Contacts of the helix formed by residues 165 - 175 (chain C) in PDB entry 2A3W
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 PRO 165 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C VAL 3.6 6.3 - - - +
164C LEU* 1.3 89.6 - - + +
166C PRO* 1.3 77.4 - - + +
167C GLU* 3.2 20.9 - - + +
168C ASN* 3.0 43.6 + - - +
169C ILE* 3.2 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 4.0 21.3 - - + -
106C GLU* 6.1 0.7 - - - +
108C TRP* 3.9 34.7 - - + -
164C LEU 4.5 1.1 - - - +
165C PRO* 1.3 86.2 - - + +
167C GLU* 1.3 63.5 + - - +
169C ILE* 3.1 8.3 + - + +
170C LEU* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C PRO* 3.6 24.4 - - + +
166C PRO* 1.3 84.1 - - - +
168C ASN* 1.3 70.7 + - - +
170C LEU* 3.5 8.4 + - - +
171C SER* 3.0 30.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C TRP* 5.6 0.2 - - - -
164C LEU* 3.6 30.4 - - + +
165C PRO* 3.0 31.3 + - - +
167C GLU* 1.3 82.9 - - - +
169C ILE* 1.3 64.6 + - - +
171C SER* 3.7 8.1 + - - -
172C ALA* 3.2 21.7 + - - +
177C PRO* 5.3 0.9 - - - +
178C LEU* 3.5 42.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
34C THR* 3.8 23.1 - - + -
93C HIS* 4.5 1.9 - - + -
95C CYS* 3.8 28.3 - - + -
96C VAL 6.2 0.2 - - - -
97C SER* 5.7 2.2 - - - -
108C TRP* 3.7 52.3 - - + +
111C GLY* 4.9 4.7 - - - -
164C LEU* 3.9 18.4 - - + +
165C PRO 3.2 15.4 + - - +
166C PRO* 3.1 11.8 + - + +
168C ASN* 1.3 75.8 - - - +
170C LEU* 1.3 68.6 + - + +
172C ALA* 3.1 8.6 + - - +
173C TYR* 3.0 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C TRP* 4.5 11.2 - - + -
111C GLY* 3.5 36.3 - - - +
166C PRO* 2.9 23.1 + - + +
167C GLU* 3.8 8.1 - - - +
169C ILE* 1.3 76.9 - - + +
171C SER* 1.3 57.6 + - - +
173C TYR* 3.1 10.2 + - + +
174C GLN* 2.8 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLU 3.0 20.0 + - - -
168C ASN* 3.7 10.8 + - - -
169C ILE 3.2 0.2 - - - -
170C LEU* 1.3 78.0 - - - +
172C ALA* 1.3 61.3 + - - +
174C GLN* 3.3 10.1 + - - -
175C GLY 3.1 5.0 + - - -
176C THR* 2.8 51.8 + - - -
178C LEU* 4.7 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C CYS* 4.2 17.0 - - + -
38C ARG* 3.2 11.3 + - - -
93C HIS* 3.7 17.8 + - + +
156C ASP* 5.9 0.9 - - - +
158C TYR* 5.9 0.7 - - + -
160C TRP* 4.4 6.7 - - + -
168C ASN 3.2 13.3 + - - +
169C ILE 3.1 10.1 + - - +
171C SER* 1.3 75.0 - - - +
173C TYR* 1.3 63.1 + - - +
175C GLY* 3.2 11.4 + - - -
177C PRO* 3.9 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 2.9 30.9 + - - -
93C HIS* 3.5 36.9 - + + +
110C ASN* 3.4 50.0 + - + +
111C GLY* 4.0 12.3 - - - +
169C ILE* 3.0 11.7 + - + +
170C LEU* 3.4 15.0 - - + +
172C ALA* 1.3 76.5 - - - +
174C GLN* 1.3 67.7 + - + +
175C GLY 3.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 4.4 0.7 - - - -
170C LEU* 2.8 35.5 + - - +
171C SER* 3.9 11.5 + - - +
172C ALA 3.3 0.2 - - - -
173C TYR* 1.3 88.7 - - + +
175C GLY* 1.3 58.7 + - - +
176C THR* 3.6 8.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 3.9 10.5 - - - -
156C ASP* 5.8 1.6 - - - -
171C SER 3.1 1.8 + - - -
172C ALA 3.2 11.1 + - - -
173C TYR 3.2 1.2 - - - -
174C GLN* 1.3 78.1 - - - +
176C THR* 1.3 65.9 + - - +
177C PRO* 3.3 11.6 - - - +
----------------------------------------------------------
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