Contacts of the helix formed by residues 792 - 797 (chain F) in PDB entry 6M04
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 GLU 792 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769F LYS* 3.2 13.2 - - - +
791F PRO* 1.3 73.4 - - - +
793F LYS* 1.3 55.7 + - - +
794F VAL 3.2 0.2 - - - -
795F GLY* 2.9 26.1 + - - -
796F GLN* 3.4 6.5 + - - +
816F GLN* 3.3 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 793 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767F LEU* 3.5 23.8 - - - +
768F PRO 3.4 20.4 - - - +
769F LYS* 3.0 29.9 - - - +
771F LEU* 3.7 25.9 - - + +
772F PHE* 3.7 25.7 - - + +
780F LEU* 5.1 3.2 - - - +
790F LEU* 3.4 23.0 - - + +
791F PRO* 3.1 27.7 - - + -
792F GLU* 1.3 76.9 - - - +
794F VAL* 1.3 59.9 + - - +
795F GLY 3.2 0.2 - - - -
796F GLN* 2.9 24.4 + - - +
797F LEU* 3.0 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 794 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790F LEU* 3.7 26.2 - - + -
791F PRO 3.3 16.8 + - - +
793F LYS* 1.3 80.2 - - - +
795F GLY* 1.3 60.8 + - - +
797F LEU* 3.4 25.9 + - + +
803F LEU* 3.7 30.1 - - + -
816F GLN* 3.6 24.9 - - + +
817F LEU* 3.7 26.7 - - + -
819F GLN 4.5 1.0 - - - +
820F CYS* 4.2 10.8 - - - -
823F LEU* 5.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 795 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792F GLU* 2.9 15.2 + - - -
794F VAL* 1.3 82.1 - - - +
796F GLN* 1.3 60.3 + - - +
797F LEU 3.4 0.2 - - - -
798F SER* 4.0 14.2 + - - -
816F GLN* 4.0 8.6 + - - +
819F GLN* 4.1 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 796 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771F LEU 5.2 0.9 - - - +
772F PHE* 3.3 40.4 + - + +
774F CYS* 4.5 13.4 - - - +
777F LEU* 5.1 1.5 - - - +
792F GLU 3.4 3.1 + - - +
793F LYS* 2.9 23.7 + - - +
795F GLY* 1.3 74.5 - - - +
797F LEU* 1.3 55.1 + - - +
798F SER* 3.0 16.0 + - - -
799F GLN* 4.1 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 797 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771F LEU* 3.9 11.2 - - + -
777F LEU* 3.7 34.5 - - + -
780F LEU* 3.8 19.7 - - + -
790F LEU* 5.7 1.6 - - + -
793F LYS* 3.0 21.6 + - - +
794F VAL* 3.4 38.8 - - + +
795F GLY 3.4 0.2 - - - -
796F GLN* 1.3 73.1 - - - +
798F SER* 1.3 58.7 + - - +
799F GLN 3.2 1.1 - - - +
800F LEU* 3.2 47.3 + - + +
803F LEU* 3.8 9.4 - - + -
823F LEU* 4.0 9.0 - - + +
----------------------------------------------------------
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