Contacts of the helix formed by residues 176 - 188 (chain C) in PDB entry 3OFN
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 176 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C GLN* 3.6 3.6 - - - +
175C THR* 1.3 79.6 - - - +
177C LYS* 1.3 63.5 + - - +
178C THR 3.6 1.3 - - - -
179C ALA* 3.6 18.4 - - - +
180C VAL* 3.2 30.1 + - - +
354C LEU* 3.4 3.8 - - - +
359C PHE* 4.7 7.0 - - - -
365C PRO* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ILE* 3.6 21.4 - - + +
170C ILE* 4.0 2.9 - - - -
171C GLY 3.6 18.3 + - - +
172C ASP 2.7 32.5 + - - -
173C ARG* 3.7 9.7 - - - +
174C GLN 4.1 4.6 - - - +
175C THR* 3.9 8.0 + - - +
176C GLY* 1.3 74.1 - - - +
178C THR* 1.3 66.1 + - - +
180C VAL 3.4 8.0 + - - -
181C ALA* 3.6 8.0 + - - +
271C ASP* 4.8 1.6 - - - -
272C ASP* 5.5 2.0 - - - -
328C VAL* 3.7 25.7 - - + +
329C ILE 3.3 25.4 - - - +
330C GLU* 4.0 14.8 + - - +
354C LEU* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LYS* 1.3 75.4 - - - +
179C ALA* 1.3 55.7 + - - +
181C ALA* 3.2 4.5 + - + +
182C LEU* 2.7 43.7 + - + +
205C TYR* 3.4 22.7 + - + +
210C GLN* 4.9 1.2 + - - -
218C LEU* 4.0 22.0 - - + -
271C ASP* 2.7 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLY* 3.6 23.0 - - - +
178C THR* 1.3 79.3 - - - +
180C VAL* 1.3 60.7 + - + +
182C LEU* 3.9 9.6 - - - +
183C ASP* 2.7 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C THR* 6.0 0.9 - - + -
152C LEU* 3.8 29.0 - - + +
155C VAL* 4.8 0.7 - - + -
161C ILE* 6.2 1.6 - - + -
169C ILE* 3.9 19.1 - - + -
176C GLY 3.2 22.3 + - - +
177C LYS 3.9 4.9 - - - +
178C THR 3.2 0.6 - - - -
179C ALA* 1.3 80.1 - - + +
181C ALA* 1.3 62.2 + - - +
183C ASP* 3.5 0.5 + - - +
184C THR* 3.2 21.2 + - - +
326C LEU* 5.9 1.1 - - + -
352C ILE* 4.4 20.6 - - + -
354C LEU* 4.4 12.6 - - + -
365C PRO* 4.1 26.9 - - + -
367C ILE* 5.2 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ILE* 3.6 20.0 - - + -
177C LYS 3.6 4.0 + - - +
178C THR* 3.2 9.9 + - + +
180C VAL* 1.3 77.4 - - - +
182C LEU* 1.3 64.2 + - - +
184C THR* 3.4 5.5 + - - -
185C ILE* 3.2 27.0 + - - +
205C TYR* 5.8 1.1 - - + -
267C LEU* 5.4 0.2 - - - +
269C VAL* 3.9 24.5 - - + -
326C LEU* 3.9 22.0 - - + +
328C VAL* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C THR* 2.7 28.9 + - + +
179C ALA* 3.9 8.3 - - - +
181C ALA* 1.3 73.1 - - - +
183C ASP* 1.3 68.3 + - - +
185C ILE* 3.4 10.6 + - + +
186C LEU* 3.0 36.9 + - + +
205C TYR* 6.4 1.1 - - + -
218C LEU* 3.9 31.6 - - + -
221C THR* 4.6 20.0 - - + -
222C LEU* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C THR 3.3 12.0 - - - +
152C LEU* 3.6 28.5 - - + +
179C ALA* 2.7 26.0 + - - +
180C VAL 3.5 1.5 + - - +
181C ALA 3.3 0.2 - - - -
182C LEU* 1.3 85.8 - - - +
184C THR* 1.3 59.8 + - - +
186C LEU* 3.9 14.7 - - - +
187C ASN* 3.1 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C VAL* 4.3 12.6 - - + -
149C GLN 4.0 0.9 - - - +
150C THR* 3.3 40.3 + - + +
161C ILE* 6.2 0.4 - - + -
180C VAL* 3.2 14.8 + - - +
181C ALA* 3.5 11.2 + - - -
182C LEU 3.2 0.4 - - - -
183C ASP* 1.3 76.8 - - - +
185C ILE* 1.3 68.2 + - - +
187C ASN* 3.2 9.9 + - - +
188C GLN* 3.2 35.1 + - - +
267C LEU* 4.4 15.3 - - + -
326C LEU* 4.6 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ALA* 3.2 16.0 + - + +
182C LEU* 3.4 11.0 + - + +
184C THR* 1.3 77.7 - - - +
186C LEU* 1.3 57.3 + - - +
187C ASN 3.2 0.2 + - - -
188C GLN* 3.3 5.6 + - - +
203C CYS* 3.6 37.5 - - + -
204C VAL 5.3 0.4 - - - +
205C TYR* 4.6 23.3 - - + -
218C LEU* 6.4 0.9 - - + -
222C LEU* 3.9 25.4 - - + -
227C ALA* 4.8 0.7 - - + -
230C TYR* 2.6 32.7 + - + +
231C SER* 3.8 16.2 - - - +
267C LEU* 4.2 10.3 - - + +
269C VAL* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C LEU* 3.0 30.6 + - + +
183C ASP* 3.9 16.2 - - - +
185C ILE* 1.3 76.4 - - - +
187C ASN* 1.3 62.7 + - - +
189C LYS* 3.1 14.6 + - - +
221C THR* 4.8 2.7 - - + +
222C LEU* 3.8 26.5 - - + +
225C HIS* 3.5 58.6 - - + +
227C ALA* 4.2 5.5 - - + +
230C TYR* 3.0 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C GLN* 3.2 30.3 + - - +
150C THR 3.5 9.0 - - - +
151C GLY* 3.4 21.5 - - - +
183C ASP 3.1 17.7 + - - +
184C THR 3.2 4.9 + - - +
186C LEU* 1.3 74.5 - - - +
188C GLN* 1.3 53.4 + - - +
189C LYS* 2.7 17.6 + - - +
190C ARG* 2.6 58.2 + - - +
191C TRP* 4.1 5.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C VAL* 4.0 2.8 - - - +
149C GLN 2.5 40.2 + - - +
163C ARG* 4.0 9.4 + - - -
184C THR* 3.2 26.4 + - + +
185C ILE* 3.3 9.6 + - - +
186C LEU 3.3 0.4 + - - -
187C ASN* 1.3 74.7 - - - +
189C LYS* 1.3 63.5 + - - +
190C ARG 3.0 1.1 - - - -
191C TRP* 3.0 35.7 + - + +
192C ASN* 3.0 31.2 + - - +
199C LYS 5.1 0.3 - - - +
201C LEU* 3.6 38.9 + - + +
203C CYS* 4.8 3.1 - - - -
230C TYR* 4.4 0.9 - - + -
267C LEU* 5.7 0.2 - - + -
----------------------------------------------------------
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