Contacts of the helix formed by residues 67 - 72 (chain C) in PDB entry 2EHO
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 ASP 67 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLU 3.9 5.8 + - - +
65C TRP 2.6 8.2 + - - +
66C MSE 1.3 74.0 - - - +
68C VAL* 1.3 77.0 + - - +
69C GLU* 3.9 7.8 + - - +
70C LYS* 2.9 55.7 + - + +
71C LEU* 2.9 17.8 + - - +
108C PRO* 6.1 0.9 - - - +
113C ILE* 4.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C MSE 3.8 3.4 + - - +
67C ASP* 1.3 81.3 + - - +
69C GLU* 1.3 63.2 + - + +
70C LYS 2.6 8.0 + - - -
71C LEU 2.9 0.3 + - - -
72C GLU* 2.8 31.5 + - - +
108C PRO* 4.1 21.5 - - + +
109C LYS* 4.7 4.9 - - + +
112C GLU* 2.8 40.2 - - + +
113C ILE* 4.6 16.1 - - + +
116C LEU* 3.3 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ASP* 3.9 7.2 + - - +
68C VAL* 1.3 83.2 - - + +
70C LYS* 1.3 60.7 + - - +
72C GLU* 3.7 25.0 - - - +
73C LYS* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLU* 2.9 46.4 + - - +
65C TRP* 4.0 9.0 - - - +
67C ASP* 2.9 47.7 + - + +
68C VAL 2.6 5.7 + - - -
69C GLU* 1.3 74.5 - - - +
71C LEU* 1.3 58.8 + - - +
73C LYS* 3.2 19.4 + - - +
74C MSE 3.3 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C TRP* 3.3 48.7 - - + +
66C MSE 4.3 2.7 - - + -
67C ASP 2.9 5.6 + - - +
68C VAL 2.9 4.6 + - - +
70C LYS* 1.3 69.0 - - - +
72C GLU* 1.3 53.7 + - - +
73C LYS 2.7 6.4 + - - -
74C MSE 2.4 52.9 + - + +
75C ARG* 2.8 14.7 + - - +
88C PRO* 4.4 2.9 - - + -
113C ILE* 3.3 29.2 - - + -
116C LEU* 3.6 14.8 - - + -
117C VAL* 3.9 18.4 - - + -
120C MSE 3.7 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C VAL* 2.8 31.3 + - - +
69C GLU* 3.7 23.3 - - - +
71C LEU* 1.3 77.0 - - - +
73C LYS* 1.3 55.6 + - - +
75C ARG* 3.7 14.4 - - - +
76C ASP* 2.9 25.2 - - - +
112C GLU* 4.4 5.0 - - - +
116C LEU* 3.3 22.9 - - + +
----------------------------------------------------------
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