Contacts of the helix formed by residues 795 - 812 (chain A) in PDB entry 5I9V
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 795 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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736A VAL* 3.5 15.9 - - - +
764A LEU* 4.5 11.7 - - + -
793A LYS* 3.8 3.0 + - + +
794A PHE* 1.3 82.5 - - - +
796A SER* 1.3 67.9 + - - +
797A ALA* 3.0 20.9 + - - +
798A SER* 2.9 25.3 + - - -
799A ASP 3.0 6.9 + - - -
858A ARG* 3.4 33.8 + - - +
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Residues in contact with SER 796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A ALA* 3.9 28.3 - - - -
735A TYR 5.3 2.2 - - - -
736A VAL* 4.4 3.7 - - - +
764A LEU* 5.4 5.5 - - - +
795A THR* 1.3 76.7 - - - +
797A ALA* 1.3 57.9 + - - +
799A ASP* 3.2 14.0 + - - +
800A VAL* 2.9 31.2 + - - +
863A LYS* 6.0 2.1 - - - +
864A PHE* 3.7 5.5 - - - -
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Residues in contact with ALA 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A THR* 3.0 11.0 + - - +
796A SER* 1.3 79.8 + - - +
798A SER* 1.3 65.2 + - - +
800A VAL* 3.3 11.3 + - - +
801A TRP 3.3 13.2 + - - -
858A ARG* 3.9 38.1 - - + +
861A ARG* 2.9 20.2 + - + +
862A PRO 5.9 0.2 - - - -
863A LYS* 5.8 4.9 - - + +
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Residues in contact with SER 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A VAL* 4.6 1.0 - - - +
784A THR* 5.9 0.2 - - - -
785A ALA* 3.7 15.5 + - - +
787A GLU* 3.6 15.0 + - - -
788A ALA* 4.1 13.9 - - - -
793A LYS 4.2 2.2 - - - -
794A PHE* 3.4 13.5 - - - +
795A THR* 2.9 34.6 + - - -
797A ALA* 1.3 75.5 - - - +
799A ASP* 1.3 65.3 + - - +
801A TRP* 3.2 5.7 + - - +
802A SER* 3.1 22.7 + - - -
861A ARG* 3.9 6.9 - - - +
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Residues in contact with ASP 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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727A MET* 3.5 18.0 - - + +
731A ALA* 6.0 1.2 - - - +
735A TYR 4.6 1.7 - - - +
736A VAL* 3.5 16.7 - - - +
737A HIS* 2.7 28.3 + - - +
738A ARG* 3.1 25.9 + - - -
739A ASP 4.8 0.2 + - - -
740A LEU* 3.6 7.1 - - + +
794A PHE* 5.8 0.2 - - - -
795A THR 3.0 7.7 + - - +
796A SER* 3.2 12.3 + - - +
798A SER* 1.3 78.3 + - - +
800A VAL* 1.3 56.6 + - - +
802A SER* 3.2 10.8 + - - -
803A PHE* 2.8 27.4 + - - +
864A PHE* 3.8 15.2 - - + -
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Residues in contact with VAL 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A SER* 2.9 19.2 + - - +
797A ALA* 3.5 11.9 - - - +
798A SER 3.2 0.4 - - - -
799A ASP* 1.3 72.3 - - - +
801A TRP* 1.3 67.4 + - - +
803A PHE* 3.1 4.5 + - - +
804A GLY 3.0 18.0 + - - -
853A CYS* 3.4 32.5 - - + +
861A ARG* 4.0 8.5 - - + -
862A PRO* 3.4 29.8 - - + +
863A LYS* 4.7 0.7 - - - -
864A PHE* 3.6 33.7 - - + +
867A ILE* 4.0 7.4 - - + -
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Residues in contact with TRP 801 (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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782A ARG 4.9 1.8 + - - -
783A TRP 3.7 17.1 + - - -
784A THR 3.6 9.5 + - - -
785A ALA* 3.6 20.6 - - + -
