Contacts of the helix formed by residues 164 - 180 (chain C) in PDB entry 3U1K
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 GLU 164 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LYS* 4.1 19.1 + - - -
162C VAL 3.7 1.2 + - - +
163C ASN* 1.3 70.7 - - - +
165C PRO* 1.3 75.7 - - - +
166C ASP* 3.5 16.3 + - - +
167C VAL* 4.3 4.6 + - + +
168C LEU* 3.8 18.8 - - - +
192C ARG* 4.0 7.6 - - - +
204C PRO 4.5 9.0 + - - +
206C ARG* 2.9 40.4 + - + +
209C MET* 3.6 33.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C THR* 3.9 13.0 - - + -
80C VAL* 3.6 22.4 - - + +
102C TYR* 3.4 21.1 - - - +
104C GLN* 6.1 0.2 - - - +
126C LYS* 5.9 2.0 - - - +
156C LEU* 3.8 19.3 - - + -
159C VAL* 4.4 10.5 - - + -
163C ASN 3.5 7.6 - - - +
164C GLU* 1.3 93.0 - - + +
166C ASP* 1.3 64.6 + - - +
167C VAL 3.4 0.2 - - - -
168C LEU* 3.1 6.6 + - + +
169C ALA* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TYR* 3.8 6.8 + - - +
126C LYS* 2.9 31.4 + - - +
130C THR* 3.7 26.5 + - + +
133C ILE* 5.9 4.2 - - + +
164C GLU* 3.6 9.3 - - - +
165C PRO* 1.3 79.5 - - - +
167C VAL* 1.3 77.2 + - - +
169C ALA* 3.0 14.7 + - - +
170C ILE* 3.2 18.7 + - + +
192C ARG* 2.8 42.8 + - - -
217C VAL* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 6.2 0.7 - - + -
164C GLU* 4.3 5.1 + - + +
165C PRO 3.4 0.4 - - - -
166C ASP* 1.3 85.3 + - - +
168C LEU* 1.3 76.8 + - + +
170C ILE* 3.3 16.7 + - + +
171C ASN* 2.9 40.3 + - - +
190C ALA* 3.9 9.0 - - + +
191C VAL* 4.3 2.5 - - - -
192C ARG* 3.3 36.6 - - + +
203C ASN* 3.7 26.2 - - + +
217C VAL* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 4.0 20.0 - - + -
73C VAL* 3.7 32.2 - - + +
75C SER* 3.9 20.9 - - - +
78C THR* 3.7 44.2 - - + +
80C VAL* 3.9 11.6 - - + +
163C ASN* 5.1 0.7 - - + +
164C GLU 3.8 15.3 - - - +
165C PRO* 3.1 7.9 + - + +
167C VAL* 1.3 85.5 - - + +
169C ALA* 1.3 51.2 + - - +
171C ASN* 3.3 5.3 + - - +
172C GLY* 2.8 31.4 + - - -
203C ASN* 5.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C VAL* 4.0 17.7 - - + +
82C VAL* 3.6 6.7 - - - +
102C TYR* 3.7 24.9 - - + -
134C ILE* 3.6 21.9 - - + +
154C CYS* 4.1 4.5 - - - -
165C PRO 3.0 7.1 + - - +
166C ASP 3.0 10.1 + - - +
168C LEU* 1.3 74.7 - - - +
170C ILE* 1.3 66.1 + - - +
172C GLY* 3.0 1.2 + - - -
173C ALA* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C THR* 5.7 0.9 - - + -
133C ILE* 3.7 29.2 - - + -
134C ILE* 3.6 25.1 - - + -
137C SER* 3.7 28.5 - - - +
138C ILE* 5.1 2.1 - - + +
166C ASP* 3.2 15.5 + - + +
167C VAL* 3.7 11.0 - - - +
168C LEU 3.3 0.2 - - - -
169C ALA* 1.3 78.0 - - - +
