Contacts of the helix formed by residues 719 - 726 (chain B) in PDB entry 5B2R
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 719 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B ASP* 1.3 74.5 - - - +
720B LEU* 1.3 56.2 + - - +
721B HIS* 3.6 6.3 + - - +
722B GLU* 3.3 36.1 + - - +
723B HIS* 2.7 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 720 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719B SER* 1.3 75.0 - - - +
721B HIS* 1.3 59.3 + - - +
723B HIS* 3.1 8.4 + - + +
724B ILE* 2.9 55.9 + - + +
738B LEU* 4.0 17.3 - - + -
741B VAL* 3.8 19.1 - - + -
742B LYS* 6.3 0.7 - - + -
934B ILE* 4.0 24.5 - - + -
938B ARG* 3.6 31.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 721 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A A 2.9 37.8 + + + -
66A U 3.2 40.1 + - - -
719B SER* 3.4 5.8 + - - +
720B LEU* 1.3 80.1 - - - +
722B GLU* 1.3 60.7 + - + +
724B ILE* 3.3 6.4 + - + -
725B ALA* 2.9 33.7 + - + +
738B LEU* 4.3 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 722 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B ASP* 3.8 22.4 - - - +
719B SER* 3.3 33.8 + - - +
720B LEU 3.3 0.2 - - - -
721B HIS* 1.3 77.8 - - + +
723B HIS* 1.3 63.9 + - - +
725B ALA* 3.3 6.1 + - - +
726B ASN* 2.9 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 723 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B ASP* 3.7 20.2 + - + +
719B SER 2.7 23.2 + - - +
720B LEU* 3.4 9.9 - - + +
722B GLU* 1.3 73.5 - - - +
724B ILE* 1.3 62.5 + - + +
726B ASN* 3.2 12.7 + - - +
727B LEU* 3.4 31.9 + - + +
930B HIS* 4.7 9.7 + + - -
933B GLN* 4.3 10.0 + - - -
934B ILE* 3.7 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 724 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B LEU* 2.9 43.7 + - + +
721B HIS* 3.9 6.1 - - + +
723B HIS* 1.3 72.7 - - + +
725B ALA* 1.3 63.5 + - - +
727B LEU* 3.1 22.3 + - + +
734B LYS* 3.2 44.1 - - + +
737B ILE* 4.0 18.8 - - + -
738B LEU* 3.8 39.9 - - + +
741B VAL* 4.5 4.9 - - + -
934B ILE* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 725 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A A 4.8 6.5 - - - +
721B HIS* 2.9 29.1 + - + +
722B GLU* 3.6 7.2 - - - +
724B ILE* 1.3 77.0 - - - +
726B ASN* 1.3 65.2 + - - +
734B LYS* 2.6 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 726 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B ASP* 3.7 18.4 - - - +
722B GLU* 2.9 24.0 + - - +
723B HIS* 3.2 7.4 + - - +
724B ILE 3.2 0.4 - - - -
725B ALA* 1.3 80.5 + - - +
727B LEU* 1.3 63.6 + - - +
728B ALA 3.8 0.7 + - - -
----------------------------------------------------------
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