Contacts of the helix formed by residues 775 - 785 (chain X) in PDB entry 6AH0
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 VAL 775 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743X LYS 5.7 6.2 + - - -
744X ASN* 6.2 2.2 - - - +
745X ILE 6.2 1.1 - - - +
772X ASP 3.0 10.0 + - - -
774X ALA* 1.3 77.5 - - - +
776X PHE* 1.3 56.8 + - - +
777X TYR 3.3 3.3 + - - -
778X GLU* 3.4 4.2 + - - +
779X LEU* 2.8 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 776 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772X ASP 3.6 5.0 + - - -
773X SER* 3.2 14.7 + - - +
774X ALA 3.5 0.2 - - - -
775X VAL* 1.3 78.0 - - - +
777X TYR* 1.3 57.1 + - - +
779X LEU* 3.8 1.1 - - - +
780X LYS* 2.8 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 777 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773X SER 4.7 1.8 + - - -
774X ALA 5.2 1.4 + - - -
775X VAL 3.3 0.6 - - - -
776X PHE* 1.3 76.2 - - - +
778X GLU* 1.3 57.8 + - - +
780X LYS* 3.3 1.8 + - - +
781X GLN* 3.0 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 778 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745X ILE* 6.2 4.7 - - - +
775X VAL* 3.4 5.6 + - - +
776X PHE 3.3 0.2 - - - -
777X TYR* 1.3 73.2 - - - +
779X LEU* 1.3 59.7 + - - +
781X GLN* 3.2 2.3 + - - +
782X ALA* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 779 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775X VAL 2.8 17.9 + - - -
776X PHE* 3.8 1.6 - - - +
778X GLU* 1.3 72.1 - - - +
780X LYS* 1.3 66.0 + - - +
782X ALA* 3.2 3.5 + - - +
783X ILE* 3.1 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 780 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776X PHE 2.8 17.6 + - - -
777X TYR 3.7 2.0 - - - -
779X LEU* 1.3 77.2 - - - +
781X GLN* 1.3 56.5 + - - +
783X ILE* 3.3 1.3 + - - +
784X LEU* 2.9 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 781 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777X TYR 3.0 14.2 + - - -
778X GLU* 3.2 4.4 + - - +
780X LYS* 1.3 76.9 - - - +
782X ALA* 1.3 63.4 + - - +
784X LEU* 3.3 1.6 + - - +
785X GLU* 3.0 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 782 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778X GLU 2.9 14.7 + - - -
779X LEU* 3.2 4.4 + - - +
781X GLN* 1.3 76.4 - - - +
783X ILE* 1.3 59.1 + - - +
785X GLU* 3.7 7.3 + - - -
786X SER* 3.7 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 783 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779X LEU 3.1 12.6 + - - -
780X LYS* 3.9 1.8 - - - +
782X ALA* 1.3 76.0 - - - +
784X LEU* 1.3 65.2 + - - +
785X GLU 3.0 1.8 - - - -
786X SER* 2.9 22.6 + - - +
789X SER* 5.1 5.0 - - - +
790X SER 5.6 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 784 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780X LYS 2.9 16.9 + - - -
781X GLN* 3.8 1.8 - - - +
783X ILE* 1.3 76.0 - - - +
785X GLU* 1.3 55.9 + - - +
786X SER 3.2 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 785 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781X GLN 3.0 15.9 + - - -
782X ALA 3.9 5.8 - - - -
783X ILE 3.0 0.4 - - - -
784X LEU* 1.3 76.3 - - - +
786X SER* 1.3 56.6 + - - +
787X PRO 3.9 2.8 - - - -
----------------------------------------------------------
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