Contacts of the helix formed by residues 1987 - 2004 (chain A) in PDB entry 4UXL
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 THR1987 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1986A SER* 1.3 75.2 + - - +
1988A ASP* 1.3 68.2 + - + +
1989A GLN* 3.1 31.9 - - + +
1990A GLU* 2.7 43.5 + - + +
1991A LYS* 3.1 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1988 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1986A SER 3.5 3.3 + - - -
1987A THR* 1.3 74.7 - - + +
1989A GLN* 1.3 58.5 + - - +
1991A LYS* 3.5 12.0 + - - +
1992A ILE* 3.0 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1989 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1987A THR* 3.0 17.4 - - + +
1988A ASP* 1.3 78.2 - - - +
1990A GLU* 1.3 66.2 + - + +
1992A ILE* 3.0 22.4 + - + +
1993A GLU* 3.2 12.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1990 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1956A PHE* 3.5 51.7 - - + +
1982A LEU* 4.3 5.9 - - + +
1986A SER* 3.2 17.4 - - - +
1987A THR* 2.7 45.9 + - + +
1989A GLN* 1.3 76.4 - - + +
1991A LYS* 1.3 60.4 + - - +
1993A GLU* 3.2 11.0 + - - +
1994A PHE* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1991 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1982A LEU* 4.3 19.9 - - + +
1986A SER* 5.5 1.6 - - - -
1987A THR 3.1 11.2 + - - +
1988A ASP* 3.6 17.5 - - - +
1989A GLN 3.2 0.2 - - - -
1990A GLU* 1.3 77.1 - - - +
1992A ILE* 1.3 60.5 + - + +
1994A PHE* 3.3 8.8 - - + +
1995A LEU* 2.9 42.2 + - + +
2020A GLU* 3.6 19.7 + - - +
2022A GLN* 3.0 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1992 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1988A ASP* 3.0 29.6 - - - +
1989A GLN* 3.0 14.3 + - + +
1991A LYS* 1.3 81.3 - - + +
1993A GLU* 1.3 54.5 + - - +
1995A LEU* 3.2 17.7 + - + +
1996A LYS* 2.7 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1993 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1956A PHE* 5.0 15.3 - - + -
1989A GLN* 3.2 8.7 + - + +
1990A GLU* 3.2 11.0 + - - +
1992A ILE* 1.3 77.5 - - - +
1994A PHE* 1.3 63.1 + - - +
1996A LYS* 3.3 25.6 + - - +
1997A GLU* 2.7 47.2 + - - +
2104A GLY* 3.4 33.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1994 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1980A LYS* 3.6 37.5 - - + -
1981A THR 3.8 17.9 - - - -
1982A LEU* 3.7 30.7 - - + -
1990A GLU 2.9 14.5 + - - +
1991A LYS* 3.3 13.7 - - - +
1993A GLU* 1.3 77.9 - - - +
1995A LEU* 1.3 66.4 + - + +
1997A GLU* 3.4 13.5 + - - +
1998A ALA* 3.2 20.6 + - - +
2017A LEU* 4.6 4.5 - - + -
2022A GLN* 3.3 31.0 - - + -
2024A ILE* 3.4 37.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
1937A LEU* 5.0 6.1 - - + -
1991A LYS* 2.9 38.7 + - + +
1992A ILE* 3.5 17.5 - - + +
1994A PHE* 1.3 76.6 - - + +
1996A LYS* 1.3 67.0 + - - +
1998A ALA* 3.2 6.0 + - + +
1999A HIS* 3.0 35.7 + - + +
2017A LEU* 3.7 35.9 - - + -
2022A GLN* 5.6 4.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
1992A ILE* 2.7 22.5 + - + +
1993A GLU* 3.3 28.3 + - - +
1995A LEU* 1.3 72.7 - - - +
1997A GLU* 1.3 62.9 + - + +
1999A HIS* 3.1 8.7 + - - +
2000A LEU* 3.0 37.5 + - + +
2104A GLY 4.9 1.8 - - - +
2106A ALA 5.0 0.4 - - - +
2107A ARG* 3.5 40.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1997 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1980A LYS* 3.1 34.4 - - - +
