Contacts of the helix formed by residues 754 - 760 (chain B) in PDB entry 5M64
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 754 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B ASN* 3.6 28.5 - - - +
703B LEU* 4.7 7.0 + - - +
753B LYS* 1.3 84.2 + - - +
755B ASN* 1.3 68.1 + - - +
756B LEU* 3.0 13.0 - - + +
757B TYR* 3.1 20.9 + - - +
758B ASP 4.1 1.4 + - - -
980B ASP* 3.3 5.8 - - - -
981B SER* 3.1 16.4 + - - +
982B THR* 4.2 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 755 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA* 5.8 3.1 - - + -
692B THR* 6.2 2.2 - - - +
694B THR* 5.9 1.0 - - - +
753B LYS* 5.9 1.1 - - - +
754B ALA* 1.3 75.8 - - - +
756B LEU* 1.3 78.7 + - - +
757B TYR 3.4 0.2 - - - -
758B ASP* 3.7 7.5 + - - +
759B ASP* 3.0 26.3 + - - +
980B ASP* 3.4 22.5 + - - +
982B THR* 5.0 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 756 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.6 3.8 - - + -
547B HIS* 3.3 38.4 - - + +
548B LYS* 5.2 1.6 - - - +
694B THR* 5.3 5.6 - - + -
702B ASN* 3.3 29.2 - - + +
703B LEU* 5.6 1.6 - - + +
754B ALA* 3.0 6.3 - - + -
755B ASN* 1.3 105.7 + - - +
757B TYR* 1.3 60.9 + - - +
758B ASP 3.2 1.6 - - - -
759B ASP* 3.6 25.8 - - + +
760B TYR* 2.9 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 757 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B TYR* 4.4 5.8 - - - -
703B LEU* 3.5 35.3 - - + +
749B THR* 3.3 36.6 + - - -
750B PRO* 3.6 19.9 - - + +
753B LYS* 3.5 25.6 - - + -
754B ALA* 3.1 14.2 + - - +
756B LEU* 1.3 78.7 - - - +
758B ASP* 1.3 58.7 + - + +
762B MET* 3.0 67.1 + - + -
763B ASP* 3.7 24.2 + - + -
765B PHE 4.8 3.1 + - - -
766B PRO* 4.8 6.2 - - - +
767B ASN* 5.0 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 758 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 2.3 47.6 + - - +
24B ARG* 5.8 2.3 + - - -
35B PHE* 4.6 6.2 - - - +
753B LYS* 4.6 14.8 - - - +
754B ALA 4.1 1.0 + - - +
755B ASN* 3.7 9.8 + - - +
756B LEU 3.2 0.2 - - - -
757B TYR* 1.3 79.9 - - + +
759B ASP* 1.3 63.1 + - - +
760B TYR 3.2 2.2 - - - -
761B GLY* 3.2 13.2 + - - +
763B ASP* 5.8 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 759 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 3.2 22.4 - - - +
37B LEU* 3.3 42.7 - - + +
755B ASN 3.0 19.5 + - - +
756B LEU* 3.4 19.8 + - + +
758B ASP* 1.3 76.0 - - - +
760B TYR* 1.3 63.5 + - - +
761B GLY 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 760 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 4.5 3.8 - - - -
37B LEU* 3.5 38.9 - - + +
38B LEU* 3.3 38.2 - - + +
41B ALA* 5.5 6.0 - - + +
493B PHE* 4.9 0.2 - - - -
501B ARG* 5.6 2.8 + - - -
547B HIS* 3.0 49.0 + + - -
548B LYS* 5.4 0.3 - - - +
699B ILE* 4.1 30.8 - - + +
756B LEU* 2.9 27.7 + - + +
759B ASP* 1.3 82.1 - - - +
761B GLY* 1.3 64.0 + - - +
762B MET* 3.1 20.6 + - + +
----------------------------------------------------------
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