Contacts of the strand formed by residues 722 - 726 (chain B) in PDB entry 1WBB
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 LEU 722 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B PRO* 4.0 17.5 - - + -
577B GLY* 3.4 32.1 - - - +
578B ILE* 4.0 18.6 - - + -
603B LEU* 4.0 24.0 - - + -
604B SER 3.5 28.5 - - - +
605B PRO* 5.2 0.7 - - + -
608B ARG* 3.3 12.6 - - + -
650B ILE* 5.9 5.8 - - + -
686B GLU 4.6 2.4 + - - +
687B TYR 6.1 0.7 - - - -
688B SER 3.2 16.1 + - - +
689B LEU* 3.5 8.6 - - + +
690B VAL 3.0 23.4 + - - -
720B LYS 3.6 2.2 + - - +
721B ALA* 1.3 72.8 - - - +
723B THR* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 723 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LEU* 4.3 5.6 - - - +
608B ARG 2.9 11.7 + - - +
609B MET* 3.3 32.3 - - + +
610B LEU 3.1 23.7 + - - -
689B LEU* 5.5 0.2 - - - -
690B VAL* 3.2 21.8 - - + +
692B MET* 4.8 0.4 - - + -
715B LEU* 4.1 23.6 - - + +
721B ALA* 3.1 20.3 + - - +
722B LEU* 1.3 75.4 + - - +
724B LEU* 1.3 76.3 + - - +
725B PHE* 4.2 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 724 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B LEU* 4.0 12.3 - - + -
603B LEU* 4.5 8.7 - - + -
610B LEU* 3.8 39.0 - - + -
612B ILE* 4.1 9.2 - - + -
623B TYR* 4.1 12.3 - - + -
624B MET* 3.4 26.7 - - + +
627B THR* 3.6 27.4 - - + +
689B LEU* 5.7 0.6 - - + +
690B VAL 2.9 8.7 + - - +
691B LEU* 3.6 25.1 - - + -
692B MET* 2.9 26.7 + - - +
723B THR* 1.3 77.1 - - - +
725B PHE* 1.3 60.0 - - - +
726B ALA 3.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 725 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B MET* 4.4 3.8 - - + -
610B LEU 2.8 14.9 + - - +
611B ILE* 3.5 25.5 - - + +
612B ILE* 2.8 23.9 + - - +
692B MET* 3.6 34.8 - - + -
695B ILE* 4.1 17.0 - - + -
708B ALA* 3.3 24.7 - - + -
711B CYS* 4.0 7.0 - - + -
712B ALA* 3.7 23.8 - - + -
715B LEU* 4.3 4.0 - - + -
723B THR* 3.9 14.6 - - + -
724B LEU* 1.3 69.1 - - - +
726B ALA* 1.3 72.5 + - - +
727B THR* 3.6 5.7 + - - -
732B LEU* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 726 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ILE* 3.5 11.4 - - + +
620B LYS* 3.7 21.1 - - + -
624B MET* 3.3 24.2 - - + -
692B MET* 2.9 20.4 + - - +
693B ASP* 4.2 1.8 - - - +
694B GLU* 2.9 28.8 + - + +
695B ILE 4.4 1.4 + - - -
724B LEU 3.6 1.6 + - - -
725B PHE* 1.3 80.4 - - - +
727B THR* 1.3 63.0 + - - +
----------------------------------------------------------
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