Contacts of the helix formed by residues 1987 - 1997 (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 ASP1987 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1981A TYR* 3.9 5.3 - - - -
1986A ILE* 1.3 77.5 - - - +
1988A LYS* 1.3 63.4 + - - +
1989A THR* 3.2 12.1 + - - +
1990A THR* 2.6 45.3 + - - -
1991A LEU* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1988 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1981A TYR* 3.7 36.4 - - + +
1987A ASP* 1.3 75.5 - - - +
1989A THR* 1.3 62.1 + - - +
1991A LEU* 3.5 9.0 + - + +
1992A ASP* 2.6 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1989 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1987A ASP* 3.2 11.9 + - - -
1988A LYS* 1.3 77.5 - - - +
1990A THR* 1.3 65.8 + - - +
1992A ASP* 3.5 4.5 + - - +
1993A LYS* 3.2 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1990 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1986A ILE* 4.1 18.7 - - + +
1987A ASP* 2.6 36.3 + - - -
1989A THR* 1.3 73.1 - - - +
1991A LEU* 1.3 62.3 - - - +
1993A LYS* 3.4 9.9 + - - +
1994A LEU* 3.2 22.3 + - + +
1999A LYS* 4.9 12.9 + - + +
2004A VAL* 3.8 38.6 - - + -
2007A GLU* 5.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1991 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1977A ALA* 3.6 40.4 - - + +
1978A MET* 4.0 26.5 - - + -
1981A TYR* 3.6 34.8 - - + -
1986A ILE* 4.1 10.7 - - + +
1987A ASP 3.1 17.9 + - - +
1988A LYS* 3.8 13.9 - - + +
1989A THR 3.3 0.2 - - - -
1990A THR* 1.3 77.5 - - - +
1992A ASP* 1.3 65.2 + - - +
1994A LEU* 3.2 15.6 + - + +
1995A LEU* 3.2 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1992 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1988A LYS* 2.6 50.0 + - - +
1989A THR* 4.1 5.0 - - - +
1990A THR 3.3 0.4 - - - -
1991A LEU* 1.3 77.4 - - - +
1993A LYS* 1.3 61.5 + - + +
1995A LEU* 3.1 18.2 + - - +
1996A LYS* 2.9 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1993 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1989A THR* 3.2 39.4 + - + +
1990A THR* 3.7 4.5 - - - +
1991A LEU 3.3 0.2 - - - -
1992A ASP* 1.3 76.5 - - + +
1994A LEU* 1.3 57.3 + - - +
1996A LYS* 4.4 4.9 - - + +
1997A GLY* 2.8 22.7 + - - -
1998A LYS* 2.9 44.3 + - + +
1999A LYS* 3.1 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1994 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1961A VAL* 3.3 19.2 - - - +
1966A LEU* 4.0 18.2 - - + +
1968A PHE* 4.3 13.0 - - + -
1977A ALA* 3.9 24.7 - - + -
1986A ILE* 4.3 16.4 - - + -
1990A THR 3.2 17.4 + - - +
1991A LEU* 3.3 8.5 - - - +
1992A ASP 3.1 0.2 - - - -
1993A LYS* 1.3 79.3 - - - +
1995A LEU* 1.3 61.8 + - - +
1996A LYS 3.1 0.7 + - - -
1997A GLY* 3.7 4.9 + - - -
1999A LYS* 3.6 19.5 - - + +
2000A SER 3.6 21.8 - - - +
2001A VAL* 4.1 13.5 - - + +
2004A VAL* 3.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1995 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1960A THR* 3.3 19.6 - - + +
1961A VAL* 3.1 26.3 + - - -
1963A THR* 3.9 21.5 - - + -
1966A LEU* 3.7 21.1 - - + -
1978A MET* 4.1 29.4 - - + -
1991A LEU* 3.2 19.9 + - + +
1992A ASP* 3.1 23.6 + - - +
1994A LEU* 1.3 76.3 - - - +
1996A LYS* 1.3 61.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1996 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1960A THR* 4.9 10.5 + - + +
1961A VAL* 4.8 8.1 + - - +
1992A ASP* 2.9 36.1 + - - +
1993A LYS* 4.2 4.2 - - + +
1994A LEU 4.3 0.4 - - - -
1995A LEU* 1.3 84.2 - - + +
1997A GLY* 1.3 58.9 + - - +
1998A LYS* 4.4 34.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1997 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1961A VAL* 5.3 7.2 - - - -
1993A LYS 2.8 7.2 + - - -
1994A LEU 3.7 5.6 + - - -
1996A LYS* 1.3 79.1 - - - +
1998A LYS* 1.3 65.8 + - - +
1999A LYS 3.2 11.0 + - - +
----------------------------------------------------------
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