Contacts of the helix formed by residues 2041 - 2055 (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 SER2041 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2040A ILE* 1.3 72.4 - - - +
2042A PRO* 1.3 66.0 - - - +
2043A GLU* 3.5 14.2 + - - +
2044A SER* 2.6 42.8 + - - -
2045A THR* 2.7 22.0 + - - -
2173A VAL* 5.1 0.9 - - - +
2174A ASP 3.7 4.5 + - - -
2175A PRO 3.1 22.7 + - - -
2176A VAL 5.0 3.4 - - - -
2177A THR 5.0 1.1 + - - -
2178A LYS* 6.0 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO2042 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2035A LYS* 3.6 30.6 - - + +
2040A ILE 3.7 2.9 - - - +
2041A SER* 1.3 84.9 - - - +
2043A GLU* 1.3 78.1 + - - +
2045A THR* 3.3 7.8 + - - -
2046A VAL* 3.2 23.6 + - - +
2082A ASP* 5.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2043 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2041A SER* 3.5 12.8 - - - +
2042A PRO* 1.3 96.0 - - - +
2044A SER* 1.3 61.4 + - - +
2046A VAL* 3.5 13.4 + - - +
2047A MET* 3.5 22.7 + - + +
2173A VAL* 4.4 11.4 - - + -
2178A LYS* 5.3 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2044 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2040A ILE* 3.2 15.5 - - - +
2041A SER* 2.6 33.2 + - - -
2043A GLU* 1.3 76.0 - - - +
2045A THR* 1.3 63.8 + - - +
2047A MET* 3.8 4.3 - - - +
2048A LEU* 3.0 33.6 + - - +
2173A VAL* 3.6 36.0 - - - +
2174A ASP 3.9 3.4 - - - -
2175A PRO* 3.5 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2045 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2031A LEU* 3.6 28.1 + - + +
2032A VAL* 4.6 3.1 - - - -
2035A LYS* 3.4 29.8 - - + +
2040A ILE* 3.4 14.6 - - - +
2041A SER 2.7 19.5 + - - -
2042A PRO 3.4 9.6 - - - -
2043A GLU 3.2 0.4 - - - -
2044A SER* 1.3 77.7 + - - +
2046A VAL* 1.3 63.0 + - + +
2048A LEU* 3.6 5.4 + - - +
2049A LEU* 3.1 36.3 + - + +
2079A ASP* 4.9 4.5 - - - +
2082A ASP* 5.4 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2046 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2042A PRO 3.2 17.5 - - - +
2043A GLU* 3.8 8.1 - - - +
2044A SER 3.3 0.6 - - - -
2045A THR* 1.3 76.2 - - - +
2047A MET* 1.3 59.0 + - + +
2049A LEU* 3.1 9.6 + - - +
2050A GLU* 2.8 50.6 + - + +
2082A ASP* 3.4 43.5 - - + +
2085A GLN* 4.2 14.4 - - + -
2086A ILE* 5.1 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2047 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2043A GLU* 3.5 17.0 + - + +
2044A SER* 3.4 6.7 + - - +
2046A VAL* 1.3 76.5 - - + +
2048A LEU* 1.3 57.5 + - + +
2050A GLU* 3.3 13.9 + - - +
2051A ALA 3.1 20.8 + - - -
2123A ARG* 3.4 43.3 - - - +
2171A ASN 3.9 7.2 - - - +
2172A PHE* 3.3 28.1 - - + -
2173A VAL* 3.6 50.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2048 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2018A ILE* 4.2 15.9 - - + +
2031A LEU* 3.7 34.5 - - + +
2040A ILE* 4.9 9.9 - - + -
2044A SER* 3.0 28.0 + - - +
2045A THR* 4.0 1.8 - - - +
2047A MET* 1.3 76.5 - - + +
2049A LEU* 1.3 61.8 + - - +
2051A ALA* 3.4 5.7 + - - +
2052A GLN* 3.2 26.5 + - - +
2172A PHE* 4.5 6.5 - - + -
2173A VAL 6.0 0.2 - - - +
2175A PRO* 5.3 2.7 - - + -
2183A TYR* 4.1 21.5 + - + -
2186A LEU* 4.0 25.4 - - + -
2201A LEU* 4.5 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2049 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2031A LEU* 3.7 20.9 - - + -
