Contacts of the helix formed by residues 178 - 189 (chain C) in PDB entry 1C72
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 178 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C GLN* 1.3 76.5 - - - +
179C ASN* 1.3 65.6 + - - -
180C LEU 3.2 2.7 - - - -
181C SER* 3.0 14.8 + - - -
182C GLN* 3.1 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C SER* 2.7 54.5 + - - +
141C LEU* 3.7 15.6 - - + +
142C GLY* 3.1 30.4 + - - +
178C GLY* 1.3 70.8 - - - -
180C LEU* 1.3 66.4 + - - +
182C GLN* 3.6 20.6 - - + +
183C PHE* 3.0 26.7 + - - +
186C ARG* 5.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C LEU* 3.6 40.4 - - + +
137C LEU* 4.3 19.5 - - + +
138C SER* 4.3 5.8 - - - +
141C LEU* 4.1 19.5 - - + -
147C PHE* 4.4 8.7 - - + -
163C LEU* 4.0 25.9 - - + +
175C GLU 4.1 15.7 - - - +
176C LEU* 4.0 15.3 - - + +
177C GLN 5.3 0.4 + - - +
178C GLY 3.2 0.8 - - - -
179C ASN* 1.3 87.2 + - - +
181C SER* 1.3 65.2 + - - +
183C PHE* 3.5 4.5 + - + +
184C LEU* 3.3 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU 3.3 20.1 + - - -
177C GLN* 3.8 16.7 + - - +
178C GLY 3.0 16.0 + - - -
180C LEU* 1.3 75.4 - - - +
182C GLN* 1.3 66.4 + - - +
184C LEU* 3.3 10.6 + - - +
185C GLN* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C GLY* 3.1 13.7 + - - +
179C ASN* 3.6 27.5 - - - +
181C SER* 1.3 76.7 - - - +
183C PHE* 1.3 61.7 + - - +
185C GLN* 3.5 18.0 - - - +
186C ARG* 3.1 47.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 4.1 12.3 - - + -
145C SER 4.3 9.0 - - - -
146C TRP* 3.4 39.0 - + - -
147C PHE* 3.8 33.9 - + - -
156C ASP* 3.5 28.7 - - + -
159C ALA* 4.1 1.6 - - + -
160C TYR* 3.9 28.5 - + + -
163C LEU* 4.0 7.9 - - + -
179C ASN 3.0 16.4 + - - +
180C LEU* 3.6 6.1 - - + +
181C SER 3.1 0.4 - - - -
182C GLN* 1.3 76.6 - - - +
184C LEU* 1.3 76.9 + - + +
186C ARG* 3.3 9.4 + - - +
187C PHE* 3.1 24.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C TYR* 3.5 29.9 - - + +
163C LEU* 3.7 39.0 - - + +
164C ASP 4.8 0.7 - - - +
167C ARG* 3.7 41.3 - - + +
176C LEU* 4.5 15.0 - - + -
180C LEU 3.3 15.5 + - - +
181C SER* 3.3 9.4 + - - +
183C PHE* 1.3 82.4 - - + +
185C GLN* 1.3 57.5 + - - +
187C PHE* 3.3 2.9 + - - +
188C GLU* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C SER* 3.1 17.6 + - - +
182C GLN* 3.5 25.4 + - - +
184C LEU* 1.3 75.4 - - - +
186C ARG* 1.3 58.4 + - - +
188C GLU* 3.2 15.4 + - - +
189C ALA* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 5.4 2.4 - - - +
144C ARG 4.1 7.5 + - - -
145C SER* 2.8 47.0 + - - +
146C TRP* 3.8 24.0 - - + -
179C ASN 5.1 1.0 + - - -
182C GLN* 3.1 46.5 + - - +
183C PHE* 3.3 26.1 + - - +
185C GLN* 1.3 77.2 - - - +
187C PHE* 1.3 60.1 + - - +
189C ALA* 3.5 13.3 + - - +
190C LEU* 3.6 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LEU* 4.2 9.6 - - + -
146C TRP* 4.2 20.4 - + + -
152C LEU* 4.9 2.0 - - + -
156C ASP 4.2 16.2 - - - -
157C PHE* 3.6 53.2 - + - -
160C TYR* 3.5 46.7 - + + -
183C PHE* 3.1 20.0 + + + +
184C LEU 3.6 3.8 - - - +
186C ARG* 1.3 75.4 - - - +
188C GLU* 1.3 62.6 + - - +
190C LEU* 3.3 29.5 + - + +
193C ILE* 3.5 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C TYR* 2.9 32.2 + - + +
167C ARG* 3.0 34.5 + - - -
184C LEU 3.0 21.3 + - - +
185C GLN* 3.2 16.7 + - - +
187C PHE* 1.3 76.2 - - - +
189C ALA* 1.3 57.9 + - - +
190C LEU 3.3 0.2 - - - -
193C ILE* 4.1 7.6 - - - -
194C SER* 3.1 29.1 - - - -
197C MET* 3.6 21.6 - - - +
204C LYS* 5.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C GLN 2.8 17.2 + - - +
186C ARG* 3.9 9.4 - - - +
187C PHE 3.2 0.8 - - - -
188C GLU* 1.3 74.6 - - - +
190C LEU* 1.3 66.1 + - - +
191C GLU* 3.4 2.8 + - - -
194C SER* 3.7 5.6 + - - -
----------------------------------------------------------
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