Contacts of the helix formed by residues 809 - 825 (chain A) in PDB entry 3L6X
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 SER 809 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A GLU* 2.8 39.9 + - - -
807A ASN 4.0 0.4 + - - -
808A ARG* 1.3 79.5 - - - +
810A GLU* 1.3 60.7 + - - +
811A LYS* 3.7 3.7 + - - -
812A GLU* 3.1 15.7 + - - +
813A VAL* 2.9 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 810 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A SER* 1.3 72.4 - - - +
811A LYS* 1.3 58.4 + - + +
813A VAL* 3.2 7.1 + - - +
814A ARG* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 811 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A GLU* 3.9 15.0 + - - +
767A ASP* 4.7 8.7 + - - -
770A ILE* 3.9 31.3 - - + +
809A SER* 3.3 2.5 + - - +
810A GLU* 1.3 79.3 - - + +
812A GLU* 1.3 57.7 + - - +
814A ARG* 3.8 6.5 - - - +
815A ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 812 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A GLU* 4.0 19.8 - - + +
769A VAL* 3.4 30.9 - - + +
770A ILE* 4.0 20.2 - - + -
773A LEU* 4.0 1.5 - - + +
802A ILE* 3.8 14.3 - - + +
808A ARG* 2.6 53.9 + - + +
809A SER* 3.1 19.9 + - - +
811A LYS* 1.3 77.2 - - - +
813A VAL* 1.3 66.7 + - - +
815A ALA* 3.3 2.6 + - - +
816A ALA 3.1 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 813 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A ILE 3.8 17.9 - - - +
803A ASN* 3.2 43.8 - - - +
805A SER 4.6 9.2 - - - +
808A ARG* 4.2 15.7 - - + +
809A SER 2.9 19.9 + - - +
810A GLU* 3.7 7.0 - - - +
812A GLU* 1.3 77.0 - - - +
814A ARG* 1.3 63.3 + - - +
816A ALA* 3.1 3.6 + - - +
817A ALA* 3.0 18.3 + - + +
844A GLN 5.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 814 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A GLU 2.8 17.7 + - - +
811A LYS* 3.8 6.9 - - - +
813A VAL* 1.3 76.2 - - - +
815A ALA* 1.3 67.1 + - - +
817A ALA* 2.9 17.0 + - - +
818A LEU* 3.0 33.9 + - + +
845A VAL* 3.2 34.3 - - + +
846A ASN 2.5 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 815 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A ILE* 4.2 15.3 - - + -
773A LEU* 3.8 19.1 - - + +
774A ASN* 4.1 18.5 - - - +
811A LYS 2.9 18.2 + - - +
812A GLU 3.3 5.1 + - - +
814A ARG* 1.3 77.2 - - - +
816A ALA* 1.3 62.2 + - - +
818A LEU* 3.4 20.7 + - - +
819A VAL* 3.5 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 816 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A LEU* 3.9 17.4 - - + +
799A LEU* 3.7 20.6 - - - +
802A ILE* 3.6 31.9 - - + -
803A ASN* 3.9 5.2 - - + +
812A GLU 3.1 5.9 + - - -
813A VAL 3.6 6.1 - - - +
814A ARG 3.1 0.4 - - - -
815A ALA* 1.3 76.5 - - - +
817A ALA* 1.3 65.2 + - - +
819A VAL* 3.4 4.7 + - - +
820A LEU* 3.1 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 817 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A ASN* 3.5 17.0 + - - +
813A VAL* 3.0 8.3 + - + +
814A ARG* 2.9 10.2 + - - +
816A ALA* 1.3 75.7 - - - +
818A LEU* 1.3 53.2 + - - +
820A LEU* 3.0 10.0 + - - +
821A GLN* 2.7 38.1 + - - +
843A PHE 3.8 9.6 - - - +
844A GLN 3.5 24.7 - - - +
845A VAL* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 818 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A ASN* 5.3 6.7 - - - +
