Contacts of the helix formed by residues 156 - 165 (chain C) in PDB entry 2PK2
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 HIS 156 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ASP* 5.2 4.2 + - - +
152C HIS 4.6 1.3 + - - -
153C PRO* 3.9 14.1 - - + -
154C HIS 2.8 5.0 + - - -
155C THR* 1.3 92.1 + - - +
157C VAL* 1.3 54.7 + - - +
158C VAL 3.0 2.0 - - - -
159C LYS* 2.6 17.5 + - + +
160C CYS* 2.5 38.4 + - - +
193C PRO* 3.6 12.2 - - + +
194C PRO* 3.6 38.9 - - + +
197C ALA* 3.7 7.9 - - - +
225C VAL* 3.1 37.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C PRO 4.5 6.5 - - - +
154C HIS* 2.5 26.6 + - + +
156C HIS* 1.3 75.2 + - - +
158C VAL* 1.3 63.8 + - + +
159C LYS 3.5 0.2 + - - -
160C CYS* 3.9 4.7 + - - +
161C THR* 3.6 16.5 + - - -
174C SER* 3.6 39.1 - - - +
175C TYR 4.4 1.3 - - - +
178C ALA* 5.5 0.4 - - + -
197C ALA* 3.3 44.4 - - + +
200C CYS* 4.8 4.9 - - + -
201C ILE* 3.6 22.0 - - + +
225C VAL* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C HIS* 2.6 42.1 + - + +
155C THR* 3.9 7.2 - - - +
157C VAL* 1.3 77.0 - - + +
159C LYS* 1.3 53.0 - - - +
160C CYS 3.7 0.2 - - - -
161C THR* 4.6 3.5 - - - -
162C GLN* 2.7 32.3 + - - +
175C TYR* 4.8 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C THR* 3.0 26.2 - - - +
156C HIS* 2.6 23.4 + - + +
158C VAL* 1.3 71.6 - - - +
160C CYS* 1.3 57.8 + - - +
162C GLN* 2.9 11.9 - - - +
163C LEU* 2.8 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C HIS* 2.5 18.9 + - + +
157C VAL* 3.9 1.1 + - - +
159C LYS* 1.3 75.4 - - - +
161C THR* 1.3 62.9 + - - +
163C LEU* 4.2 1.7 - - - -
164C VAL* 2.8 52.7 + - - +
201C ILE* 4.3 21.8 - - + -
212C ILE* 6.0 2.7 - - - -
221C TRP* 4.7 15.9 - - - -
224C TYR* 4.6 21.1 - - + -
225C VAL* 4.9 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C VAL 3.6 15.6 + - - -
158C VAL* 4.7 3.1 - - - -
159C LYS 3.4 0.4 - - - -
160C CYS* 1.3 74.7 - - - +
162C GLN* 1.3 72.3 + - + +
164C VAL* 2.9 7.6 - - - +
165C ARG 2.6 31.0 + - - -
166C ALA* 2.9 20.7 + - + +
167C SER 5.0 1.1 - - - +
171C ALA* 3.1 38.5 + - + +
174C SER* 4.8 1.2 + - - -
201C ILE* 5.2 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C VAL* 2.7 29.6 + - - +
159C LYS* 2.9 27.6 - - - +
161C THR* 1.3 82.5 - - + +
163C LEU* 1.3 64.7 + - + +
165C ARG* 2.5 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LYS* 2.8 40.8 - - + +
160C CYS* 4.5 2.9 - - - +
161C THR 3.6 0.2 - - - -
162C GLN* 1.3 84.4 + - + +
164C VAL* 1.3 61.3 + - + +
165C ARG* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C CYS* 2.8 50.7 - - - +
161C THR* 2.9 11.4 - - - +
162C GLN 3.0 0.4 - - - -
163C LEU* 1.3 80.8 - - + +
165C ARG* 1.3 74.5 + - - +
166C ALA* 3.8 11.7 - - + +
201C ILE* 6.4 1.3 - - + -
212C ILE* 4.8 26.7 - - + +
221C TRP* 5.7 4.0 - - + -
224C TYR* 5.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C THR 2.6 5.8 + - - -
162C GLN* 2.5 25.7 + - - +
163C LEU* 3.0 26.3 + - - +
164C VAL* 1.3 79.0 + - - +
166C ALA* 1.3 66.7 + - - +
167C SER* 5.1 0.2 + - - -
210C TRP* 5.4 6.9 + - - -
212C ILE* 5.6 2.2 - - - +
----------------------------------------------------------
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