Contacts of the helix formed by residues 816 - 828 (chain B) in PDB entry 3ZNS
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 816 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B ASP* 2.6 32.6 + - - -
803B ALA* 5.9 0.4 - - - -
804B GLU* 6.2 0.9 - - - -
814B HIS 3.6 2.5 + - - -
815B VAL* 1.3 73.2 - - - +
817B ALA* 1.3 62.9 + - - +
818B LYS* 3.6 8.1 + - - +
819B CYS* 3.1 17.0 + - - +
820B PHE* 3.1 27.2 + - - -
872B TRP* 4.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 817 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B SER* 1.3 72.6 - - - +
818B LYS* 1.3 63.2 + - + +
820B PHE* 3.2 5.1 + - - +
821B GLY 2.8 23.7 + - - -
850B ASP* 3.3 44.4 - - + +
851B ALA* 3.8 10.1 - - - +
854B ALA* 3.0 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 818 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B SER* 3.4 7.0 + - - +
817B ALA* 1.3 77.6 - - + +
819B CYS* 1.3 52.3 - - - +
821B GLY* 3.2 1.3 + - - +
822B TYR* 2.7 36.2 + - - +
854B ALA* 4.6 5.6 - - + -
864B VAL* 4.0 20.4 - - + +
869B GLU* 3.9 21.5 - - - +
872B TRP* 3.9 14.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 819 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B ASP* 3.3 44.0 - - - +
774B TYR* 4.2 12.8 - - - -
775B LEU* 4.2 18.8 - - - -
815B VAL* 3.8 13.7 - - + -
816B SER* 3.1 15.4 + - - +
818B LYS* 1.3 74.0 - - - +
820B PHE* 1.3 60.3 + - - +
822B TYR* 3.2 1.4 + - - +
823B MET* 2.8 39.6 + - - +
872B TRP* 3.6 11.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 820 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B TRP* 3.6 40.2 - + + -
774B TYR* 6.0 1.3 - + - -
799B GLY 3.9 0.4 - - - -
800B PHE* 3.8 26.5 - + + -
802B ALA* 4.3 7.6 - - + -
803B ALA* 3.9 29.4 - - + -
815B VAL* 3.7 23.3 - - + -
816B SER 3.1 23.0 + - - -
817B ALA 3.2 5.8 + - - +
819B CYS* 1.3 78.0 - - - +
821B GLY* 1.3 59.0 + - - +
823B MET* 3.3 24.6 + - + +
824B THR* 2.9 31.7 + - - -
851B ALA* 3.8 16.2 - - + -
855B CYS* 3.7 16.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 821 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817B ALA 2.8 14.0 + - - -
818B LYS* 3.5 4.0 - - - -
820B PHE* 1.3 76.9 - - - +
822B TYR* 1.3 55.5 + - - +
824B THR 3.3 1.0 + - - -
825B GLN* 2.9 25.2 + - - +
854B ALA* 3.7 29.0 - - - +
855B CYS* 4.2 2.0 - - - -
858B ALA* 3.3 14.6 - - - +
864B VAL* 4.7 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 822 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B LEU* 3.6 21.5 - - + -
818B LYS 2.7 20.2 + - - +
819B CYS* 3.2 4.0 + - - +
821B GLY* 1.3 70.9 - - - +
823B MET* 1.3 60.6 + - - +
825B GLN* 3.3 31.7 + - - +
826B GLN* 3.0 67.4 + - + +
864B VAL* 3.8 27.3 - - + +
866B PRO* 3.1 27.9 - - + +
872B TRP* 3.7 19.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 823 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B TRP* 3.9 21.1 - - + -
774B TYR* 4.0 33.0 - - + +
775B LEU* 5.3 3.8 - - + -
778B PHE* 3.5 50.8 - - + -
815B VAL* 4.6 1.6 - - + -
819B CYS* 2.8 27.8 + - - +
820B PHE* 3.3 47.6 - - + +
822B TYR* 1.3 69.5 - - - +
824B THR* 1.3 63.1 + - - +
826B GLN* 3.3 3.8 + - - +
827B LEU* 3.2 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 824 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B TRP* 3.3 15.7 - - - -
820B PHE 2.9 16.6 + - - -
821B GLY* 3.4 9.0 - - - -
823B MET* 1.3 75.9 - - - +
825B GLN* 1.3 62.6 + - - +
827B LEU* 3.2 8.3 + - - +
828B MET* 3.1 24.1 + - + +
835B VAL* 5.3 1.5 - - + +
837B LEU* 3.5 12.6 - - + +
855B CYS* 3.3 37.4 - - - +
858B ALA* 3.8 8.3 - - + -
859B LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 825 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821B GLY 2.9 16.4 + - - +
822B TYR* 3.5 32.7 - - - +
823B MET 3.3 0.2 - - - -
824B THR* 1.3 77.0 - - - +
826B GLN* 1.3 60.5 + - + +
828B MET* 3.4 30.2 - - + +
829B ASN* 3.7 10.3 + - - +
858B ALA* 4.1 5.6 - - + +
862B ASN 4.2 5.0 + - - +
863B ARG* 3.5 30.7 - - + +
864B VAL* 3.0 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 826 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B LEU* 4.3 8.9 + - - +
778B PHE* 3.5 37.8 - - + +
779B ARG* 4.9 3.9 + - - +
783B MET* 3.2 33.8 - - + +
822B TYR* 3.0 61.4 + - + +
823B MET* 3.7 5.7 - - - +
824B THR 3.2 0.2 - - - -
825B GLN* 1.3 73.4 - - + +
827B LEU* 1.3 67.2 + - - +
828B MET 3.1 1.8 - - - -
829B ASN* 3.1 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 827 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B VAL* 4.0 25.6 - - + -
706B TRP* 3.7 23.6 - - + -
778B PHE* 3.9 18.6 - - + -
782B VAL* 4.5 4.0 - - + -
783B MET* 4.2 6.3 - - - -
794B VAL* 4.5 6.1 - - + +
796B VAL* 3.5 31.2 - - + -
823B MET 3.2 9.3 + - - +
824B THR* 3.7 7.4 - - - +
826B GLN* 1.3 76.2 - - - +
828B MET* 1.3 56.6 + - - +
829B ASN 3.1 0.2 - - - -
830B LEU* 2.9 47.8 + - + +
835B VAL* 3.5 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 828 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B LYS* 4.7 9.0 - - - -
659B ASN* 4.3 9.2 - - - +
824B THR* 3.1 22.1 + - + +
825B GLN* 3.4 22.7 - - + +
826B GLN 3.1 0.6 - - - -
827B LEU* 1.3 77.3 - - - +
829B ASN* 1.3 59.1 + - - +
830B LEU 3.2 1.3 - - - -
833B GLY* 3.3 25.2 + - - +
835B VAL* 3.9 18.2 - - + -
858B ALA 3.1 36.6 - - - +
859B LEU* 3.8 27.1 - - + +
861B GLY* 4.5 9.4 - - - +
863B ARG* 6.3 0.9 - - - +
----------------------------------------------------------
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