Contacts of the helix formed by residues 176 - 188 (chain C) in PDB entry 4KEU
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 ASN 176 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ASN 4.1 1.2 + - - -
174C HIS 3.9 1.1 - - - -
175C ASN* 1.3 78.9 + - - +
177C THR* 1.3 58.9 + - - +
178C GLY 3.1 2.9 - - - -
179C LEU* 3.1 17.2 + - + +
180C GLU* 2.9 35.4 + - + +
208C TYR* 3.3 38.7 + - - -
211C LYS* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ALA* 4.0 22.7 - - + -
141C ASP 3.6 20.0 - - - +
144C GLY* 3.8 16.8 - - - -
145C ILE* 4.2 6.7 - - + +
171C SER* 3.5 1.7 - - - -
172C ASN 2.9 25.2 + - - -
175C ASN* 2.8 28.8 + - - +
176C ASN* 1.3 75.8 - - - +
178C GLY* 1.3 58.0 + - - +
180C GLU* 3.3 8.7 + - - +
181C GLN* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C SER* 3.6 21.0 + - - -
172C ASN 4.6 0.8 + - - -
176C ASN 3.1 0.8 - - - -
177C THR* 1.3 83.0 + - - +
179C LEU* 1.3 61.2 + - - +
181C GLN* 3.3 5.2 + - - +
182C GLN* 3.1 23.2 + - - +
197C ILE* 3.7 23.1 - - - +
208C TYR* 3.4 8.4 + - - -
212C ILE* 4.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ASN* 3.1 23.5 + - - +
178C GLY* 1.3 75.5 - - - +
180C GLU* 1.3 59.7 + - + +
182C GLN* 3.5 24.0 + - - +
183C ARG* 2.9 28.8 + - + +
208C TYR* 3.0 24.4 + - + +
211C LYS* 3.9 42.4 - - + +
212C ILE* 4.1 13.8 - - + +
215C LYS* 4.8 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ILE* 3.7 29.1 - - + +
176C ASN* 2.9 25.5 + - + +
177C THR* 3.6 4.5 - - - +
179C LEU* 1.3 76.7 - - + +
181C GLN* 1.3 66.7 + - - +
183C ARG* 2.6 49.5 + - - +
184C ILE* 2.8 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ILE* 4.7 7.9 - - + +
139C ALA* 3.7 6.3 + - - +
140C ALA* 3.4 20.0 - - - +
145C ILE* 4.5 3.8 - - + +
153C ILE* 4.2 24.9 - - + -
169C THR* 2.6 36.8 + - + +
170C HIS 2.8 26.3 + - - -
171C SER* 3.6 12.1 - - - -
177C THR 2.8 23.2 + - - +
178C GLY* 3.5 7.6 - - - +
180C GLU* 1.3 71.7 - - - +
182C GLN* 1.3 64.4 + - - +
184C ILE* 3.4 1.0 + - - +
185C LEU* 3.0 32.5 + - + +
197C ILE* 4.0 6.1 - - + +
----------------------------------------------------------
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 10.0 + - - +
179C LEU* 3.6 22.2 - - - +
180C GLU 3.2 0.2 - - - -
181C GLN* 1.3 78.5 - - - +
183C ARG* 1.3 60.1 + - - +
185C LEU* 4.0 3.7 - - - +
186C THR* 2.8 43.0 + - + +
195C ILE* 4.8 4.3 - - + -
197C ILE* 4.0 13.2 - - + +
212C ILE* 2.9 34.1 + - - +
215C LYS* 3.2 35.6 + - + +
217C SER* 2.8 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ILE* 6.3 0.2 - - - +
154C ARG* 6.0 1.0 - - - +
179C LEU* 2.9 16.1 + - + +
180C GLU* 2.6 48.6 + - - +
182C GLN* 1.3 78.0 - - - +
184C ILE* 1.3 84.0 + - - +
186C THR* 2.8 20.3 + - - +
187C GLU* 2.9 59.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ILE* 4.0 26.7 - - + -
150C GLU* 4.0 17.0 - - + -
153C ILE* 3.8 27.8 - - + -
154C ARG* 4.0 37.5 - - + +
180C GLU* 2.8 24.3 + - + +
181C GLN 4.0 2.0 - - - +
183C ARG* 1.3 97.8 - - - +
185C LEU* 1.3 63.6 + - - +
187C GLU* 3.4 9.5 + - - +
188C GLU* 3.1 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ILE* 4.3 10.5 - - + -
153C ILE* 3.4 35.2 - - + +
156C ALA* 4.6 1.1 - - + -
157C ALA* 3.9 11.0 - - + -
167C ILE* 3.9 33.4 - - + -
169C THR* 4.7 2.0 - - + -
181C GLN 3.0 24.4 + - - +
182C GLN 4.0 0.2 - - - +
184C ILE* 1.3 76.6 - - - +
186C THR* 1.3 62.7 + - - +
188C GLU* 3.0 10.6 + - - +
189C GLY 3.3 0.5 + - - -
190C VAL* 3.0 27.6 + - + +
195C ILE* 3.7 44.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C GLN* 2.8 31.8 + - + +
183C ARG* 2.8 15.2 + - - -
185C LEU* 1.3 71.5 - - - +
187C GLU* 1.3 66.5 + - - +
189C GLY* 2.9 15.1 + - - -
190C VAL 3.6 12.0 - - - +
192C PRO* 3.7 36.1 - - + -
195C ILE* 4.4 3.8 - - + -
215C LYS* 5.5 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ARG* 5.3 6.6 + - - -
183C ARG* 2.9 62.1 + - + +
184C ILE* 3.6 8.4 - - - +
186C THR* 1.3 79.1 + - - +
188C GLU* 1.3 65.5 + - - +
189C GLY* 3.2 3.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
154C ARG* 2.3 43.8 + - + +
157C ALA* 3.7 23.3 - - + -
161C LYS* 2.9 38.0 + - - +
184C ILE* 3.1 17.8 + - + +
185C LEU* 3.0 11.2 + - - +
187C GLU* 1.3 82.0 - - - +
189C GLY* 1.3 58.1 + - - +
190C VAL* 3.6 0.7 - - - -
----------------------------------------------------------
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