Contacts of the helix formed by residues 836 - 845 (chain v) in PDB entry 6FF7
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 836 (chain v).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824v VAL* 5.3 13.2 - - + -
834v LEU 2.9 10.6 + - - +
835v ALA* 1.3 71.1 - - - +
837v GLU* 1.3 63.4 + - - +
838v MET 3.3 1.1 - - - -
839v ALA* 3.6 9.7 + - + +
840v ALA* 3.4 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 837 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835v ALA* 3.2 4.8 - - + +
836v ALA* 1.3 76.7 - - - +
838v MET* 1.3 60.1 + - - +
840v ALA* 3.6 4.0 + - - +
841v ALA* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 838 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823v MET* 6.1 3.1 - - + -
835v ALA* 3.9 20.5 + - + +
836v ALA 3.3 0.6 - - - -
837v GLU* 1.3 78.8 - - - +
839v ALA* 1.3 55.8 + - - +
841v ALA* 3.4 6.0 + - - +
842v PHE* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 839 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820v ALA* 3.8 43.3 - - + +
823v MET* 4.5 12.7 - - + +
824v VAL* 5.1 4.9 - - + +
835v ALA 4.4 2.3 + - - +
836v ALA* 3.6 13.5 + - + +
837v GLU 3.4 0.2 - - - -
838v MET* 1.3 79.8 - - - +
840v ALA* 1.3 56.1 + - - +
842v PHE* 3.2 7.7 + - - +
843v LEU* 2.9 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 840 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836v ALA 3.4 14.6 + - - +
837v GLU* 4.2 4.0 - - - +
839v ALA* 1.3 78.3 - - - +
841v ALA* 1.3 57.9 + - - +
843v LEU* 3.6 8.2 - - - +
844v ASN* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 841 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837v GLU 2.9 21.1 + - - +
838v MET* 3.7 7.0 - - - +
840v ALA* 1.3 77.9 - - - +
842v PHE* 1.3 59.8 + - - +
844v ASN* 4.4 1.5 - - - -
845v GLU* 3.3 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 842 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276v ASN* 6.6 0.2 - - + -
816v LYS* 5.5 5.2 - - - +
819v MET* 6.3 2.9 - - + -
838v MET 2.9 17.1 + - - +
839v ALA* 3.6 7.2 - - - +
841v ALA* 1.3 76.1 - - - +
843v LEU* 1.3 62.6 + - - +
845v GLU* 3.5 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 843 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816v LYS* 5.4 12.1 - - + +
820v ALA* 5.6 6.3 - - + -
839v ALA 2.9 14.3 + - - +
840v ALA* 3.2 11.6 + - - +
842v PHE* 1.3 79.3 - - - +
844v ASN* 1.3 62.6 + - + +
845v GLU 3.3 4.2 + - - +
846v ASN* 4.8 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 844 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840v ALA 2.9 19.0 + - - +
841v ALA* 5.0 1.3 - - - +
843v LEU* 1.3 72.5 - - + +
845v GLU* 1.3 59.0 + - - +
846v ASN* 3.8 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 845 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841v ALA 3.3 18.8 + - - +
842v PHE* 3.5 13.5 - - - +
843v LEU 3.2 3.0 - - - -
844v ASN* 1.3 76.7 - - - +
846v ASN* 1.3 61.8 + - - +
847v LEU* 3.8 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