Contacts of the helix formed by residues 2078 - 2093 (chain A) in PDB entry 5XJY
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 LYS2078 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2076A ASP 3.7 0.2 - - - -
2077A PRO* 1.3 82.9 - - + +
2079A ALA* 1.3 55.6 + - - +
2080A ARG 3.2 6.1 + - - -
2081A ARG* 3.7 4.1 + - - +
2082A PHE* 2.8 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2079 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2048A GLY 6.0 2.0 - - - +
2052A LYS* 6.3 3.4 - - + -
2072A THR* 5.1 0.9 - - - -
2075A MET* 3.6 26.1 + - + +
2078A LYS* 1.3 77.8 - - + +
2080A ARG* 1.3 58.7 + - - +
2082A PHE* 3.7 9.0 - - - -
2083A LEU* 2.8 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2080 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2072A THR* 4.8 10.1 - - - -
2075A MET* 3.0 23.9 + - + +
2076A ASP* 5.1 4.9 - - - +
2078A LYS 3.2 1.0 + - - -
2079A ALA* 1.3 77.1 - - - +
2081A ARG* 1.3 53.5 + - - +
2083A LEU* 4.6 0.3 - - - +
2084A TRP* 2.7 37.1 + - - +
2106A GLU* 4.9 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2081 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2078A LYS 3.7 4.2 + - - +
2080A ARG* 1.3 77.8 - - - +
2082A PHE* 1.3 57.7 + - - +
2084A TRP* 3.8 7.1 - - - -
2085A ASN* 2.9 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2082 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2078A LYS* 2.8 30.8 + - + +
2079A ALA* 3.7 3.6 - - - -
2081A ARG* 1.3 76.0 - - - +
2083A LEU* 1.3 62.0 + - - +
2084A TRP 3.3 0.4 - - - -
2085A ASN* 3.1 8.1 + - - +
2086A CYS* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2083 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2052A LYS* 6.1 7.4 - - + -
2071A PRO* 5.0 11.7 - - + +
2072A THR* 6.0 0.4 - - - -
2075A MET* 5.9 0.2 - - + -
2079A ALA* 2.8 28.6 + - + +
2082A PHE* 1.3 75.5 - - - +
2084A TRP* 1.3 58.5 + - - +
2086A CYS* 3.1 10.6 + - - +
2087A ALA* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP2084 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2080A ARG 2.7 25.6 + - - +
2081A ARG* 3.8 6.3 - - - -
2083A LEU* 1.3 76.9 - - - +
2085A ASN* 1.3 57.6 + - - +
2087A ALA* 3.4 9.5 + - - +
2088A LEU* 2.9 25.1 + - - +
2106A GLU* 4.7 9.0 - - + +
2110A LEU* 4.3 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2085 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2081A ARG 2.9 23.0 + - - +
2082A PHE* 3.1 10.7 + - - +
2084A TRP* 1.3 75.7 - - - +
2086A CYS* 1.3 59.6 + - - +
2088A LEU* 3.2 10.3 + - + +
2089A SER* 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS2086 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2031A LYS 5.3 8.5 - - - +
2032A LEU* 5.7 5.8 - - - -
2082A PHE 2.9 12.9 + - - +
2083A LEU* 3.1 13.2 + - - +
2085A ASN* 1.3 75.0 - - - +
2087A ALA* 1.3 59.8 + - - +
2089A SER* 3.3 8.5 + - - +
2090A VAL* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2087 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2083A LEU 3.0 12.2 + - - +
2084A TRP* 3.5 12.3 - - - +
2085A ASN 3.3 0.2 - - - -
2086A CYS* 1.3 77.6 - - - +
2088A LEU* 1.3 56.3 + - - +
2090A VAL* 3.0 8.7 + - - +
2091A VAL* 2.9 31.9 + - - +
2097A VAL* 5.4 1.4 - - - +
2110A LEU* 6.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2088 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2084A TRP 2.9 15.1 + - - +
2085A ASN* 3.2 14.3 + - + +
2087A ALA* 1.3 75.0 - - - +
2089A SER* 1.3 53.0 + - - +
2091A VAL* 5.4 1.6 - - - -
2092A LYS* 2.6 42.6 + - + +
2110A LEU* 5.6 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2089 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2085A ASN 2.9 13.1 + - - -
2086A CYS* 3.6 11.0 - - - -
2087A ALA 3.2 0.2 - - - -
2088A LEU* 1.3 74.1 - - - +
2090A VAL* 1.3 60.4 + - - +
2092A LYS* 4.3 3.4 - - - -
2093A GLU* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2090 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2066A VAL* 6.1 3.4 - - + -
2086A CYS 3.0 14.5 + - - +
2087A ALA* 3.0 12.5 + - - +
2089A SER* 1.3 76.4 - - - +
2091A VAL* 1.3 62.7 + - - +
2093A GLU* 3.2 14.7 + - - +
2094A GLY 3.5 0.7 + - - -
2095A ARG* 3.3 26.9 + - + +
2097A VAL* 5.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2091 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1939A GLY 3.8 15.9 - - - +
1940A GLU 3.8 19.5 - - - +
1941A CYS* 4.1 18.6 - - + -
2087A ALA 2.9 16.2 + - - +
2088A LEU* 4.9 1.3 - - - +
2090A VAL* 1.3 74.9 - - - +
2092A LYS* 1.3 60.7 + - - +
2094A GLY* 3.2 12.1 + - - -
2095A ARG* 3.9 8.7 + - - +
2096A SER 4.1 2.6 + - - +
2097A VAL* 4.1 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2092 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2088A LEU* 2.6 25.4 + - + +
2089A SER* 4.2 3.6 - - - +
2091A VAL* 1.3 77.1 - - - +
2093A GLU* 1.3 58.4 + - - +
2094A GLY 3.2 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2093 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2089A SER 2.9 20.9 + - - +
2090A VAL* 3.2 6.8 + - - +
2092A LYS* 1.3 75.4 - - - +
2094A GLY* 1.3 59.9 + - - +
2095A ARG* 5.9 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