Contacts of the helix formed by residues 798 - 815 (chain A) in PDB entry 2VWU
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 798 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737A VAL* 3.6 16.2 - - - +
790A GLU* 4.8 0.2 + - - -
796A LYS* 4.0 17.4 + - + +
797A PHE* 1.3 79.3 - - - +
799A SER* 1.3 65.4 + - - +
800A ALA* 3.2 20.8 + - - +
801A SER* 2.8 28.4 + - - -
802A ASP 3.1 5.2 + - - -
861A ARG* 4.0 26.6 + - - +
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Residues in contact with SER 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A ALA* 3.5 35.2 + - - +
735A SER* 5.7 1.2 - - - -
736A TYR 4.4 3.6 + - - -
737A VAL* 3.6 14.7 - - - +
798A THR* 1.3 74.5 - - - +
800A ALA* 1.3 56.7 + - - +
802A ASP* 3.2 14.4 + - - +
803A ALA* 2.9 23.4 + - - +
867A PHE* 3.7 12.6 - - - -
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Residues in contact with ALA 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A THR* 3.0 12.5 + - - +
799A SER* 1.3 76.4 - - - +
801A SER* 1.3 62.2 + - - +
803A ALA* 3.4 7.7 + - - +
804A TRP 3.3 12.6 + - - -
861A ARG* 3.7 37.2 - - + +
862A ASN* 5.8 0.9 - - - +
864A ARG* 3.0 22.2 + - + +
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Residues in contact with SER 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A VAL* 4.7 1.0 - - - +
788A ALA* 3.6 28.6 + - - +
790A GLU* 3.7 8.0 + - - -
791A ALA* 4.2 13.2 - - - -
796A LYS 4.3 1.1 - - - -
797A PHE* 3.4 12.7 - - - -
798A THR* 2.8 38.2 + - - -
800A ALA* 1.3 73.1 - - - +
802A ASP* 1.3 64.3 + - - +
804A TRP* 3.3 5.9 + - - +
805A SER* 3.2 23.1 + - - -
864A ARG* 3.8 1.2 - - - +
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Residues in contact with ASP 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A MET* 3.7 20.9 - - + +
736A TYR 4.3 1.4 - - - +
737A VAL* 3.5 12.0 - - - +
738A HIS* 2.7 33.1 + - - +
739A ARG* 3.0 27.8 + - - -
740A ASP 4.8 0.2 + - - -
741A LEU* 3.7 5.5 - - + +
798A THR 3.1 12.6 + - - +
799A SER* 3.2 13.6 + - - +
801A SER* 1.3 76.4 + - - +
803A ALA* 1.3 59.7 + - - +
805A SER* 3.3 9.9 + - - -
806A TYR* 2.8 28.4 + - - +
867A PHE* 3.6 5.8 - - + -
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Residues in contact with ALA 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A SER 2.9 12.5 + - - +
800A ALA* 3.5 14.4 - - - +
801A SER 3.2 0.4 - - - -
802A ASP* 1.3 72.5 - - - +
804A TRP* 1.3 66.3 + - - +
806A TYR* 3.3 4.1 + - - +
807A GLY 3.1 17.2 + - - -
856A CYS* 3.4 17.3 - - - +
864A ARG* 4.6 9.0 - - + -
865A PRO 3.7 23.3 - - - +
866A ARG* 5.7 0.4 - - - -
867A PHE* 3.7 19.2 - - + -
870A VAL* 5.8 1.1 - - + -
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Residues in contact with TRP 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A ARG 5.0 1.4 + - - -
786A TRP 3.6 16.0 + - - -
787A THR 3.8 8.3 + - - -
788A ALA* 3.7 17.5 - - + -
789A PRO* 3.4 30.3 - - + -
800A ALA 3.3 4.4 + - - -
801A SER 3.4 11.0 - - - +
803A ALA* 1.3 77.0 - - - +
805A SER* 1.3 64.3 + - - +
807A GLY 3.1 10.2 + - - -
808A ILE* 3.2 20.8 + - + +
821A TYR* 4.6 3.9 + - - -
833A ILE* 3.7 36.6 - - + -
838A ARG* 3.8 12.1 - - - -
856A CYS 3.3 13.1 + - - +
857A TRP* 3.1 60.1 + + + -
858A GLN 3.8 6.1 - - - -
864A ARG* 3.5 21.8 - - - +
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Residues in contact with SER 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A ARG 5.4 4.2 + - - -
741A LEU* 3.5 33.7 + - - +
786A TRP* 2.7 26.5 + - - +
787A THR* 4.6 2.4 - - - -
801A SER 3.2 12.8 + - - -
802A ASP* 3.3 13.0 + - - -
804A TRP* 1.3 79.0 - - - +
806A TYR* 1.3 62.9 + - - +
808A ILE* 3.0 9.1 + - - +
809A VAL* 2.9 23.6 + - - +
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Residues in contact with TYR 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A LEU* 2.6 35.7 + - + +
724A ILE* 3.8 20.0 - - + -
725A ALA* 3.7 26.2 - - + -
728A MET* 4.7 0.4 - - + -
741A LEU* 3.6 13.2 - - + +
802A ASP 2.8 17.4 + - - +
803A ALA 3.4 8.5 - - - +
804A TRP 3.2 0.2 - - - -
805A SER* 1.3 71.7 - - - +
807A GLY* 1.3 59.7 + - - +
809A VAL* 3.0 7.7 + - + +
810A MET* 2.8 58.6 + - + +
856A CYS* 4.3 8.7 - - - -
867A PHE* 3.7 23.1 - + + -
870A VAL* 3.5 21.3 - - + -
874A LEU* 3.2 15.9 - - + +
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Residues in contact with GLY 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A ALA 3.1 7.3 + - - -
804A TRP 3.1 9.0 + - - -
806A TYR* 1.3 77.3 - - - +