1993A GLU* 2.7 51.4 + - - +
1994A PHE* 3.5 15.4 - - - +
1996A LYS* 1.3 75.7 - - + +
1998A ALA* 1.3 64.9 + - - +
2000A LEU* 3.1 22.5 + - - +
2001A MET* 3.1 29.3 + - + +
2024A ILE* 6.0 2.6 - - + +
2102A ASP* 5.2 3.4 - - - +
2103A PHE* 4.7 4.8 + - + +
2104A GLY* 4.2 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1998 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1937A LEU* 4.3 17.5 - - + -
1994A PHE 3.2 7.0 + - - +
1995A LEU* 3.2 11.2 + - + +
1997A GLU* 1.3 79.9 - - - +
1999A HIS* 1.3 60.6 + - - +
2001A MET 3.4 0.5 + - - -
2002A SER* 3.0 14.6 + - - -
2012A GLN* 2.9 44.0 - - - +
2017A LEU* 5.3 2.0 - - + -
2024A ILE* 3.4 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1999 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1935A GLU* 3.9 37.9 - - + +
1937A LEU* 3.6 38.4 - - + +
1995A LEU* 3.0 31.2 + - + +
1996A LYS* 3.5 9.2 - - - +
1997A GLU 3.1 0.2 - - - -
1998A ALA* 1.3 75.4 - - - +
2000A LEU* 1.3 65.2 + - - +
2002A SER* 3.3 3.3 + - - -
2003A LYS* 3.0 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2000 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1996A LYS* 3.0 32.4 + - + +
1997A GLU* 3.1 10.7 + - - +
1999A HIS* 1.3 75.9 - - - +
2001A MET* 1.3 61.1 + - - +
2003A LYS* 3.3 21.4 + - + +
2004A PHE* 3.1 32.4 - - + -
2075A PHE* 3.2 41.5 - - + -
2103A PHE* 3.3 36.6 - - + +
2106A ALA* 4.1 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2001 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1980A LYS* 6.4 2.0 - - + -
1997A GLU* 3.1 31.8 + - + +
1998A ALA 3.9 4.5 - - - +
1999A HIS 3.1 0.2 - - - -
2000A LEU* 1.3 75.6 - - - +
2002A SER* 1.3 65.1 + - - +
2004A PHE* 3.3 22.1 + - - +
2009A ILE* 5.4 1.6 - - + -
2010A LEU* 3.6 33.1 - - - +
2012A GLN* 3.8 27.3 + - + +
2024A ILE* 5.0 2.7 - - + -
2026A LEU* 3.4 32.5 - - + -
2101A GLY 5.5 2.5 - - - +
2102A ASP* 6.2 0.4 - - - -
2103A PHE* 4.2 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2002 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1936A ASN 4.5 9.6 - - - -
1937A LEU* 3.1 22.6 - - - +
1938A PRO* 3.8 9.4 - - - +
1998A ALA 3.0 9.1 + - - -
1999A HIS* 3.7 7.9 - - - -
2001A MET* 1.3 77.5 - - - +
2003A LYS* 1.3 65.1 + - - +
2004A PHE 3.3 4.9 + - - +
2005A ASN* 5.7 0.5 - - - +
2012A GLN* 3.0 20.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2003 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1935A GLU* 6.0 6.1 - - + -
1999A HIS* 3.0 27.1 - - + +
2000A LEU* 3.3 12.6 - - + +
2001A MET 3.2 0.2 - - - -
2002A SER* 1.3 80.4 - - - +
2004A PHE* 1.3 65.4 + - + +
2005A ASN* 3.8 2.8 + - - +
2069A TYR* 4.0 5.2 + - - -
2073A MET* 4.1 15.8 - - + +
2075A PHE* 3.4 37.0 - - - -
2108A ASP* 5.4 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2004 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2000A LEU* 3.1 35.8 + - + +
2001A MET* 3.3 18.4 + - - +
2002A SER 3.2 4.1 - - - +
2003A LYS* 1.3 85.2 - - + +
2005A ASN* 1.3 63.1 + - - +
2006A HIS 4.2 0.2 - - - -
2009A ILE* 3.8 29.5 - - + +
2010A LEU 5.7 0.7 - - - +
2069A TYR* 3.6 20.6 - + + -
2070A LEU* 3.9 15.7 - - + -
2073A MET* 4.4 9.2 - - + -
2075A PHE* 3.7 47.8 - + + -
2103A PHE* 3.9 26.7 - + - -
2106A ALA* 5.6 1.3 - - + -
----------------------------------------------------------
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