Contacts of the helix formed by residues 132 - 139 (chain C) in PDB entry 2WOE
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 CYS 132 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 4.8 0.4 - - - +
128C ALA 3.3 19.5 - - - -
129C ALA* 3.6 13.2 + - - +
130C MET 3.6 0.8 - - - -
131C ARG* 1.3 76.5 - - - +
133C LEU* 1.3 66.1 - - - +
134C PRO* 3.4 0.4 - - - -
135C ALA* 3.1 16.3 - - - +
136C ALA* 3.3 10.4 - - - -
150C VAL* 3.9 12.5 - - + -
153C GLN* 3.3 19.3 + - - -
167C CYS* 3.4 38.8 - - - +
170C LEU* 5.3 6.5 - - + -
171C GLY* 5.4 3.4 - - - +
253C MET* 5.9 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ALA* 3.6 19.7 - - + +
14C PHE* 3.4 53.6 - - + +
17C LEU* 4.8 11.0 - - + -
65C SER* 5.3 0.4 - - - +
130C MET 5.4 0.8 + - - -
131C ARG 3.4 0.4 - - - -
132C CYS* 1.3 76.8 + - - +
134C PRO* 1.4 70.7 - - + +
136C ALA* 3.0 8.0 + - - +
137C LEU* 2.9 37.6 + - + +
174C VAL* 3.9 18.4 - - + -
253C MET* 3.7 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 4.3 10.8 - - + -
65C SER* 3.3 35.9 - - - +
68C LEU* 4.1 3.4 - - + -
69C GLY* 3.8 24.2 - - - +
72C LEU* 3.6 10.0 - - + +
131C ARG 3.4 15.9 - - - +
132C CYS 3.5 0.9 - - - -
133C LEU* 1.4 93.0 - - + +
135C ALA* 1.3 55.5 + - - +
137C LEU* 3.4 4.6 + - + +
138C ALA* 2.9 30.7 + - - +
287C LEU* 3.9 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 4.3 14.5 - - + +
72C LEU* 3.8 12.3 - - + +
78C LEU* 6.1 0.4 - - + -
132C CYS 3.1 10.0 - - - +
134C PRO* 1.3 75.1 - - - +
136C ALA* 1.3 62.3 + - - +
138C ALA* 3.7 1.7 + - - -
139C THR* 2.8 33.3 + - - +
146C LEU* 4.2 0.9 - - - +
149C TRP* 4.3 12.6 - - + +
150C VAL* 3.9 32.5 - - + +
153C GLN* 4.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C CYS 3.3 9.5 - - - -
133C LEU* 3.0 12.8 + - - +
135C ALA* 1.3 74.1 - - - +
137C LEU* 1.3 66.3 + - - +
139C THR* 3.2 4.3 + - - -
140C LEU* 3.5 2.0 + - - +
146C LEU* 3.7 12.5 - - + +
150C VAL* 4.4 0.6 - - + +
171C GLY* 4.1 17.9 - - - -
174C VAL* 3.9 29.8 - - + -
175C HIS* 2.6 29.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ALA* 4.1 25.1 - - + +
13C ALA* 4.9 0.2 - - + -
14C PHE* 4.2 20.4 - - + -
133C LEU* 2.9 43.4 + - + +
134C PRO* 3.8 6.1 - - + +
136C ALA* 1.3 75.6 - - - +
138C ALA* 1.3 62.9 + - - +
139C THR 3.1 1.4 + - - -
140C LEU* 3.3 17.9 + - + +
174C VAL* 4.3 1.3 - - + -
178C ILE* 3.4 32.8 - - + -
284C VAL* 4.7 7.9 - - + +
287C LEU* 3.9 25.2 - - + +
288C LEU* 5.4 2.9 - - + -
291C ALA* 3.3 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 4.2 8.1 - - + -
134C PRO 2.9 17.9 + - - +
135C ALA 4.1 1.3 - - - +
136C ALA 3.4 0.2 - - - -
137C LEU* 1.3 75.6 - - - +
139C THR* 1.3 58.0 + - - +
140C LEU 3.5 0.4 - - - -
142C HIS* 2.8 22.2 + - - -
149C TRP* 3.7 25.6 - - + -
287C LEU* 3.8 17.9 + - + +
290C LEU* 3.8 17.5 - - + +
291C ALA* 3.4 11.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ALA 2.8 23.6 + - - +
137C LEU 3.1 0.4 - - - -
138C ALA* 1.3 75.4 - - - +
140C LEU* 1.3 64.5 + - - +
141C GLY 3.3 2.7 - - - -
142C HIS* 3.2 31.7 + - + -
143C PRO 3.2 0.2 - - - -
145C ASP* 3.7 20.2 - - + +
146C LEU* 3.4 14.0 - - - +
149C TRP* 3.4 34.1 - - + -
175C HIS* 3.0 28.5 + - - -
----------------------------------------------------------
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