Contacts of the helix formed by residues 2000 - 2006 (chain A) in PDB entry 5DZZ
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 SER2000 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1994A LEU* 3.8 2.2 - - - -
1999A LYS* 1.3 73.2 - - - +
2001A VAL* 1.3 64.5 + - - +
2002A GLU* 2.4 31.5 + - - +
2003A GLU* 3.1 34.1 + - - -
2004A VAL* 3.2 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2001 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1965A LYS 4.2 5.8 - - - +
1966A LEU* 3.7 42.2 - - + -
1967A VAL 3.9 15.0 - - - +
1968A PHE* 3.2 34.7 - - + -
1994A LEU* 4.1 2.9 - - + +
2000A SER* 1.3 78.2 + - - +
2002A GLU* 1.3 70.9 + - + +
2004A VAL 3.4 0.3 + - - -
2005A ALA* 3.0 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2002 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2000A SER* 2.4 33.5 + - - +
2001A VAL* 1.3 88.2 + - + +
2003A GLU* 1.3 63.8 + - + +
2005A ALA* 4.0 5.8 - - - +
2006A SER* 3.2 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2003 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1998A LYS 4.4 2.9 - - - +
1999A LYS* 3.8 18.7 - - + +
2000A SER* 3.1 37.5 + - - +
2001A VAL 3.3 0.6 - - - -
2002A GLU* 1.3 79.6 - - + +
2004A VAL* 1.3 62.8 + - + +
2006A SER* 3.6 11.3 + - - -
2007A GLU* 3.3 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2004 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1968A PHE* 4.2 13.7 - - + -
1986A ILE* 4.0 18.4 - - + -
1990A THR* 3.8 30.3 - - + -
1994A LEU* 3.7 19.5 - - + -
1999A LYS* 4.1 14.4 - - + +
2000A SER 3.2 17.5 + - - +
2001A VAL 3.9 3.4 - - - +
2003A GLU* 1.3 73.9 - - + +
2005A ALA* 1.3 64.1 + - - +
2006A SER 3.1 2.0 - - - -
2007A GLU* 3.0 25.4 + - - +
2008A ILE* 3.3 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2005 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1968A PHE* 3.6 20.2 - - + -
2001A VAL* 3.0 20.3 + - + +
2002A GLU* 4.0 6.7 - - - +
2004A VAL* 1.3 76.3 - - - +
2006A SER* 1.3 54.6 - - - +
2007A GLU 3.1 1.4 + - - -
2008A ILE* 3.5 11.5 + - - +
2009A GLN* 2.6 44.7 + - - +
2012A LEU* 4.2 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2006 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2002A GLU 3.2 18.1 + - - -
2003A GLU* 3.7 9.6 - - - -
2004A VAL 3.1 1.0 - - - -
2005A ALA* 1.3 76.1 - - - +
2007A GLU* 1.3 62.2 + - - +
2008A ILE 3.6 0.2 - - - -
2009A GLN* 4.1 18.2 + - - +
----------------------------------------------------------
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