Contacts of the helix formed by residues 796 - 809 (chain A) in PDB entry 4IQJ
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 GLU 796 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A PRO* 2.8 16.2 + - + +
795A GLU* 1.3 73.3 - - - +
797A GLU* 1.3 71.6 + - + +
799A ASN* 4.1 6.8 + - - +
800A ARG* 3.1 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A GLU 4.0 12.8 - - - +
723A PHE* 3.4 25.3 - - + +
724A PRO* 3.4 21.5 - - - +
725A HIS* 3.3 36.0 + - - +
726A ALA* 3.7 7.7 + - + -
793A VAL* 4.2 6.8 - - + +
794A PRO* 3.7 22.1 - - + +
795A GLU 4.2 0.4 - - - +
796A GLU* 1.3 84.5 - - + +
798A ALA* 1.3 55.8 + - - +
800A ARG* 3.0 13.1 + - - +
801A LEU* 2.5 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A PHE* 3.5 15.8 - - + -
785A VAL* 3.7 20.2 - - + -
788A ALA* 3.6 29.6 - - + -
793A VAL* 3.8 12.9 - - + +
795A GLU* 3.9 14.7 - - - +
796A GLU 3.5 1.8 - - - +
797A GLU* 1.3 76.3 - - - +
799A ASN* 1.3 58.0 + - - +
801A LEU* 3.3 5.8 + - - -
802A PHE* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A ARG* 3.6 22.8 + - - +
785A VAL* 3.3 20.3 - - - +
795A GLU* 3.6 34.1 + - - +
796A GLU* 4.1 6.6 + - - +
797A GLU 3.2 0.6 - - - -
798A ALA* 1.3 75.8 - - - +
800A ARG* 1.3 57.5 + - - +
802A PHE* 3.3 7.0 + - - +
803A ASP* 3.0 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 800 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A GLU* 3.0 38.8 + - - +
723A PHE* 3.8 21.9 - - + -
796A GLU* 3.1 53.8 + - - +
797A GLU* 3.0 9.0 + - - +
799A ASN* 1.3 76.8 - - - +
801A LEU* 1.3 62.5 + - - +
802A PHE 3.3 0.2 - - - -
803A ASP* 3.5 17.0 + - + +
804A MET* 3.4 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 801 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A PHE* 3.5 19.9 - - + -
726A ALA* 4.1 16.6 - - + -
730A LEU* 4.0 21.3 - - + -
750A ILE* 4.9 3.8 - - + -
754A VAL* 3.8 34.1 - - + -
784A PHE* 4.0 13.7 - - + -
793A VAL* 5.2 2.2 - - + -
797A GLU* 2.5 22.1 + - + +
798A ALA* 3.6 7.2 - - - +
800A ARG* 1.3 71.5 - - - +
802A PHE* 1.3 62.6 + - - +
804A MET* 3.4 29.9 + - + +
805A LEU* 3.3 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 802 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A LEU* 4.2 26.0 - - + -
769A MET* 4.1 26.2 - - + -
777A MET* 4.2 18.8 - - + -
780A HIS* 4.3 4.5 - - + -
781A ARG* 3.4 37.7 - - + +
784A PHE* 3.7 41.9 - + + -
785A VAL* 6.1 0.7 - - + -
798A ALA 3.0 14.0 + - - +
799A ASN* 3.5 10.1 - - - +
800A ARG 3.3 0.2 - - - -
801A LEU* 1.3 74.8 - - - +
803A ASP* 1.3 62.1 + - - +
805A LEU* 3.4 9.7 + - + +
806A GLU* 3.1 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 803 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A ARG* 3.0 20.6 + - - -
799A ASN* 3.0 18.1 + - - +
800A ARG* 3.5 21.9 - - + +
801A LEU 3.3 0.2 - - - -
802A PHE* 1.3 76.2 - - - +
804A MET* 1.3 63.0 + - - +
806A GLU* 3.1 33.6 - - - +
807A ALA* 3.2 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 804 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A PHE* 3.9 24.9 - - + -
730A LEU* 4.9 5.6 - - + -
734A LEU* 5.0 5.2 - - + -
741A PRO* 4.3 18.4 - - + -
750A ILE* 4.7 9.6 - - + -
800A ARG 3.4 8.3 + - - +
801A LEU* 3.4 29.7 + - + +
802A PHE 3.2 0.4 - - - -
803A ASP* 1.3 79.2 - - - +
805A LEU* 1.3 74.8 + - + +
807A ALA* 3.3 6.0 + - - +
808A PHE* 3.1 51.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 805 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A PRO* 5.8 1.8 - - + -
747A ILE* 3.4 39.7 - - + +
750A ILE* 4.1 33.4 - - + -
751A ALA* 4.7 9.6 - - + -
765A LEU* 5.8 2.5 - - + -
769A MET* 4.1 10.1 - - + -
784A PHE* 4.0 30.3 - - + -
801A LEU* 3.3 16.2 + - + +
802A PHE* 3.9 12.1 - - + +
803A ASP 3.4 0.2 - - - -
804A MET* 1.3 85.8 - - + +
806A GLU* 1.3 59.0 + - - +
808A PHE* 4.3 3.5 - - - +
809A ALA* 2.8 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 806 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A MET* 3.4 32.4 - - + +
777A MET* 4.1 12.0 - - + +
781A ARG* 3.9 8.0 + - - -
802A PHE* 3.1 30.7 + - - +
803A ASP* 3.1 42.6 - - - +
805A LEU* 1.3 78.5 - - - +
807A ALA* 1.3 60.2 + - - +
809A ALA* 3.8 4.9 + - - +
810A ASN* 3.4 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 807 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A ASP 3.2 18.3 + - - +
804A MET* 3.5 6.7 - - - +
805A LEU 3.2 0.6 - - - -
806A GLU* 1.3 78.7 - - + +
808A PHE* 1.3 68.2 + - + +
809A ALA 3.5 0.3 + - - -
810A ASN* 3.5 23.5 + - - +
811A TYR* 4.4 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 808 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A HIS* 3.4 39.3 - + - -
740A ILE* 3.9 15.9 - - + -
741A PRO* 3.6 56.0 - - + +
747A ILE* 4.0 7.5 - - + +
804A MET* 3.1 43.1 + - + +
805A LEU* 4.3 1.8 - - - +
807A ALA* 1.3 79.9 - - + +
809A ALA* 1.3 63.6 + - - +
810A ASN 3.1 4.3 + - - -
811A TYR* 3.2 7.9 + - - +
812A GLY* 3.2 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 809 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A GLN* 5.9 0.7 - - - +
747A ILE* 3.7 19.7 - - + +
766A ARG* 5.2 15.0 - - + +
769A MET* 3.7 32.8 - - + -
770A GLY* 5.7 4.5 - - - -
805A LEU 2.8 20.5 + - - +
806A GLU 4.0 1.1 - - - +
807A ALA 3.3 0.4 - - - -
808A PHE* 1.3 76.3 - - - +
810A ASN* 1.3 62.1 + - - +
812A GLY* 3.6 9.7 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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