786A PRO* 3.5 30.5 - - + -
797A ALA 3.3 6.9 + - - +
798A SER 3.2 10.2 + - - +
800A VAL* 1.3 79.0 - - - +
802A SER* 1.3 64.9 + - - +
804A GLY 3.0 10.2 + - - -
805A ILE* 3.2 21.5 + - + +
818A TYR* 4.8 2.3 + - - -
830A ILE* 3.7 40.4 - - + -
835A ARG* 3.8 10.3 - - - -
853A CYS 3.4 13.2 + - - +
854A TRP* 3.2 57.4 + + + -
855A GLN 3.7 8.7 - - - -
856A GLN 4.5 0.4 - - - -
861A ARG* 3.7 11.9 - - - +
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Residues in contact with SER 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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738A ARG 5.5 2.9 + - - -
740A LEU* 3.4 34.8 + - - +
783A TRP* 2.7 26.6 + - - +
784A THR* 4.5 2.3 - - - -
798A SER 3.1 12.2 + - - -
799A ASP* 3.2 12.4 + - - -
801A TRP* 1.3 77.4 - - - +
803A PHE* 1.3 63.3 + - - +
805A ILE* 3.0 8.2 + - - +
806A VAL* 2.9 23.3 + - - +
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Residues in contact with PHE 803 (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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720A LEU* 3.6 29.4 - - + -
723A ILE* 3.6 32.1 - - + -
724A ALA* 3.7 20.0 - - + -
727A MET* 4.8 0.7 - - + -
740A LEU* 3.7 12.5 - - + +
799A ASP 2.8 13.7 + - - +
800A VAL* 3.1 7.8 + - - +
802A SER* 1.3 76.3 - - - +
804A GLY* 1.3 57.2 + - - +
806A VAL* 3.0 7.3 + - + +
807A MET* 2.8 58.7 + - + +
853A CYS* 4.5 1.1 - - - -
864A PHE* 3.8 21.8 - + + -
867A ILE* 3.5 33.9 - - + -
871A LEU* 4.5 2.0 - - + -
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Residues in contact with GLY 804 (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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800A VAL 3.0 11.7 + - - -
801A TRP 3.0 5.3 + - - -
803A PHE* 1.3 76.5 - - - +
805A ILE* 1.3 59.9 + - - +
807A MET* 3.2 11.9 + - - +
808A TRP 3.1 17.2 + - - -
850A MET* 3.8 3.0 - - - +
853A CYS* 3.8 18.8 - - - -
854A TRP* 3.3 25.2 - - - -
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Residues in contact with ILE 805 (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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782A ARG 3.8 15.7 - - - +
783A TRP* 3.5 31.6 - - + +
801A TRP* 3.2 26.4 + - + +
802A SER 3.0 7.9 + - - +
804A GLY* 1.3 74.4 - - - +
806A VAL* 1.3 57.9 + - - +
808A TRP* 3.1 5.1 + - - +
809A GLU* 2.8 26.6 + - + +
817A PRO* 3.6 24.5 - - + -
818A TYR* 3.7 23.1 - - - +
836A LEU* 3.8 11.9 - - + -
854A TRP* 3.3 23.1 - - + +
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Residues in contact with VAL 806 (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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720A LEU* 4.4 3.6 - - + -
723A ILE* 4.2 32.1 - - + -
740A LEU* 4.0 11.4 - - + +
741A ALA* 3.6 37.5 - - - +
742A ALA* 4.6 11.2 - - + +
745A ILE* 4.9 2.2 - - + -
783A TRP* 4.7 0.2 - - + -
802A SER 2.9 17.2 + - - +
803A PHE* 3.4 11.9 - - + +
805A ILE* 1.3 75.2 - - - +
807A MET* 1.3 62.9 + - - +
809A GLU* 3.1 8.7 + - - +
810A VAL* 2.8 29.7 + - + +
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Residues in contact with MET 807 (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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720A LEU* 3.7 22.2 - - + -
