Contacts of the helix formed by residues 78 - 86 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C SER* 4.0 0.7 - - - -
33C ARG* 4.2 11.0 - - - +
90C ASP* 3.4 34.5 - - - +
91C GLY* 4.5 7.9 - - - -
92C GLY 6.1 0.2 - - - +
77D ALA* 1.3 84.8 - - - +
79D VAL* 1.3 60.7 + - - +
80D LYS* 3.8 7.8 + - - +
81D GLU* 3.1 32.7 + - - +
82D TYR* 2.9 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PHE* 4.7 3.1 - - + -
26C LEU* 3.9 19.1 - - + -
29C SER* 4.0 11.9 - - - +
79C VAL* 3.9 35.5 - - + +
83C THR* 3.6 24.2 - - - +
90C ASP* 2.9 27.8 + - - +
25D PHE* 4.1 17.3 - - + -
78D THR* 1.3 69.7 - - - +
80D LYS* 1.3 61.3 + - + +
82D TYR* 3.8 8.8 - - + +
83D THR* 2.9 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ASP* 5.2 0.6 + - - -
78D THR* 3.2 7.9 + - - +
79D VAL* 1.3 83.1 - - + +
81D GLU* 1.3 59.2 + - + +
83D THR* 3.4 6.8 + - - -
84D GLU* 3.0 60.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ARG* 5.9 0.2 - - - -
22D SER* 4.5 0.2 - - - -
76D VAL* 3.7 31.1 - - + +
77D ALA* 3.1 19.9 + - - +
78D THR* 3.1 28.6 + - - +
80D LYS* 1.3 78.2 - - + +
82D TYR* 1.3 65.4 + - - +
84D GLU* 3.2 7.0 + - - +
85D HIS* 3.0 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C SER* 4.4 5.5 + - - -
32C HIS* 4.9 2.4 - - - +
36C TRP* 3.4 21.5 - - - -
21D LEU* 4.3 11.9 - - + -
22D SER* 3.5 28.4 - - - +
25D PHE* 3.4 53.2 - + + -
26D LEU* 4.2 16.8 - - + -
76D VAL* 3.6 27.8 - - + -
77D ALA* 3.4 19.6 - - - -
78D THR 2.9 28.8 + - - -
79D VAL* 3.8 13.7 - - - +
81D GLU* 1.3 73.0 - - - +
83D THR* 1.3 62.5 + - - +
86D ALA* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C VAL* 3.5 22.6 - - + +
26D LEU* 4.4 12.1 - - + +
79D VAL 2.9 22.4 + - - -
80D LYS* 3.7 6.5 - - - -
82D TYR* 1.3 76.7 - - - +
84D GLU* 1.3 64.4 + - + +
85D HIS 3.4 0.2 + - - -
86D ALA* 3.9 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LYS* 3.0 52.9 + - + +
81D GLU* 3.2 8.7 + - - +
83D THR* 1.3 78.6 - - + +
85D HIS* 1.3 69.5 + - + +
86D ALA 4.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ASN 5.8 0.6 + - - -
18D ASN* 4.2 14.7 - - + +
19D THR* 2.9 33.2 + - - +
22D SER* 3.4 15.7 - - - +
76D VAL* 3.9 25.6 - - + +
81D GLU* 3.0 36.6 + - - +
84D GLU* 1.3 87.5 + - + +
86D ALA* 1.3 66.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D THR* 4.1 1.6 - - - -
22D SER* 3.6 14.5 - - - -
23D ASN* 3.4 14.1 - - - +
26D LEU* 3.6 14.6 - - + -
82D TYR 3.1 19.1 + - - +
83D THR 3.9 8.6 + - - +
84D GLU 3.8 1.4 - - - +
85D HIS* 1.3 80.5 - - - +
87D SER* 1.3 59.2 + - - +
88D ILE 3.6 17.5 - - - +
----------------------------------------------------------
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