Contacts of the strand formed by residues 811 - 816 (chain B) in PDB entry 2WAC
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 ALA 811 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B THR* 4.2 6.3 - - - +
717B PHE* 4.2 15.9 - - + -
718B ALA 3.4 7.2 - - - +
719B GLN* 4.3 1.1 - - + -
784B ILE 3.4 13.1 + - - +
785B ASP 3.5 26.0 + - - +
786B TYR* 3.6 20.2 - - - +
809B PRO* 3.3 10.3 - - - +
810B TYR* 1.3 78.3 - - - +
812B THR* 1.3 65.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 812 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B PHE* 3.3 4.2 - - - -
718B ALA 2.9 30.1 + - - -
809B PRO 4.6 6.1 + - - -
810B TYR 5.2 1.0 - - - -
811B ALA* 1.3 76.2 + - - +
813B GLU* 1.3 68.1 + - - +
814B TYR* 3.4 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 813 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B THR* 4.1 7.3 - - - +
715B THR* 2.7 30.1 + - - +
716B PHE 3.3 7.9 - - - +
717B PHE* 3.7 38.5 - - + -
812B THR* 1.3 82.2 - - - +
814B TYR* 1.3 68.6 + - - +
856B PRO* 3.5 36.7 - - + +
857B ASN 4.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 814 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B GLU* 4.7 9.0 + - - -
705B VAL* 5.8 2.3 - - + +
715B THR* 3.3 6.4 - - - -
716B PHE* 2.8 56.9 + + + -
718B ALA* 4.4 8.1 - - + -
812B THR* 3.4 44.5 + - + +
813B GLU* 1.3 75.8 - - - +
815B ALA* 1.3 60.4 + - - +
846B LEU* 3.7 33.1 - - + +
848B VAL* 3.9 22.7 - - + +
856B PRO* 3.8 6.5 - - - -
857B ASN* 3.6 22.9 - - + +
859B ALA* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 815 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B THR* 4.4 13.7 - - + -
716B PHE* 4.2 1.8 - - - -
814B TYR* 1.3 72.9 - - - +
816B LEU* 1.3 61.4 + - - +
817B ALA 3.1 1.7 + - - -
856B PRO* 3.7 16.4 - - + +
857B ASN 2.8 13.2 + - - +
858B LEU* 3.5 17.1 - - + -
859B ALA* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 816 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714B LEU* 3.6 26.9 + - + +
716B PHE* 4.1 12.0 - - + -
814B TYR 4.0 1.0 + - - -
815B ALA* 1.3 70.0 - - - +
817B ALA* 1.3 67.6 + - - +
818B LEU 3.3 0.7 + - - -
819B VAL* 3.2 49.2 + - + +
835B PHE* 3.7 45.3 - - + -
858B LEU* 5.4 0.6 - - - +
859B ALA 3.7 11.7 - - - +
860B THR* 5.3 0.9 - - - -
861B LEU* 4.5 11.4 - - + +
871B GLY* 4.1 19.5 - - - +
874B LEU* 4.2 6.1 - - + -
----------------------------------------------------------
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