803A PHE* 2.8 53.0 + - + +
804A GLY* 3.2 8.7 + - - +
806A VAL* 1.3 73.8 - - - +
808A TRP* 1.3 57.5 + - - +
810A VAL* 3.2 1.7 + - - +
811A MET* 3.0 34.5 + - - +
846A ILE* 3.5 43.1 - - + +
849A LEU* 3.7 27.1 - - + -
850A MET* 3.9 26.9 - - + +
853A CYS* 4.5 1.8 - - - -
871A LEU* 4.9 2.2 - - + -
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Residues in contact with TRP 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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804A GLY 3.1 8.1 + - - +
805A ILE 3.1 9.9 + - - +
807A MET* 1.3 77.0 - - - +
809A GLU* 1.3 69.0 + - - +
811A MET* 3.4 1.0 + - - +
812A THR* 2.9 41.1 + - + +
815A GLU* 3.7 31.4 - - + -
816A ARG 3.8 11.0 - - - -
817A PRO* 3.5 31.0 - - + -
819A TRP* 3.5 38.6 - + - -
836A LEU* 3.7 29.7 - - + +
837A PRO 2.8 27.3 + - - -
838A THR 4.6 0.2 - - - -
839A PRO* 3.7 19.7 - - + +
850A MET* 3.9 19.0 - - - -
854A TRP* 4.3 5.8 - + + -
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Residues in contact with GLU 809 (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 ASP* 4.3 9.2 - - - +
704A LEU* 4.2 1.4 - - - +
705A ARG* 4.6 6.8 + - - -
742A ALA* 2.9 41.1 + - + +
743A ARG 4.7 1.2 + - - -
783A TRP* 2.8 41.3 + - - +
805A ILE 2.8 18.4 + - - +
806A VAL* 3.5 14.2 - - - +
808A TRP* 1.3 73.6 - - - +
810A VAL* 1.3 62.6 + - - +
812A THR* 3.2 8.7 + - - -
814A GLY* 2.7 33.3 + - - +
815A GLU 4.2 8.4 - - - +
817A PRO* 4.1 16.9 - - + +
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Residues in contact with VAL 810 (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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700A LEU* 3.8 29.2 - - + -
704A LEU* 3.7 15.6 - - + +
716A LEU* 3.9 51.4 - - + +
719A MET* 4.7 6.7 - - + -
720A LEU* 3.8 22.7 - - + -
723A ILE* 4.6 1.6 - - + -
742A ALA* 5.2 0.7 - - + -
806A VAL* 2.8 26.6 + - + +
807A MET 3.8 3.8 - - - +
809A GLU* 1.3 74.0 - - + +
811A MET* 1.3 64.0 + - - +
813A TYR* 3.1 13.9 + - - -
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Residues in contact with MET 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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713A VAL* 4.6 9.4 - - + -
716A LEU* 3.8 37.6 - - + +
717A VAL* 4.7 5.4 - - + -
720A LEU* 4.1 17.3 - - + -
807A MET 3.0 21.6 + - - +
810A VAL* 1.3 76.3 - - - +
812A THR* 1.3 58.2 + - - +
813A TYR* 3.4 11.3 + - - -
839A PRO* 3.8 28.1 - - + +
840A MET 4.2 8.4 + - - +
841A ASP 4.5 7.6 - - - +
842A CYS* 4.2 3.8 - - - -
843A PRO* 3.9 28.3 - - + -
846A ILE* 4.1 20.9 - - + -
850A MET* 4.2 4.5 - - + -
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Residues in contact with THR 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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708A ASP* 4.5 3.3 - - - +
808A TRP* 2.9 47.3 + - + +
809A GLU* 3.2 5.7 + - - -
810A VAL 3.2 0.2 - - - -
811A MET* 1.3 75.6 - - - +
813A TYR* 1.3 71.8 + - - +
814A GLY 3.4 0.2 + - - -
815A GLU* 3.1 51.4 + - - +
839A PRO* 3.6 24.9 - - + -
840A MET 5.5 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
------------------------------------------------------------
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