU* 1.3 65.7 + - - +
788A LEU* 3.8 3.4 - - - +
789A LYS* 2.9 30.0 + - + +
821A VAL* 3.3 9.7 - - - +
822A PRO 4.2 24.1 + - - +
832A ASN* 3.4 25.1 + - - +
836A LEU* 4.7 22.0 - - + +
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Residues in contact with GLU 786 (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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751A THR* 6.1 0.7 - - + -
755A PHE* 4.4 4.6 - - - -
784A THR* 2.8 13.8 - - + +
785A GLU* 1.3 79.9 - - - +
787A ARG* 1.3 57.8 + - + +
789A LYS* 3.8 8.6 + - - +
790A GLY* 3.0 22.9 + - - -
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Residues in contact with ARG 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A GLU* 2.9 50.0 + - - +
750A LYS* 3.9 12.0 - - - +
751A THR* 2.7 44.0 + - + +
754A LEU* 3.7 25.8 - - + -
755A PHE* 4.0 4.9 - - - -
781A THR 4.5 4.5 + - - -
782A VAL* 3.8 6.5 - - + -
783A ASP* 2.6 43.5 + - - -
784A THR* 3.1 28.7 + - + +
785A GLU 3.0 0.4 - - - -
786A GLU* 1.3 79.3 - - + +
788A LEU* 1.3 59.6 + - - +
790A GLY* 3.2 0.9 + - - -
791A VAL* 2.8 35.0 + - - +
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Residues in contact with LEU 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A VAL* 3.4 16.3 - - + +
784A THR 2.9 15.5 + - - +
785A GLU* 3.8 6.1 - - - +
787A ARG* 1.3 74.6 - - - +
789A LYS* 1.3 59.6 + - - +
791A VAL* 3.7 3.2 - - + +
792A ILE* 2.9 38.5 + - + +
816A LEU* 5.1 10.3 - - + +
819A LEU* 5.5 7.4 - - + +
821A VAL* 3.9 28.3 - - + -
832A ASN* 4.4 10.8 - - - +
833A PHE* 3.7 42.0 - - + -
836A LEU* 3.3 26.2 - - + -
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Residues in contact with LYS 789 (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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785A GLU* 2.9 20.5 + - + +
786A GLU* 4.1 8.3 - - - +
788A LEU* 1.3 78.0 - - - +
790A GLY* 1.3 57.3 + - - +
792A ILE* 3.8 7.3 - - + +
793A ASP* 3.0 62.2 + - - +
836A LEU* 4.4 19.2 - - + +
840A ARG* 5.2 4.0 - - - +
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Residues in contact with GLY 790 (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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755A PHE* 3.8 20.2 - - - -
786A GLU 3.0 17.8 + - - -
787A ARG 3.2 2.9 + - - -
789A LYS* 1.3 76.9 - - - +
791A VAL* 1.3 54.8 + - - +
793A ASP* 3.1 10.7 + - - +
794A LEU* 2.8 37.7 + - - +
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Residues in contact with VAL 791 (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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754A LEU* 3.8 26.7 - - + -
755A PHE* 4.0 2.6 - - + -
758A VAL* 3.9 32.1 - - + -
780A LEU* 5.6 1.3 - - + -
782A VAL* 4.4 11.4 - - + -
787A ARG 2.8 21.6 + - - +
788A LEU* 3.7 6.3 - - + +
790A GLY* 1.3 74.1 - - - +
792A ILE* 1.3 61.3 + - + +
794A LEU* 2.8 28.6 + - - +
795A VAL* 2.9 14.1 + - + +
812A MSE 5.6 0.4 - - + -
816A LEU* 4.3 32.5 - - + -
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Residues in contact with ILE 792 (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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788A LEU* 2.9 28.1 + - + +
789A LYS* 3.8 6.3 - - + +
791A VAL* 1.3 79.5 - - + +
793A ASP* 1.3 62.6 + - - +
795A VAL* 3.1 9.3 + - - +
796A PHE* 3.1 45.0 + - + -
813A CYS* 5.8 2.9 - - - -
816A LEU* 5.7 2.9 - - + -
833A PHE* 3.5 40.6 - - + -
836A LEU* 3.9 29.8 - - + +
837A LEU* 4.6 8.1 - - + +
840A ARG* 4.1 16.6 - - + -
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Residues in contact with ASP 793 (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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789A LYS* 3.0 54.2 + - - +
790A GLY* 3.3 12.2 - - - +
792A ILE* 1.3 75.9 - - - +
794A LEU* 1.3 65.2 + - + +
796A PHE* 3.3 1.6 + - - +
797A GLU* 3.0 41.1 + - - +
840A ARG* 3.0 35.6 + - - +
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Residues in contact with LEU 794 (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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755A PHE* 3.7 51.8 - - + +