2032A VAL* 5.6 2.2 - - + +
2045A THR* 3.1 33.8 + - + +
2046A VAL* 3.1 7.9 + - - +
2048A LEU* 1.3 76.3 - - - +
2050A GLU* 1.3 64.2 + - - +
2052A GLN* 3.3 21.0 + - - +
2053A ALA* 3.2 19.8 + - - +
2058A ILE* 3.5 27.9 - - + +
2077A LEU 4.3 17.7 - - - +
2078A ILE* 4.6 6.1 - - + -
2079A ASP* 5.2 5.4 - - - +
2082A ASP* 5.4 4.3 - - - +
2086A ILE* 3.6 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2050 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2046A VAL* 2.8 29.3 + - + +
2047A MET* 3.4 12.0 + - - +
2049A LEU* 1.3 77.9 - - - +
2051A ALA* 1.3 60.5 + - - +
2053A ALA 3.5 0.7 + - - -
2054A ALA* 3.1 24.8 + - - +
2085A GLN* 3.2 37.3 + - + +
2086A ILE* 4.9 5.6 - - + +
2089A ALA* 3.6 24.9 - - + +
2120A THR* 3.7 9.5 - - - +
2123A ARG* 3.1 42.1 + - + +
2124A LEU* 3.7 7.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2051 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2047A MET 3.1 12.8 + - - +
2048A LEU 3.6 8.5 - - - +
2049A LEU 3.2 0.2 - - - -
2050A GLU* 1.3 76.0 - - - +
2052A GLN* 1.3 56.8 + - - +
2054A ALA* 3.3 2.6 + - - -
2055A THR* 2.6 38.7 + - - +
2124A LEU* 5.2 1.6 - - - -
2127A ALA* 3.7 19.3 - - + -
2172A PHE* 4.1 4.9 - - + -
2183A TYR* 3.6 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2052 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2017A SER* 4.1 11.8 + - - +
2018A ILE 2.7 28.9 + - - +
2019A ALA* 3.2 25.3 + - - +
2031A LEU* 3.4 18.3 - - - +
2048A LEU 3.2 11.5 + - - +
2049A LEU* 3.6 22.1 - - - +
2050A GLU 3.3 0.2 - - - -
2051A ALA* 1.3 78.2 - - - +
2053A ALA* 1.3 55.5 + - - +
2055A THR* 3.3 6.2 + - - -
2056A GLY 3.2 8.5 + - - -
2057A GLY 2.7 39.8 + - - +
2058A ILE* 3.7 5.8 - - - +
2059A ILE* 3.1 27.5 + - + +
2183A TYR* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2053 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1972A ARG* 5.4 0.5 + - - -
2049A LEU 3.2 13.1 + - - +
2050A GLU 3.9 4.3 - - - +
2051A ALA 3.3 0.2 - - - -
2052A GLN* 1.3 78.8 - - - +
2054A ALA* 1.3 56.6 + - - +
2055A THR 3.4 0.2 - - - -
2056A GLY 4.7 0.2 - - - -
2057A GLY* 3.9 14.7 + - - -
2058A ILE* 3.8 15.2 - - + +
2069A VAL* 4.7 1.6 - - + -
2086A ILE* 3.9 14.6 - - + +
2089A ALA* 3.8 2.5 - - + -
2090A GLU* 3.6 37.9 - - + +
2093A ILE* 3.5 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2054 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2050A GLU 3.1 17.7 + - - +
2051A ALA* 3.8 5.6 - - - +
2052A GLN 3.1 0.6 - - - -
2053A ALA* 1.3 77.5 - - - +
2055A THR* 1.3 60.5 + - + +
2089A ALA 3.6 10.1 - - - +
2092A ALA* 3.7 11.9 - - + -
2093A ILE* 3.4 10.5 - - - +
2124A LEU* 3.7 31.6 - - + +
2128A GLN* 3.0 27.3 + - - +
2135A VAL* 4.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2055 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1971A LEU* 3.9 10.9 - - - +
2013A ARG 4.2 8.7 - - - +
2014A GLY* 4.8 1.7 - - - -
2017A SER* 3.4 22.1 + - - -
2051A ALA 2.6 22.4 + - - +
2052A GLN 3.3 5.4 + - - -
2054A ALA* 1.3 84.5 - - - +
2056A GLY* 1.3 54.7 + - - +
2066A LYS* 5.1 1.0 + - - -
2093A ILE* 3.6 4.9 - - - -
2127A ALA* 3.5 24.9 - - + +
2128A GLN* 3.9 6.7 - - + +
2131A SER* 3.5 27.4 - - - +
2142A PHE* 3.9 15.9 - - + -
2183A TYR* 6.1 0.2 - - + -
----------------------------------------------------------
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