777A ASN* 3.9 17.9 - - + +
814A ARG* 3.0 39.1 + - + +
815A ALA* 3.6 15.3 - - - +
816A ALA 3.2 0.2 - - - -
817A ALA* 1.3 75.4 - - - +
819A VAL* 1.3 63.5 + - + +
821A GLN* 3.1 6.2 + - + +
822A THR* 3.0 23.4 + - - -
845A VAL* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 819 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A LEU* 3.4 33.4 - - + +
776A ILE* 3.8 20.9 - - + -
777A ASN* 3.5 19.9 + - + +
780A ILE* 3.9 12.8 - - + -
799A LEU* 3.6 31.4 - - + -
815A ALA 3.5 12.1 + - - +
816A ALA 3.4 7.1 + - - +
817A ALA 3.3 0.4 - - - -
818A LEU* 1.3 76.2 - - - +
820A LEU* 1.3 58.4 + - - +
822A THR* 3.1 4.0 + - - -
823A ILE* 2.9 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 820 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A ILE* 4.7 10.5 - - + -
799A LEU* 4.0 33.2 - - + +
800A VAL* 4.4 13.2 - - + -
803A ASN* 3.8 23.6 - - + -
816A ALA 3.1 18.0 + - - +
817A ALA* 3.0 7.7 + - - +
819A VAL* 1.3 77.3 - - - +
821A GLN* 1.3 59.9 + - - +
823A ILE* 3.1 12.1 + - + +
824A TRP* 2.8 29.8 + - - +
833A LEU* 5.8 2.9 - - + -
843A PHE* 3.6 49.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 821 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A ALA 2.7 21.6 + - - +
818A LEU* 3.1 8.2 + - + +
820A LEU* 1.3 69.7 + - - +
822A THR* 1.3 65.0 + - - +
824A TRP* 3.3 19.9 + - - +
825A GLY* 3.3 15.9 + - - -
840A LYS* 3.3 25.8 + - - +
843A PHE* 2.9 37.8 + - - +
844A GLN* 4.9 2.0 - - - +
845A VAL* 4.0 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 822 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A ASN* 2.7 27.5 + - - +
780A ILE* 3.8 35.2 - - + +
781A ALA* 3.9 17.8 - - + +
818A LEU 3.0 7.5 + - - -
819A VAL 3.1 5.4 + - - -
821A GLN* 1.3 74.0 - - - +
823A ILE* 1.3 67.9 + - - +
825A GLY* 3.0 15.0 + - - -
826A TYR* 3.6 11.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 823 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A ILE* 3.7 15.0 - - + -
787A ALA* 5.2 0.2 - - + -
790A LEU* 3.3 28.0 - - + -
796A ILE* 3.5 22.7 - - + -
799A LEU* 3.5 22.2 - - + -
819A VAL* 2.9 16.0 + - + +
820A LEU* 3.4 13.9 - - + +
822A THR* 1.3 76.5 - - - +
824A TRP* 1.3 64.4 + - + +
825A GLY 3.2 1.0 + - - -
826A TYR* 3.2 24.5 + - - +
829A LEU* 3.9 33.6 - - + +
830A ARG 4.7 0.3 + - - -
833A LEU* 4.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 824 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A LEU 2.8 15.5 + - - +
821A GLN* 3.6 20.6 - - - +
822A THR 3.1 0.4 - - - -
823A ILE* 1.3 77.1 - - + +
825A GLY* 1.3 57.0 + - - +
826A TYR 3.2 2.5 + - - +
830A ARG* 2.9 61.6 + - + +
833A LEU* 4.4 31.0 - - + -
834A GLU* 3.8 20.9 - - + -
838A TRP* 3.7 23.3 - - + -
839A LYS* 3.7 7.2 - - + -
840A LYS* 3.3 49.7 - - + +
843A PHE* 4.7 12.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 825 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A GLN 3.3 7.6 + - - -
822A THR* 3.0 13.3 + - - -
824A TRP* 1.3 78.2 - - - +
826A TYR* 1.3 62.1 + - - +
827A LYS 3.8 2.3 + - - -
830A ARG* 3.9 7.9 + - - -
----------------------------------------------------------
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