808A ILE* 1.3 60.3 + - - +
810A MET* 3.3 14.8 - - - +
811A TRP 3.1 16.3 + - - -
853A MET* 3.7 4.3 - - - +
856A CYS* 3.8 18.2 - - - -
857A TRP* 3.3 23.6 - - - -
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Residues in contact with ILE 808 (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 ARG 3.7 19.7 - - - +
786A TRP* 3.4 33.0 - - + +
804A TRP* 3.2 26.1 + - + +
805A SER 3.0 9.1 + - - +
807A GLY* 1.3 75.4 - - - +
809A VAL* 1.3 57.9 + - - +
811A TRP* 3.0 6.3 + - + +
812A GLU* 2.9 25.5 + - - +
820A PRO* 3.6 23.1 - - + -
821A TYR* 3.7 24.0 - - + +
839A LEU* 4.2 4.7 - - + -
857A TRP* 3.5 25.4 - - + +
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Residues in contact with VAL 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A LEU* 4.8 0.4 - - + -
721A LEU* 4.5 3.6 - - + -
724A ILE* 4.2 30.5 - - + -
741A LEU* 3.9 17.7 - - + -
742A ALA* 3.7 31.2 - - - -
743A ALA* 4.5 12.8 - - + +
746A ILE* 5.0 2.2 - - + -
786A TRP* 4.9 0.2 - - + -
805A SER 2.9 18.2 + - - +
806A TYR* 3.0 10.5 + - + +
808A ILE* 1.3 73.0 - - - +
810A MET* 1.3 66.0 + - - +
812A GLU* 3.2 10.4 + - - +
813A VAL* 2.9 29.6 + - + +
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Residues in contact with MET 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A LEU* 3.7 21.3 - - + +
806A TYR* 2.8 55.4 + - + +
807A GLY* 3.3 11.7 - - - +
809A VAL* 1.3 71.1 - - - +
811A TRP* 1.3 58.3 + - - +
813A VAL* 3.3 2.3 + - - +
814A MET* 3.0 34.1 + - - +
849A LEU* 3.6 48.5 - - + +
852A LEU* 3.9 26.2 - - + +
853A MET* 3.7 19.1 - - + -
856A CYS* 4.8 0.7 - - - -
874A LEU* 4.8 2.0 - - + -
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Residues in contact with TRP 811 (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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807A GLY 3.1 8.3 + - - +
808A ILE* 3.0 11.9 + - - +
810A MET* 1.3 76.2 - - - +
812A GLU* 1.3 65.4 + - - +
814A MET 3.5 0.2 + - - -
815A SER* 2.9 44.0 + - - -
818A GLU* 3.5 33.4 - - + -
819A ARG 3.7 11.4 - - - -
820A PRO* 3.6 26.0 - - + -
822A TRP* 3.6 35.7 - + - -
839A LEU* 3.6 30.8 - - + +
840A PRO* 2.9 29.0 + - + -
842A PRO* 3.7 22.9 - - + +
853A MET* 4.0 19.2 - - - +
857A TRP* 4.2 6.7 - + + -
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Residues in contact with GLU 812 (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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702A ASP* 4.6 6.9 - - - +
705A LEU* 4.8 0.9 - - - -
743A ALA* 2.9 45.2 + - + +
744A ARG 4.8 1.2 + - - -
786A TRP* 3.0 36.1 + - - -
808A ILE 2.9 14.4 + - - +
809A VAL* 3.5 16.3 - - - +
811A TRP* 1.3 76.8 - - - +
813A VAL* 1.3 60.4 + - - +
815A SER* 3.1 10.2 + - - -
817A GLY* 2.7 34.1 + - - -
818A GLU 4.2 9.1 - - - +
820A PRO* 3.9 19.5 - - + +
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Residues in contact with VAL 813 (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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701A LEU* 3.8 29.2 - - + -
705A LEU* 3.7 15.9 - - + +
717A LEU* 3.9 41.1 - - + +
720A MET* 5.0 5.6 - - + -
721A LEU* 3.7 32.8 - - + -
724A ILE* 4.8 1.1 - - + -
743A ALA* 5.4 0.2 - - + -
809A VAL* 2.9 22.6 + - + +
810A MET 3.7 4.3 - - - +
812A GLU* 1.3 79.2 - - + +
814A MET* 1.3 59.4 + - - +
816A PHE* 3.0 19.8 + - - -
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Residues in contact with MET 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A VAL* 4.4 11.7 - - + -
717A LEU* 3.7 41.2 - - + +
721A LEU* 4.1 14.1 - - + -
810A MET 3.0 20.2 + - - +
813A VAL* 1.3 75.9 - - - +
815A SER* 1.3 58.5 + - - +
816A PHE* 3.4 11.4 + - - -
842A PRO* 3.7 19.0 - - + +
843A PRO* 4.3 9.0 - - - +
844A ASP 5.5 0.4 - - - +
845A CYS* 3.9 27.1 - - + -
846A PRO* 4.1 16.4 - - + -
849A LEU* 3.8 29.2 - - + -
853A MET* 4.0 7.0 - - + -
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Residues in contact with SER 815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A ASP* 4.7 2.1 - - - +
811A TRP* 2.9 29.9 + - - -
812A GLU* 3.1 10.9 + - - -
813A VAL 3.1 0.2 - - - -
814A MET* 1.3 78.0 - - - +
816A PHE* 1.3 67.3 + - - +
818A GLU* 3.1 33.9 + - - +
842A PRO* 3.9 16.2 - - - -
843A PRO* 5.4 4.7 - - - -
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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) + - + + + + + -
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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