758A VAL* 4.0 12.6 - - + -
759A ARG* 3.4 43.1 - - + +
762A LEU* 3.9 15.3 - - + +
790A GLY 2.8 18.0 + - - +
791A VAL* 2.8 12.1 + - - +
793A ASP* 1.3 79.1 - - + +
795A VAL* 1.3 60.6 + - - +
797A GLU* 3.5 12.2 + - + +
798A LYS* 3.1 22.5 + - - +
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Residues in contact with VAL 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A LEU* 4.0 23.1 - - + -
791A VAL* 2.9 20.2 + - + +
792A ILE* 3.1 9.8 + - - +
794A LEU* 1.3 75.0 - - - +
796A PHE* 1.3 61.6 + - + +
798A LYS* 3.2 2.9 + - - +
799A ALA* 2.8 26.3 + - - +
809A TYR* 3.9 26.4 - - + +
812A MSE 4.2 19.3 - - + -
813A CYS* 4.0 15.9 - - - -
816A LEU* 4.8 10.5 - - + -
895A PHE* 4.0 14.8 - - + -
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Residues in contact with PHE 796 (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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792A ILE* 3.1 26.6 + - + +
793A ASP 3.9 5.8 - - - +
795A VAL* 1.3 73.9 - - + +
797A GLU* 1.3 61.0 + - - +
799A ALA* 3.0 5.3 + - - +
800A ILE* 2.7 41.3 + - + +
813A CYS* 5.2 1.8 - - - -
837A LEU* 3.4 28.7 - - + -
840A ARG* 3.4 52.5 - - + +
841A CYS* 3.6 36.8 - - - -
844A GLU* 5.3 1.8 - - + -
892A ASN* 4.5 13.7 - - - -
895A PHE* 3.6 32.5 - + - -
896A ILE* 5.1 0.7 - - + -
899A LEU* 4.1 0.7 - - + -
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Residues in contact with GLU 797 (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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759A ARG* 4.1 20.5 + - - +
793A ASP* 3.0 34.8 + - - +
794A LEU* 3.7 12.1 - - + +
796A PHE* 1.3 77.2 - - - +
798A LYS* 1.3 60.5 + - - +
800A ILE* 3.5 8.0 + - - +
801A ASP* 3.3 20.1 + - - +
840A ARG* 5.0 9.8 + - - +
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Residues in contact with LYS 798 (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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762A LEU* 3.7 43.1 - - + -
763A ASN* 2.9 28.5 + - - +
794A LEU 3.1 12.8 + - - +
795A VAL 3.6 7.4 - - - +
796A PHE 3.1 0.6 - - - -
797A GLU* 1.3 78.4 - - - +
799A ALA* 1.3 57.8 + - - +
801A ASP* 3.0 15.7 + - - +
802A GLU* 3.0 51.1 + - - +
809A TYR* 3.4 19.5 - - + +
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Residues in contact with ALA 799 (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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795A VAL 2.8 17.7 + - - +
796A PHE 3.6 4.0 - - - +
798A LYS* 1.3 76.2 - - - +
800A ILE* 1.3 63.3 + - + +
802A GLU 4.0 0.4 - - - -
803A PRO* 3.2 27.4 - - - +
806A SER* 5.1 1.1 - - - -
809A TYR* 3.6 25.0 - - + -
891A GLY 4.9 3.3 - - - +
895A PHE* 3.7 40.0 - - + +
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Residues in contact with ILE 800 (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* 2.7 39.9 + - + +
797A GLU* 3.8 9.0 - - - +
799A ALA* 1.3 76.8 - - + +
801A ASP* 1.3 61.5 + - - +
802A GLU 3.8 0.2 + - - -
803A PRO* 4.0 11.1 - - - +
840A ARG* 5.7 2.5 - - - +
844A GLU* 4.6 11.7 - - - +
888A ARG* 3.7 41.6 - - + +
892A ASN* 3.5 40.6 - - + +
895A PHE* 5.5 1.8 - - + -
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Residues in contact with ASP 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A GLU 3.3 12.8 + - - +
798A LYS* 3.0 20.2 + - + +
800A ILE* 1.3 79.9 - - - +
802A GLU* 1.3 81.8 + - - +
803A PRO* 3.7 5.6 - - - +
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Residues in contact with GLU 802 (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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765A LEU* 4.9 9.8 - - - +
798A LYS* 3.0 32.1 + - - +
799A ALA 3.5 3.1 - - - +
801A ASP* 1.3 95.4 - - - +
803A PRO* 1.3 67.5 - - - +
804A SER* 3.1 6.4 + - - +
805A PHE* 3.0 44.8 + - + +
806A SER 4.1 0.2 + - - -
809A TYR* 3.4 27.1 + - - +
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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