Contacts of the strand formed by residues 104 - 109 (chain C) in PDB entry 2E52
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 GLY 104 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ALA 3.3 10.5 - - - -
97C LEU* 3.8 13.7 - - - -
103C TYR* 1.3 78.8 - - - +
105C LEU* 1.3 61.7 + - - +
136C LYS* 3.7 11.9 - - - -
137C ASP* 3.0 27.9 + - - +
138C TYR* 3.1 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PHE* 4.0 25.1 - - + -
80C LEU* 4.3 9.4 - - + -
95C ILE* 3.4 9.8 - - - +
96C ALA* 2.8 52.0 + - + +
103C TYR* 4.6 2.5 - - + -
104C GLY* 1.3 75.5 - - - +
106C VAL* 1.3 74.5 - - - +
107C ALA* 4.1 4.9 - - + +
136C LYS* 3.7 8.7 - - - +
138C TYR* 3.3 22.2 - - + +
140C VAL* 4.1 7.2 - - + -
192C TRP* 3.8 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 5.0 1.8 - - + -
92C GLY* 3.9 26.0 - - - +
94C VAL 3.4 12.8 - - - +
95C ILE* 3.8 15.3 - - + -
105C LEU* 1.3 78.5 - - - +
107C ALA* 1.3 66.7 + - - +
129C LEU* 4.2 9.4 - - + -
132C TRP 4.2 9.2 - - - +
133C ARG* 3.3 40.8 - - + +
136C LYS* 4.2 0.8 - - + +
138C TYR 2.9 10.3 + - - +
139C ALA* 3.3 10.8 - - + -
140C VAL* 2.8 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 3.9 11.9 - - + -
75C PHE* 3.8 29.4 - - + -
93C ASP* 3.0 8.2 + - - +
94C VAL* 2.8 38.9 + - + +
105C LEU* 4.1 3.1 - - + -
106C VAL* 1.3 79.3 - - - +
108C ASP* 1.3 60.2 + - - +
129C LEU* 4.7 1.3 - - - -
140C VAL* 3.1 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 3.8 3.0 - - - +
91C ALA 4.6 0.3 - - - +
92C GLY* 3.6 7.1 - - - -
93C ASP* 3.2 33.8 + - - +
107C ALA* 1.3 72.4 - - - +
109C ALA* 1.3 56.7 + - - +
110C LYS* 3.6 26.2 + - + +
124C PHE 5.2 2.8 - - - +
125C LYS* 5.3 0.5 - - - +
129C LEU* 4.0 27.3 - - + +
132C TRP* 3.8 20.1 - - - -
140C VAL 3.0 6.5 + - - +
141C LEU* 4.6 4.0 - - + +
142C THR* 2.8 34.7 + - - -
5F A 4.0 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C SER* 5.1 4.0 + - - +
67C GLY* 3.8 14.6 - - - +
68C ASP* 3.5 19.3 - - - +
71C LEU* 3.9 10.3 - - + +
93C ASP* 3.0 18.7 + - - +
108C ASP* 1.3 73.6 - - - +
110C LYS* 1.3 63.9 + - - +
111C SER* 5.5 0.4 - - - -
142C THR 3.6 3.8 - - - -
169C TRP* 3.6 26.5 - - + -
5F A 4.3 3.8 + - - +
6F G 4.1 6.8 + - - -
----------------------------------------------------------
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