Contacts of the helix formed by residues 78 - 86 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 4.0 1.1 - - - -
33A ARG* 4.2 10.5 - - - +
90A ASP* 3.3 36.8 - - - +
91A GLY* 4.3 7.9 - - - -
77B ALA* 1.3 85.8 - - - +
79B VAL* 1.3 53.6 + - - +
80B LYS* 3.8 7.2 + - - +
81B GLU* 3.0 35.1 + - - +
82B TYR* 2.9 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 4.5 3.4 - - + -
26A LEU* 3.9 25.1 - - + -
29A SER* 3.9 10.5 - - - +
79A VAL* 3.9 35.7 - - + +
83A THR* 3.4 25.8 - - - +
90A ASP* 2.9 24.2 + - - +
25B PHE* 4.2 15.7 - - + -
78B THR* 1.3 68.9 - - - +
80B LYS* 1.3 68.6 + - + +
82B TYR* 3.8 8.2 - - - +
83B THR* 3.0 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASP* 5.1 0.6 + - - -
78B THR* 3.3 7.7 + - - +
79B VAL* 1.3 85.0 - - + +
81B GLU* 1.3 65.3 + - + +
83B THR* 3.4 5.6 + - - -
84B GLU* 3.1 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 6.0 0.2 - - - -
22B SER* 4.6 0.2 - - - -
76B VAL* 3.8 32.3 - - + +
77B ALA* 3.4 6.8 + - - +
78B THR* 3.0 41.3 + - - +
80B LYS* 1.3 78.4 - - + +
82B TYR* 1.3 60.7 + - - +
84B GLU* 4.4 6.3 - - - +
85B HIS* 2.8 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 4.4 6.4 + - - -
32A HIS* 5.0 2.3 - - - +
36A TRP* 3.4 31.9 - + - -
21B LEU* 4.2 11.2 - - + -
22B SER* 3.4 29.1 - - - +
25B PHE* 3.4 53.6 - + + -
26B LEU* 4.2 15.5 - - + -
76B VAL* 3.6 27.4 - - + -
77B ALA* 3.4 11.1 - - - -
78B THR 2.9 31.6 + - - +
79B VAL* 3.8 9.2 - - - +
80B LYS 3.4 0.4 - - - -
81B GLU* 1.3 71.4 - - - +
83B THR* 1.3 63.5 + - - +
86B ALA* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.4 22.2 - - - +
26B LEU* 4.3 12.0 - - + +
79B VAL 3.0 20.6 + - - -
80B LYS* 3.6 7.3 - - - -
81B GLU 3.2 0.2 - - - -
82B TYR* 1.3 79.9 - - - +
84B GLU* 1.3 65.0 + - + +
86B ALA* 4.0 10.4 + - - +
88B ILE 5.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LYS* 3.1 51.4 + - - +
81B GLU* 3.2 6.6 + - - +
83B THR* 1.3 80.0 - - + +
85B HIS* 1.3 68.4 + - + +
86B ALA 4.6 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASN 5.4 0.8 + - - -
18B ASN* 4.1 21.1 - - + +
19B THR* 3.3 27.8 + - - +
22B SER* 3.4 15.0 - - - +
76B VAL* 3.8 28.0 - - + +
81B GLU* 2.8 38.4 + - + +
84B GLU* 1.3 81.1 - - + +
86B ALA* 1.3 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR 4.1 0.9 - - - -
22B SER* 3.6 14.8 - - - -
23B ASN* 3.2 15.3 - - - +
26B LEU* 3.6 11.9 - - + -
82B TYR 3.0 18.9 + - - +
83B THR 4.0 6.6 + - - +
84B GLU 3.7 3.0 - - - +
85B HIS* 1.3 80.1 - - - +
87B SER* 1.3 60.8 + - - +
88B ILE 3.3 20.2 - - - +
----------------------------------------------------------
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