Contacts of the helix formed by residues 816 - 829 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771C ASP* 2.6 32.2 + - - -
804C GLU* 6.1 2.5 - - - -
814C HIS 3.4 4.1 + - - -
815C VAL* 1.3 77.1 - - - +
817C ALA* 1.3 64.3 + - - +
818C LYS* 3.8 5.4 + - - +
819C CYS* 3.2 23.4 + - - +
820C PHE* 3.3 12.3 - - - -
872C TRP* 4.4 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 817 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816C SER* 1.3 73.1 - - - +
818C LYS* 1.3 65.9 + - + +
820C PHE* 3.1 20.8 + - - +
821C GLY 3.1 9.9 + - - -
847C ALA 5.3 0.4 - - - +
850C ASP* 3.4 45.3 - - + +
851C ALA* 3.8 3.4 - - - +
854C ALA* 3.2 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 818 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816C SER* 3.4 6.6 + - - +
817C ALA* 1.3 80.0 - - + +
819C CYS* 1.3 57.2 + - - +
821C GLY* 3.5 2.2 + - - +
822C TYR* 2.9 28.9 + - - +
854C ALA* 4.6 6.5 - - + -
864C VAL* 4.2 24.1 - - + +
869C GLU* 3.5 26.1 + - - +
872C TRP* 4.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 819 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771C ASP* 3.2 48.9 - - - +
774C TYR* 4.4 6.3 - - - -
775C LEU* 4.3 18.6 - - - +
815C VAL* 3.8 11.4 - - + -
816C SER* 3.2 16.9 + - - +
817C ALA 3.1 0.2 - - - -
818C LYS* 1.3 75.8 - - - +
820C PHE* 1.3 59.9 + - - +
822C TYR* 3.4 2.0 + - - +
823C MET* 3.0 39.7 + - - +
872C TRP* 3.9 10.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 820 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706C TRP* 3.5 42.8 - + + -
774C TYR* 5.9 1.1 - + - -
799C GLY 3.9 1.3 - - - -
800C PHE* 3.6 22.2 - + - -
802C ALA* 4.4 5.6 - - + -
803C ALA* 3.7 25.6 - - + -
815C VAL* 3.5 36.1 - - + -
816C SER 3.3 19.0 + - - -
817C ALA* 3.1 7.6 + - - +
819C CYS* 1.3 73.9 - - - +
821C GLY* 1.3 56.5 + - - +
823C MET* 3.3 20.8 + - + +
824C THR* 2.7 36.9 + - - -
851C ALA* 3.7 16.2 - - + -
855C CYS* 3.9 15.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 821 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817C ALA 3.1 11.6 + - - -
818C LYS* 3.5 3.8 + - - -
820C PHE* 1.3 77.4 - - - +
822C TYR* 1.3 55.3 + - - +
824C THR* 3.3 4.6 + - - -
825C GLN* 2.8 24.8 + - - +
854C ALA* 3.7 29.5 - - - +
855C CYS* 4.1 1.1 - - - -
858C ALA* 3.3 13.5 - - - +
864C VAL* 4.3 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 822 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775C LEU* 3.6 22.0 - - + -
818C LYS 2.9 17.9 + - - +
819C CYS* 3.8 5.2 - - - +
820C PHE 3.3 0.4 - - - -
821C GLY* 1.3 73.4 - - - +
823C MET* 1.3 60.4 + - - +
825C GLN* 3.4 28.7 - - - +
826C GLN* 2.9 71.4 + - + +
864C VAL* 3.8 26.6 - - + +
866C PRO* 3.2 27.8 - - + +
872C TRP* 4.0 16.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 823 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706C TRP* 3.9 18.6 - - + -
774C TYR* 4.1 25.6 - - + +
775C LEU* 5.8 2.7 - - + -
778C PHE* 3.5 50.6 - - + -
815C VAL* 4.1 14.4 - - + -
819C CYS* 3.0 35.3 + - - +
820C PHE* 3.3 35.4 + - + +
822C TYR* 1.3 74.5 - - - +
824C THR* 1.3 58.7 + - - +
826C GLN* 3.4 3.9 + - - +
827C LEU* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 824 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706C TRP* 3.4 12.3 - - - -
820C PHE 2.7 19.6 + - - -
821C GLY* 3.4 9.9 - - - -
822C TYR 3.2 0.2 - - - -
823C MET* 1.3 75.2 - - - +
825C GLN* 1.3 65.9 + - - +
827C LEU* 3.1 8.0 + - - +
828C MET* 3.0 28.5 + - + +
835C VAL* 5.3 1.1 - - + -
837C LEU* 4.1 14.8 - - + -
855C CYS* 3.3 28.2 - - - +
858C ALA* 4.4 1.1 - - + -
859C LEU* 3.2 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 825 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821C GLY 2.8 19.2 + - - +
822C TYR* 3.4 26.2 - - + +
824C THR* 1.3 72.3 - - - +
826C GLN* 1.3 63.9 + - - +
828C MET* 3.2 27.9 + - + +
829C ASN* 3.7 11.6 + - - +
858C ALA* 4.3 7.1 - - + +
862C ASN 4.2 7.1 - - - +
863C ARG* 3.4 48.3 - - + +
864C VAL* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 826 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775C LEU* 4.2 8.5 + - - +
778C PHE* 3.8 32.3 - - + +
779C ARG* 4.9 5.7 + - - +
783C MET* 3.1 43.8 - - + +
822C TYR* 2.9 62.0 + - + +
823C MET* 3.6 7.1 - - - +
825C GLN* 1.3 75.6 - - - +
827C LEU* 1.3 62.4 + - - +
829C ASN* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 827 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702C LEU* 4.9 0.9 - - + -
704C VAL* 3.8 28.7 - - + -
706C TRP* 3.9 20.9 - - + -
778C PHE* 3.9 10.3 - - + -
782C VAL* 4.7 3.4 - - + -
783C MET* 3.8 14.4 - - - -
794C VAL* 4.4 4.4 - - + +
796C VAL* 3.7 28.9 - - + -
823C MET 3.0 16.5 + - - +
824C THR* 3.1 6.7 + - - +
826C GLN* 1.3 74.5 - - - +
828C MET* 1.3 57.6 + - - +
829C ASN 3.2 0.2 - - - -
830C LEU* 3.1 45.1 + - + +
835C VAL* 3.3 23.1 - - + +
837C LEU* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 828 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658C LYS* 3.9 17.9 - - - +
659C ASN* 3.6 25.6 - - - +
824C THR 3.0 20.2 + - - +
825C GLN* 3.2 18.0 + - + +
827C LEU* 1.3 73.3 - - - +
829C ASN* 1.3 64.5 + - - +
830C LEU 3.1 2.2 - - - -
832C GLY 4.4 0.2 - - - -
833C GLY* 3.2 27.6 + - - +
835C VAL* 3.8 18.2 - - + -
858C ALA 3.2 35.2 - - - +
859C LEU* 3.7 19.3 - - + +
861C GLY* 4.5 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 829 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783C MET* 5.3 0.4 - - - +
787C ARG* 3.5 33.8 + - - +
825C GLN* 3.7 10.7 + - - +
826C GLN* 3.3 18.8 + - - +
827C LEU 3.2 0.6 - - - -
828C MET* 1.3 78.6 - - - +
830C LEU* 1.3 60.8 + - - +
831C ALA 4.2 0.2 + - - -
832C GLY* 4.4 5.4 + - - -
----------------------------------------------------------
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