Contacts of the helix formed by residues 806 - 822 (chain A) in PDB entry 5M9O
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 ASP 806 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A PRO* 3.4 1.4 - - - +
805A GLN* 1.3 76.3 - - - +
807A ASP* 1.3 60.6 + - - +
808A ASP* 3.2 15.0 + - - +
809A ALA* 2.9 35.9 + - + +
810A ARG* 2.8 30.9 + - - +
892A LEU* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 807 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A GLN 3.8 3.8 - - - +
806A ASP* 1.3 75.0 + - - +
808A ASP* 1.3 62.3 + - - +
810A ARG* 2.9 35.3 + - - +
811A THR* 2.8 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 808 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A ASP* 3.2 12.6 + - - +
807A ASP* 1.3 80.4 - - - +
809A ALA* 1.3 58.2 + - - +
811A THR* 3.3 8.5 + - - -
812A ASP* 3.0 35.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
804A PRO* 3.9 11.5 - - + +
806A ASP* 2.9 26.1 + - + +
808A ASP* 1.3 73.1 - - - +
810A ARG* 1.3 66.1 + - - +
812A ASP* 3.2 12.4 + - - +
813A ALA* 3.0 22.9 + - - +
860A LEU 4.5 2.6 - - - +
892A LEU* 3.9 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 810 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A ASP* 3.2 28.7 + - - +
693A ASP* 4.2 11.6 + - - +
694A LEU* 5.1 0.9 - - + +
803A VAL* 3.4 32.1 - - + -
804A PRO* 3.2 26.5 + - + +
805A GLN* 3.1 27.3 + - - +
806A ASP 2.8 14.3 + - - +
807A ASP* 2.9 28.9 + - - +
809A ALA* 1.3 72.9 - - - +
811A THR* 1.3 56.9 + - - +
813A ALA* 3.1 3.6 + - - +
814A VAL* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 811 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A ASP* 2.8 24.7 + - - +
808A ASP* 3.5 10.5 + - - +
810A ARG* 1.3 72.7 - - - +
812A ASP* 1.3 58.9 + - - +
814A VAL* 3.8 5.7 - - - +
815A ASP* 2.8 57.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 812 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A ASP* 3.0 21.9 + - - +
809A ALA* 3.2 13.2 + - - +
811A THR* 1.3 78.4 - - - +
813A ALA* 1.3 57.6 + - - +
815A ASP* 3.9 7.2 - - - +
816A SER* 3.1 29.5 + - - -
819A ARG* 5.0 1.6 + - - -
860A LEU* 3.8 19.9 - - + +
891A ASN* 4.6 8.4 - - - +
894A ARG* 4.5 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 813 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A LEU* 3.9 14.1 - - + -
804A PRO* 4.5 4.5 - - + -
809A ALA 3.0 11.9 + - - +
810A ARG* 3.5 7.9 - - - +
812A ASP* 1.3 75.3 - - - +
814A VAL* 1.3 65.2 + - - +
816A SER* 3.3 5.3 + - - -
817A VAL* 3.0 26.5 + - - +
855A LEU* 4.2 2.4 - - + +
860A LEU* 4.0 28.2 - - + +
861A VAL* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 814 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ILE* 4.1 10.9 - - + +
691A THR 3.4 31.0 - - - +
692A ASP* 3.6 27.6 - - - +
694A LEU* 3.7 23.3 - - + +
810A ARG* 2.9 20.7 + - + +
811A THR* 3.8 7.4 - - + +
813A ALA* 1.3 75.3 - - - +
815A ASP* 1.3 62.2 + - - +
817A VAL* 3.1 4.0 + - - +
818A VAL* 2.9 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 815 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A THR* 2.8 43.8 + - - +
812A ASP* 3.9 7.5 + - - +
814A VAL* 1.3 77.0 - - - +
816A SER* 1.3 58.3 + - - +
818A VAL* 3.4 9.0 + - - +
819A ARG* 3.0 52.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 816 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A ASP 3.1 18.6 + - - -
813A ALA 3.5 5.4 - - - -
815A ASP* 1.3 74.9 - - - +
817A VAL* 1.3 60.7 + - - +
819A ARG* 3.4 20.4 + - - +
820A ASP* 2.8 47.8 + - - +
855A LEU* 3.9 3.3 - - - +
858A GLU* 5.6 0.2 - - - +
860A LEU* 3.4 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 817 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ILE* 3.6 20.0 - - + -
694A LEU* 3.9 13.0 - - + -
696A PHE* 5.4 0.2 - - + -
798A PHE* 4.1 14.4 - - + -
813A ALA 3.0 18.1 + - - +
814A VAL 3.7 5.8 - - - +
816A SER* 1.3 71.6 - - - +
818A VAL* 1.3 58.8 + - - +
820A ASP* 4.0 7.0 - - - +
821A ILE* 2.8 62.1 + - + +
851A VAL* 5.1 2.5 - - + -
855A LEU* 3.5 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 818 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ILE* 3.6 34.3 - - + +
814A VAL* 2.9 29.5 + - + +
815A ASP* 3.6 9.2 - - - +
817A VAL* 1.3 75.7 - - - +
819A ARG* 1.3 65.6 + - + +
822A GLN* 3.1 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 819 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A ASP 5.0 1.6 + - - -
815A ASP* 3.0 45.3 + - - +
816A SER* 3.6 25.1 + - - +
818A VAL* 1.3 82.3 - - + +
820A ASP* 1.3 62.5 + - - +
822A GLN 5.0 1.2 + - - +
824A THR* 5.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 820 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A SER* 2.8 42.2 + - - +
817A VAL* 3.2 8.2 + - - +
819A ARG* 1.3 77.0 - - - +
821A ILE* 1.3 71.7 + - + +
824A THR* 4.1 11.2 + - - +
844A PHE* 3.7 27.4 - - + -
851A VAL* 4.9 8.4 - - + +
854A GLY 6.0 1.0 - - - -
855A LEU* 4.4 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 821 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A VAL* 3.4 25.4 - - + +
690A ILE* 3.9 7.4 - - + -
696A PHE* 4.9 2.7 - - + -
798A PHE* 4.3 6.1 - - + -
817A VAL* 2.8 44.3 + - + +
820A ASP* 1.3 80.0 - - + +
822A GLN* 1.3 66.5 + - - +
823A ASN 3.2 0.7 + - - -
824A THR* 2.6 28.5 + - - +
826A CYS* 3.9 11.7 - - - -
842A LEU* 3.6 25.6 - - + -
844A PHE* 3.8 20.0 - - + -
851A VAL* 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 822 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A VAL* 4.0 6.3 - - - -
688A THR 3.5 28.9 + - - +
689A GLU* 4.3 14.5 + - - +
690A ILE* 4.6 9.3 - - + +
817A VAL 3.8 0.4 + - - -
818A VAL* 3.1 45.7 + - - +
819A ARG 5.5 0.9 - - - +
820A ASP 5.5 0.2 - - - -
821A ILE* 1.3 79.0 - - - +
823A ASN* 1.3 89.6 + - - +
824A THR* 3.5 6.6 - - - +
113B 2MR 5.7 3.4 - - - -
----------------------------------------------------------
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