Contacts of the helix formed by residues 2056 - 2074 (chain A) in PDB entry 4ASI
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 PHE2056 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2007A THR* 4.0 11.4 - - - -
2049A GLN 5.1 3.1 - - - -
2050A GLN* 3.9 28.0 - - + +
2051A ALA* 3.5 43.3 - - + -
2054A VAL* 3.5 26.7 - - + -
2055A TRP* 1.3 77.2 - - - +
2057A PRO* 1.3 76.3 - - + +
2058A ASP* 3.2 17.0 - - - +
2059A SER* 3.6 6.3 - - - -
2060A ALA* 2.8 23.0 + - - +
2087A SER* 3.6 24.5 - - - -
2092A ASP* 3.7 17.5 - - - -
2097A VAL* 4.4 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO2057 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2056A PHE* 1.3 89.3 - - + +
2058A ASP* 1.3 63.1 + - - +
2060A ALA* 3.6 4.7 - - + +
2061A PHE* 2.9 25.2 + - - +
2092A ASP* 3.5 39.3 - - + +
2095A ASP* 3.7 31.2 - - + +
2097A VAL* 3.9 18.6 - - + -
2100A PHE* 4.2 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2058 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2004A TRP* 3.8 22.6 - - + +
2005A ALA* 3.4 27.7 + - + +
2032A LEU* 4.3 8.8 - - - +
2050A GLN* 2.9 28.5 + - - +
2056A PHE* 3.4 10.1 - - - +
2057A PRO* 1.3 79.7 - - - +
2059A SER* 1.3 84.5 + - - +
2061A PHE* 3.1 4.9 + - - +
2062A LYS 2.8 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2059 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2005A ALA* 3.7 9.4 - - - +
2007A THR* 2.9 45.4 + - - +
2008A VAL* 3.7 8.5 - - - +
2055A TRP* 3.7 10.1 - - - -
2056A PHE* 3.3 16.3 + - - +
2058A ASP* 1.3 91.0 + - - +
2060A ALA* 1.3 53.8 + - - +
2062A LYS* 3.5 2.3 + - - +
2063A THR* 2.7 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2060 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2055A TRP* 3.6 16.3 - - + +
2056A PHE 2.8 18.5 + - - +
2057A PRO* 3.6 3.8 - - + +
2059A SER* 1.3 78.0 - - - +
2061A PHE* 1.3 58.5 + - - +
2063A THR* 3.2 2.9 + - - -
2064A TYR* 2.9 29.1 + - - +
2086A PHE* 4.3 15.5 - - + -
2097A VAL 5.3 0.9 - - - +
2100A PHE* 3.8 28.2 - - + +
2101A GLY 4.4 0.2 - - - +
2104A ILE* 4.1 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2061 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1870A ARG* 5.1 7.2 - - - -
2004A TRP* 4.0 22.4 - + + -
2057A PRO 2.9 17.1 + - - +
2058A ASP* 3.5 4.7 - - - +
2060A ALA* 1.3 74.5 - - - +
2062A LYS* 1.3 66.3 + - - +
2064A TYR* 3.1 25.1 + + - +
2065A GLN* 2.9 41.2 + - - +
2100A PHE* 3.7 39.7 - + + +
2103A TYR* 5.3 2.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2062 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1999A GLU* 4.4 4.4 + - - -
2000A ILE 3.9 3.4 + - - -
2001A MET* 2.6 39.8 + - + +
2002A GLN* 3.9 8.7 + - - +
2004A TRP* 3.0 55.2 + - + +
2005A ALA* 3.5 8.7 + - + +
2008A VAL* 3.2 34.8 + - + -
2009A VAL* 4.5 0.4 - - - +
2010A VAL* 3.9 22.0 - - + +
2058A ASP 2.8 17.5 + - - +
2059A SER 3.7 4.3 - - - +
2061A PHE* 1.3 74.4 - - - +
2063A THR* 1.3 55.4 + - - +
2065A GLN* 3.7 2.9 - - - +
2066A ALA* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2063 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008A VAL* 3.6 15.7 - - - +
2010A VAL* 5.0 2.7 - - - -
2023A VAL* 4.1 21.8 - - + -
2055A TRP* 3.1 32.4 + - + -
2059A SER 2.7 28.1 + - - -
2060A ALA 3.6 4.3 - - - -
2061A PHE 3.1 0.4 - - - -
2062A LYS* 1.3 74.9 - - - +
2064A TYR* 1.3 63.6 + - - +
2066A ALA* 3.6 4.6 - - - +
2067A ILE* 3.0 45.4 + - + +
2079A VAL* 6.4 0.7 - - + -
2083A TRP* 5.0 0.7 - - + -
2104A ILE* 4.4 6.3 - - + -
2133A ILE* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR2064 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2060A ALA 2.9 13.6 + - - +
2061A PHE* 3.4 31.9 - + - +
2063A THR* 1.3 77.7 - - - +
2065A GLN* 1.3 63.6 + - - +
2067A ILE* 3.2 10.5 + - - +
2068A LYS* 3.0 61.3 + - + +
2100A PHE 5.0 0.2 - - - +
2103A TYR* 3.4 58.4 - + + -
2104A ILE* 4.1 7.1 - - + +
2106A ASP* 4.9 5.7 - - + +
2107A GLY* 4.0 14.6 - - - -
2110A GLU* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2065 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1848A TYR* 4.1 4.4 + - - -
1870A ARG* 3.2 23.3 + - - +
1873A GLN* 3.2 27.7 + - - +
1916A GLY 5.6 1.1 - - - +
