Contacts of the helix formed by residues 167 - 174 (chain C) in PDB entry 3PRJ
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 167 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO* 5.6 1.8 - - - -
164C ALA* 3.1 18.1 + - - +
165C GLU 3.1 1.4 + - - -
166C GLY* 1.3 85.7 - - - +
168C ALA* 1.3 61.2 + - - +
169C ILE 3.3 2.7 - - - -
170C LYS* 3.7 23.5 + - + +
171C ASP* 3.0 40.6 + - - -
339C LYS* 4.5 6.8 + - - +
341C ASP* 5.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TYR 5.4 0.2 - - - +
18C PRO* 4.4 11.9 - - + -
54C GLU* 2.6 34.7 + - + +
55C PRO 5.6 0.4 + - - -
163C LEU* 3.7 26.5 - - + -
164C ALA 3.8 4.9 - - - +
167C THR* 1.3 73.1 - - - +
169C ILE* 1.3 58.2 + - + +
171C ASP* 3.7 2.8 - - - +
172C LEU* 2.8 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PRO* 4.8 7.0 - - + -
22C VAL* 3.8 21.8 - - + -
54C GLU* 4.3 3.1 + - + -
55C PRO 3.5 25.0 + - - +
56C GLY* 3.9 16.2 - - - +
57C LEU* 3.9 28.3 - - + +
60C VAL* 4.0 23.3 - - + -
167C THR 3.3 0.4 - - - -
168C ALA* 1.3 76.9 - - + +
170C LYS* 1.3 68.7 + - - +
171C ASP 3.1 0.2 + - - -
172C LEU* 3.2 3.1 + - - +
173C LYS* 3.1 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C THR* 3.7 25.4 + - + +
169C ILE* 1.3 78.6 - - - +
171C ASP* 1.3 68.2 + - - +
173C LYS* 4.0 5.2 - - - +
174C ASN* 3.1 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C PHE 4.8 1.8 - - - +
163C LEU* 4.0 15.6 - - - -
164C ALA* 3.1 27.2 + - - +
167C THR* 3.0 38.8 + - - +
168C ALA 3.7 3.6 - - - +
170C LYS* 1.3 87.6 + - - +
172C LEU* 1.3 61.8 + - - +
174C ASN 4.7 3.1 - - - +
175C PRO* 3.1 33.0 - - + +
260D ARG* 5.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PRO* 3.8 16.8 - - + +
19C THR* 3.8 40.8 - - - +
22C VAL* 4.0 20.0 - - + -
161C GLU* 3.5 26.7 - - - +
163C LEU* 3.9 16.2 - - + -
168C ALA 2.8 26.0 + - - +
169C ILE* 3.2 3.6 + - - +
171C ASP* 1.3 76.3 - - - +
173C LYS* 1.3 59.6 + - - +
175C PRO* 3.3 10.4 - - - +
199C TYR* 6.3 2.2 - - + -
202C TRP* 2.9 28.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C VAL* 4.4 11.7 - - + -
25C HIS* 4.1 23.4 + - - -
26C MET* 3.7 26.4 - - + +
60C VAL* 4.3 12.0 - - - +
169C ILE* 3.1 35.4 + - + +
170C LYS* 4.0 5.4 - - - +
172C LEU* 1.3 77.7 - - - +
174C ASN* 1.3 59.3 + - + +
175C PRO* 3.3 4.3 - - - +
202C TRP* 3.2 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LYS* 3.1 15.2 + - + +
171C ASP* 3.5 6.0 - - - +
173C LYS* 1.3 79.6 - - + +
175C PRO* 1.4 67.3 - - - +
176C ASP* 3.6 4.7 + - - +
204C PRO* 5.9 1.7 - - - +
207C LYS* 3.1 26.8 + - - +
----------------------------------------------------------
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