Contacts of the helix formed by residues 798 - 809 (chain B) in PDB entry 1WZ2
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 THR 798 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B ASP* 2.8 57.5 - - + +
675B LEU* 3.9 12.1 - - + -
701B ILE* 4.7 6.5 - - + -
794B MET* 2.9 36.1 + - + +
795B ALA 3.5 2.9 - - - -
797B PHE* 1.3 76.3 - - - +
799B PRO* 1.3 60.9 - - - +
801B ILE* 4.1 12.1 - - + +
802B CYS* 2.9 24.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 799 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TRP* 3.4 11.4 - - + -
65B ARG* 3.5 34.1 - - - +
141B GLY 4.4 0.7 - - - +
671B ASP* 2.9 13.9 - - - +
674B ARG* 3.7 27.8 - - - +
795B ALA 3.0 18.7 - - - +
797B PHE 3.4 8.7 - - - +
798B THR* 1.3 82.9 - - - +
800B HIS* 1.3 67.7 + - + +
802B CYS* 4.1 3.4 - - + +
803B GLU* 3.3 26.2 + - - +
815B VAL* 4.3 2.8 - - + +
816B SER* 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 800 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 6.1 0.2 - - + -
9B ILE* 4.5 6.1 - - + -
10B GLU* 3.8 30.3 + - + -
13B TRP* 3.7 10.6 - - + +
14B GLN* 4.0 18.6 + - + -
17B TRP* 2.9 43.6 - + - -
140B ALA 4.1 10.9 + - - -
141B GLY* 3.9 12.5 - - - -
670B ALA* 3.5 29.3 - - + +
671B ASP* 2.9 27.3 + - - +
674B ARG* 5.8 0.2 - - - -
799B PRO* 1.3 78.6 - - + +
801B ILE* 1.3 57.4 + - + +
802B CYS 2.5 15.9 + - - -
803B GLU* 2.7 16.8 + - - +
804B GLU* 3.1 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 801 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 3.5 40.8 - - + -
9B ILE* 4.9 3.4 - - + -
671B ASP* 2.9 25.4 + - + +
701B ILE* 4.0 26.0 - - + -
704B PHE* 4.2 22.0 - - + -
705B TYR* 4.3 17.3 - - + -
794B MET* 5.7 0.4 - - + -
798B THR* 4.0 17.0 - - + +
800B HIS* 1.3 72.1 - - + +
802B CYS* 1.3 68.2 + - - +
804B GLU* 3.6 9.3 - - - +
805B LEU* 2.8 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 802 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B PHE* 4.8 8.3 - - - -
791B VAL* 4.0 29.0 - - + +
794B MET* 4.2 9.9 - - - -
795B ALA* 4.3 9.2 - - - -
798B THR* 2.9 37.2 - - - +
799B PRO 4.2 3.6 - - - +
800B HIS 2.5 6.7 + - - -
801B ILE* 1.3 82.5 - - - +
803B GLU* 1.3 53.5 + - - +
804B GLU 2.9 5.2 - - - -
805B LEU* 4.1 4.0 - - - +
806B TRP* 2.6 36.8 + - - +
815B VAL* 4.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 803 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TRP* 3.0 55.5 - - + +
17B TRP* 3.5 27.4 - - + +
799B PRO 3.3 14.6 + - - +
800B HIS 2.7 6.7 + - - +
802B CYS* 1.3 75.0 - - - +
804B GLU* 1.3 60.9 + - - +
806B TRP* 3.9 3.5 - - - +
807B GLU* 3.5 12.3 + - - +
814B PHE* 3.0 28.4 - - - +
815B VAL* 2.2 52.0 + - + +
816B SER* 2.8 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 804 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.1 43.8 - - + +
12B LYS* 4.5 16.8 + - - +
13B TRP* 3.2 13.9 + - - +
705B TYR* 4.7 5.4 - - + +
800B HIS 3.1 9.1 + - - +
801B ILE* 3.6 11.0 - - - +
803B GLU* 1.3 75.4 - - - +
805B LEU* 1.3 64.8 + - + +
806B TRP 3.1 0.9 - - - -
807B GLU* 2.7 51.0 + - - +
808B LYS* 2.9 15.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 805 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B PHE* 4.4 10.8 - - + -
705B TYR* 3.0 51.8 - - + +
708B ILE* 3.4 43.5 - - + -
709B SER* 3.9 13.0 - - - +
791B VAL* 4.1 9.4 - - + -
801B ILE* 2.8 21.7 + - + +
802B CYS* 4.1 2.0 - - - +
804B GLU* 1.3 76.5 - - + +
806B TRP* 1.3 64.6 + - - +
807B GLU 2.9 2.0 - - - -
808B LYS* 3.1 13.6 + - + +
809B LEU* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 806 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B ASP* 3.4 29.8 - - - -
791B VAL* 3.8 17.9 - - + +
792B ARG* 3.4 32.8 - - + -
802B CYS 2.6 23.7 + - - +
803B GLU 3.9 5.2 - - - +
804B GLU 3.1 0.2 - - - -
805B LEU* 1.3 73.9 - - - +
807B GLU* 1.3 57.9 + - - +
809B LEU* 3.3 14.7 + - + +
811B GLY* 3.0 33.3 + - - -
812B GLU* 2.7 53.3 + - + +
813B GLY 3.6 9.6 + - - -
814B PHE 4.3 0.2 + - - -
815B VAL* 3.6 39.1 - - + +
818B ALA* 4.0 8.7 - - + -
819B LYS* 5.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 807 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 4.4 13.8 + - - -
13B TRP* 4.4 15.9 - - + -
16B ARG* 5.2 4.2 + - - -
803B GLU 3.5 9.8 + - - +
804B GLU* 2.7 33.8 + - - +
806B TRP* 1.3 77.8 - - - +
808B LYS* 1.3 56.5 + - + +
809B LEU 2.5 19.4 - - - +
810B GLY 4.4 2.4 - - - +
811B GLY* 4.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 808 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B TYR* 4.0 20.0 + - - -
708B ILE* 6.1 0.2 - - + -
709B SER* 3.4 36.0 + - - +
712B ALA* 4.0 24.4 - - + +
804B GLU* 2.9 21.5 + - + +
805B LEU* 3.1 18.6 + - + +
807B GLU* 1.3 77.9 - - + +
809B LEU* 1.3 60.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 809 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B ILE* 3.9 19.7 - - + -
712B ALA* 4.1 19.5 - - + +
784B ARG* 3.5 33.4 - - - +
787B ALA* 3.9 28.7 - - + +
788B ASP* 4.4 6.1 - - - +
791B VAL* 3.9 18.2 - - + -
805B LEU 2.9 25.5 + - - +
806B TRP* 4.0 13.2 - - + +
807B GLU 2.5 19.8 - - - +
808B LYS* 1.3 78.5 - - - +
810B GLY* 1.3 68.5 + - - +
811B GLY 2.8 3.9 + - - +
----------------------------------------------------------
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