Contacts of the helix formed by residues 78 - 86 (chain A) in PDB entry 2CHP
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 THR 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA* 1.3 84.0 - - - +
79A VAL* 1.3 65.4 + - - +
80A LYS* 3.9 7.7 + - - +
81A GLU* 3.0 35.2 + - - +
82A TYR* 2.9 28.0 + - - -
29B SER* 4.1 0.9 - - - -
33B ARG* 4.2 12.3 - - - +
90B ASP* 3.4 35.2 - - - +
91B GLY* 4.4 8.5 - - - -
92B GLY 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 4.1 17.0 - - + -
78A THR* 1.3 73.4 - - - +
80A LYS* 1.3 65.8 + - + +
82A TYR* 3.6 7.2 - - - +
83A THR* 2.9 29.6 + - - -
25B PHE* 4.6 3.6 - - + -
26B LEU* 4.0 14.6 - - + -
29B SER* 3.9 13.5 - - - +
79B VAL* 3.9 36.9 - - + +
83B THR* 3.4 25.4 - - - +
90B ASP* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 3.9 6.5 + - - +
79A VAL* 1.3 85.6 - - + +
81A GLU* 1.3 63.6 + - + +
83A THR* 3.4 6.9 + - - -
84A GLU* 3.0 51.9 + - - +
90B ASP* 5.1 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 4.5 0.9 - - - -
76A VAL* 3.8 31.5 - - + +
77A ALA* 3.2 18.5 + - - +
78A THR* 3.0 30.2 + - - +
80A LYS* 1.3 78.6 - - + +
82A TYR* 1.3 61.6 + - - +
84A GLU* 3.1 8.5 + - - +
85A HIS* 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.2 11.9 - - + -
22A SER* 3.4 27.4 - - - -
25A PHE* 3.3 55.0 - + + -
26A LEU* 4.2 17.3 - - + -
76A VAL* 3.5 27.1 - - + -
77A ALA* 3.6 10.5 - - - -
78A THR 2.9 25.4 + - - -
79A VAL* 3.6 13.5 - - - +
81A GLU* 1.3 74.3 - - - +
83A THR* 1.3 58.9 + - - +
86A ALA* 2.9 37.2 + - - +
29B SER* 4.4 6.0 + - - -
32B HIS* 5.0 2.1 - - - +
36B TRP* 3.5 30.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.3 12.0 - - + +
79A VAL 2.9 19.6 + - - -
80A LYS* 3.6 7.6 - - - -
82A TYR* 1.3 78.9 - - - +
84A GLU* 1.3 65.3 + - + +
85A HIS 3.6 0.2 + - - -
86A ALA* 4.1 8.7 + - - +
88A ILE 5.5 0.9 - - - +
79B VAL* 3.4 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LYS* 3.0 59.9 + - + +
81A GLU* 3.1 10.4 + - - +
83A THR* 1.3 83.8 - - + +
85A HIS* 1.3 67.0 + - + +
86A ALA 3.7 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN 5.5 1.0 + - - -
18A ASN* 4.3 20.0 - - + +
19A THR* 3.3 26.6 + - - +
22A SER* 3.4 21.1 - - - +
76A VAL* 3.9 24.5 - - + +
81A GLU* 2.9 32.5 + - + +
84A GLU* 1.3 86.4 + - + +
86A ALA* 1.3 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR 4.2 1.1 - - - -
22A SER* 3.6 13.6 - - - +
23A ASN* 3.2 16.8 - - - +
26A LEU* 3.5 13.5 - - + -
82A TYR 2.9 19.0 + - - +
83A THR 4.1 7.1 + - - +
84A GLU 3.7 2.5 - - - +
85A HIS* 1.3 81.3 - - - +
87A SER* 1.3 60.8 + - - +
88A ILE 3.4 20.0 - - - +
----------------------------------------------------------
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