Contacts of the helix formed by residues 834 - 849 (chain B) in PDB entry 5MJ6
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 ASN 834 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B GLN* 5.9 2.5 - - - +
833B GLY* 1.3 71.1 - - - -
835B CYS* 1.3 77.2 + - - +
836B SER* 3.4 3.1 - - - -
837B THR* 3.0 23.9 + - - -
838B THR* 3.3 19.2 + - - +
1102B NAG 1.4 78.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 835 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B PHE* 5.9 0.2 - - - -
803B ILE* 4.0 19.3 - - - -
804B GLN* 6.4 0.9 - - - -
808B TRP* 3.6 22.7 - - + -
824B LEU* 4.7 10.1 - - + -
827B ALA* 3.7 27.1 - - + -
828B CYS* 3.7 18.6 - - - +
832B LEU 3.9 8.3 + - - +
833B GLY* 3.4 3.9 - - - -
834B ASN* 1.3 89.6 - - - +
836B SER* 1.3 63.3 + - - +
837B THR 3.2 0.2 + - - -
838B THR* 3.4 3.6 + - - -
839B ALA* 3.2 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 836 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B CYS* 3.8 19.3 - - - +
831B ASN* 3.7 27.2 + - - -
832B LEU 5.1 1.6 + - - +
833B GLY 5.1 2.0 + - - -
834B ASN 3.4 0.8 - - - -
835B CYS* 1.3 78.2 - - - +
837B THR* 1.3 58.4 + - - +
839B ALA* 3.3 4.9 + - - +
840B MET* 3.0 28.8 + - - +
866B VAL* 3.7 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 837 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B ASN* 3.0 19.1 + - - +
836B SER* 1.3 76.1 + - - +
838B THR* 1.3 67.6 + - - +
840B MET* 3.1 7.8 + - - +
841B LYS* 3.1 23.0 + - + +
1102B NAG 5.4 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 838 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B TRP* 3.6 39.6 + - + +
834B ASN* 3.3 19.8 + - - +
835B CYS* 3.6 7.9 - - - -
837B THR* 1.3 78.0 - - - +
839B ALA* 1.3 56.9 + - - +
841B LYS* 3.2 8.9 + - - +
842B LEU* 3.0 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 839 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B TRP* 3.8 23.6 - - + -
828B CYS* 4.5 0.7 - - - -
835B CYS 3.2 11.1 + - - +
836B SER 3.6 7.9 - - - +
837B THR 3.2 0.2 - - - -
838B THR* 1.3 77.0 - - - +
840B MET* 1.3 61.3 + - - +
842B LEU* 3.6 5.5 + - - -
843B PHE* 2.9 27.9 + - - +
862B THR* 4.4 3.1 - - + -
863B VAL* 3.7 15.5 - - - +
866B VAL* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 840 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836B SER* 3.0 16.4 + - - +
837B THR* 3.1 8.0 + - + +
839B ALA* 1.3 74.9 - - - +
841B LYS* 1.3 60.5 + - - +
843B PHE* 3.2 16.3 + - - +
844B ASP* 2.8 51.9 + - - +
866B VAL* 3.5 33.8 - - + +
867B GLY* 4.6 0.7 - - - -
869B LYS* 5.5 0.7 - - + -
870B THR* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 841 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837B THR* 3.1 13.2 + - + +
838B THR* 3.4 11.2 - - - +
840B MET* 1.3 75.8 - - - +
842B LEU* 1.3 62.7 - - + +
844B ASP* 3.2 11.7 + - + +
845B ASP* 3.0 56.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 842 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B TRP* 3.7 44.6 - - + +
838B THR* 3.0 22.3 + - + +
839B ALA 3.8 4.0 - - - +
840B MET 3.4 0.2 - - - -
841B LYS* 1.3 73.6 - - + +
843B PHE* 1.3 65.4 + - - +
845B ASP* 3.8 9.1 + - + +
846B TRP* 3.2 22.7 + - - +
853B GLN* 4.9 3.2 - - - +
854B SER 6.0 0.4 - - - +
855B LEU* 4.1 18.7 - - + +
856B PRO* 5.0 7.0 - - + -
859B VAL* 4.8 3.4 - - + -
863B VAL* 4.1 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 843 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839B ALA 2.9 19.0 + - - +
840B MET* 3.5 12.3 - - - +
841B LYS 3.2 0.2 - - - -
842B LEU* 1.3 75.4 - - - +
844B ASP* 1.3 69.3 - - - +
846B TRP* 3.1 31.5 + + - +
847B MET* 2.9 48.7 + - + +
863B VAL* 3.6 29.6 - - + +
864B PHE* 4.3 3.1 - + - -
867B GLY* 3.5 28.0 - - - +
870B THR* 5.4 1.3 - - - -
873B GLY* 3.6 37.0 - - - -
876B PHE* 4.6 4.0 - + - -
877B LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 844 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840B MET* 2.8 36.9 + - - +
841B LYS* 3.2 12.8 + - + +
843B PHE* 1.3 81.6 - - - +
845B ASP* 1.3 61.3 + - - +
847B MET* 3.2 22.5 + - - +
848B ALA* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 845 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B LYS* 3.0 50.5 + - - +
842B LEU* 4.1 9.1 - - + +
844B ASP* 1.3 76.5 - - - +
846B TRP* 1.3 63.8 + - - +
848B ALA* 3.0 19.3 + - - +
849B SER* 3.1 12.5 + - - -
853B GLN* 3.4 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 846 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842B LEU 3.2 12.2 + - - +
843B PHE* 3.1 22.1 + + - +
845B ASP* 1.3 77.7 - - - +
847B MET* 1.3 59.9 + - - +
849B SER* 3.1 9.6 + - - -
851B GLY* 2.9 52.5 + - - -
853B GLN* 3.3 33.2 + - + +
854B SER 5.1 0.2 - - - -
855B LEU* 3.8 29.3 - - + +
864B PHE* 3.7 36.1 - + - -
876B PHE* 3.5 30.7 - + - -
877B LEU* 3.8 17.3 - - + -
880B LYS* 4.1 17.9 - - + -
889B GLU* 4.3 12.3 - - - -
893B ILE* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 847 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843B PHE* 2.9 41.7 + - + +
844B ASP* 3.6 20.6 - - - +
845B ASP 3.1 0.2 - - - -
846B TRP* 1.3 73.2 - - + +
848B ALA* 1.3 56.0 + - - +
849B SER 3.1 2.2 - - - -
850B ASN* 2.8 25.8 + - - -
872B LYS* 3.7 38.6 - - + -
873B GLY* 4.2 6.3 - - - +
876B PHE* 3.5 55.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 848 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844B ASP 2.8 17.6 + - - +
845B ASP* 3.2 15.7 - - - +
847B MET* 1.3 72.6 - - - +
849B SER* 1.3 56.9 + - - +
850B ASN* 3.1 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 849 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B ASP 3.1 8.5 + - - -
846B TRP 3.1 12.0 + - - -
847B MET 3.1 0.4 - - - -
848B ALA* 1.3 75.1 - - - +
850B ASN* 1.3 65.5 + - - +
852B THR* 3.0 22.5 + - - -
853B GLN* 3.1 36.7 + - - +
----------------------------------------------------------
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