1919A HIS* 5.3 1.6 - - + -
2001A MET* 4.5 15.5 - - + -
2004A TRP* 5.1 4.4 - - + -
2061A PHE* 2.9 33.0 + - + +
2062A LYS* 3.7 7.9 - - - +
2064A TYR* 1.3 79.1 - - - +
2066A ALA* 1.3 67.6 + - - +
2068A LYS* 3.2 11.6 + - - +
2069A ASP* 2.9 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2066 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2000A ILE* 5.7 0.7 - - - -
2001A MET* 4.4 7.4 - - - +
2010A VAL* 3.9 25.4 - - + -
2023A VAL* 4.4 6.5 - - + -
2062A LYS 2.9 13.9 + - - +
2063A THR 3.6 8.1 - - - +
2065A GLN* 1.3 77.9 - - - +
2067A ILE* 1.3 64.6 + - - +
2069A ASP* 4.7 2.9 - - - -
2070A PHE* 3.0 53.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2067 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2023A VAL* 5.1 3.6 - - + -
2063A THR* 3.0 38.6 + - + +
2064A TYR* 3.5 9.6 - - - +
2066A ALA* 1.3 82.8 - - + +
2068A LYS* 1.3 65.4 + - - +
2070A PHE* 4.2 5.1 - - - +
2071A ASN* 3.1 22.1 + - + +
2077A LEU* 4.9 17.4 - - + +
2104A ILE* 4.3 18.4 - - + +
2107A GLY* 3.7 32.3 - - - +
2108A LEU* 4.2 22.0 - - + +
2111A CYS* 4.0 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2068 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1848A TYR* 3.8 16.6 - - + +
2064A TYR* 3.0 57.6 + - + +
2065A GLN* 3.2 11.6 + - - +
2067A ILE* 1.3 78.1 - - - +
2069A ASP* 1.3 64.1 + - - +
2071A ASN* 3.2 3.6 + - - +
2072A ARG* 3.0 44.9 + - - +
2107A GLY* 5.0 3.4 - - - -
2110A GLU* 3.5 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2069 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1848A TYR* 2.4 38.4 + - - -
1873A GLN* 3.7 10.7 - - - +
1874A ARG* 3.2 19.4 + - + +
1919A HIS* 3.2 29.5 + - - +
2000A ILE* 5.9 1.8 - - + -
2001A MET* 5.0 2.4 - - - +
2012A ARG* 5.4 0.9 - - - +
2065A GLN* 2.9 36.9 + - - +
2066A ALA* 4.0 4.3 - - - +
2068A LYS* 1.3 75.8 - - - +
2070A PHE* 1.3 69.1 + - + +
2072A ARG 3.0 10.9 + - - -
2073A GLU* 3.1 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2070 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2000A ILE* 4.0 17.7 - - + -
2011A GLY* 3.1 36.6 - - - -
2012A ARG* 3.8 29.6 - - + -
2021A GLY* 3.7 13.5 - - - -
2022A VAL 3.6 13.7 - - - -
2023A VAL* 5.0 0.4 - - + -
2066A ALA* 3.0 39.1 + - + +
2067A ILE 4.2 0.7 - - - +
2069A ASP* 1.3 76.9 - - + +
2071A ASN* 1.3 63.0 + - - +
2073A GLU* 3.1 23.3 + - - +
2074A GLY 3.1 16.8 + - - -
2075A LEU* 3.2 21.9 + - + +
2077A LEU* 4.0 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2071 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2067A ILE* 3.1 21.3 + - + +
2068A LYS* 3.2 6.3 + - - +
2070A PHE* 1.3 77.1 - - - +
2072A ARG* 1.3 62.6 + - - +
2074A GLY* 3.2 17.2 + - - -
2075A LEU 4.6 2.2 - - - -
2077A LEU* 5.0 3.3 - - + +
2110A GLU* 3.3 37.6 - - - +
2111A CYS* 3.5 16.9 - - - +
2112A CYS* 3.5 17.8 - - - +
2113A GLN* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2072 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1848A TYR* 3.3 51.3 - - - +
1849A ASN* 2.9 37.3 + - - +
1850A GLU 6.0 0.7 - - - -
1851A ILE* 4.7 6.8 - - - +
1852A ILE* 4.4 7.3 - - - +
1874A ARG* 3.6 17.8 + - - +
1943A VAL* 5.6 4.7 - - - +
2068A LYS* 3.0 28.2 + - - +
2069A ASP 3.0 1.3 + - - +
2071A ASN* 1.3 81.7 + - - +
2073A GLU* 1.3 61.0 + - - +
2074A GLY 3.3 0.2 - - - -
2110A GLU* 2.6 41.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2073 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1852A ILE* 4.2 17.2 - - + +
1874A ARG* 2.7 32.2 + - - +
1939A MET* 3.6 20.1 - - + +
1940A PRO* 3.3 27.0 - - - +
2012A ARG* 2.7 42.6 + - - -
2069A ASP* 3.1 16.6 + - - +
2070A PHE* 3.1 11.4 + - - +
2072A ARG* 1.3 77.4 - - - +
2074A GLY* 1.3 59.4 + - - +
2075A LEU* 3.1 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2074 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1940A PRO* 4.8 4.6 - - - +
1947A VAL* 3.7 17.2 + - - +
2070A PHE 3.1 2.8 + - - -
2071A ASN 3.2 12.4 + - - -
2072A ARG 3.3 0.4 - - - -
2073A GLU* 1.3 80.4 - - - +
2075A LEU* 1.3 63.9 - - - +
2076A PRO* 4.1 1.4 - - - +
2113A GLN* 3.7 25.9 - - - +
----------------------------------------------------------
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