171C ASN* 1.3 62.5 + - - +
173C ALA* 3.2 4.3 + - - +
174C SER* 3.1 19.4 + - - -
188C VAL* 5.1 5.4 - - + -
190C ALA* 3.5 22.9 - - + -
217C VAL* 3.9 21.1 - - + -
219C ALA* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 4.1 11.2 - - + +
58C ILE* 5.5 1.8 - - + -
73C VAL* 4.4 12.1 - - + -
167C VAL* 2.9 26.3 + - - +
168C LEU* 3.6 7.9 - - - +
170C ILE* 1.3 79.4 - - - +
172C GLY* 1.3 61.8 + - - +
174C SER* 3.1 9.1 + - - -
175C VAL* 2.9 32.5 + - + +
188C VAL 4.4 0.3 - - - +
189C GLY* 3.5 2.9 - - - -
190C ALA 2.8 46.8 + - - -
255C ILE* 3.4 27.0 - - + +
259C ILE* 4.8 0.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ALA* 3.7 7.9 - - - +
73C VAL* 3.6 16.5 - - - +
82C VAL* 3.5 18.4 - - - -
168C LEU 2.8 18.4 + - - -
169C ALA 3.0 4.6 + - - -
171C ASN* 1.3 71.7 - - - +
173C ALA* 1.3 56.6 + - - +
175C VAL* 3.3 2.6 + - - -
176C ALA* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C VAL* 3.5 12.0 - - + +
134C ILE* 3.8 24.7 - - + -
138C ILE* 4.1 13.7 - - + -
152C VAL* 3.9 17.2 - - + +
169C ALA 2.9 11.5 + - - +
170C ILE 3.2 8.9 + - - +
172C GLY* 1.3 76.1 - - - +
174C SER* 1.3 61.4 + - - +
176C ALA* 3.8 1.1 - - - +
177C LEU* 3.0 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ILE* 4.7 2.6 - - - +
170C ILE 3.1 9.3 + - - -
171C ASN* 3.1 10.7 + - - -
173C ALA* 1.3 79.8 - - - +
175C VAL* 1.3 53.4 + - - +
178C SER* 2.7 35.9 + - - -
184C TRP* 3.4 22.9 - - - -
187C PRO* 3.9 1.2 - - - +
188C VAL* 2.6 48.3 + - - -
259C ILE* 3.6 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 3.8 31.6 - - + -
59C SER 4.8 1.1 - - - +
71C ALA* 3.2 23.6 - - + -
73C VAL* 4.4 2.5 - - + -
171C ASN* 2.9 21.7 + - + +
172C GLY* 4.0 4.7 - - - +
174C SER* 1.3 73.7 - - - +
176C ALA* 1.3 59.1 + - - +
178C SER* 3.6 6.0 - - - -
179C LEU* 2.8 52.0 + - + +
259C ILE* 4.4 22.4 - - + -
262C LEU* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLY* 3.4 11.8 - - - +
70C SER* 3.8 23.3 - - - +
71C ALA* 3.8 0.2 - - - +
82C VAL* 3.6 24.7 - - + +
83C THR 4.3 0.4 - - - -
84C ALA* 4.1 13.0 - - + +
172C GLY 2.9 17.2 + - - +
173C ALA 3.8 3.8 - - - +
175C VAL* 1.3 75.9 - - - +
177C LEU* 1.3 63.4 + - - +
179C LEU* 3.5 1.1 + - - -
180C SER* 3.0 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ALA* 3.9 13.0 - - + -
138C ILE* 4.1 19.7 - - + -
142C PHE* 3.9 24.5 - - + -
150C THR* 5.1 2.0 - - + -
152C VAL* 4.8 6.3 - - + -
173C ALA 3.0 19.5 + - - +
174C SER 3.8 0.2 - - - +
176C ALA* 1.3 76.2 - - - +
178C SER* 1.3 59.5 + - - +
180C SER* 2.7 20.7 + - - -
182C ILE* 3.8 34.7 - - + +
184C TRP* 3.5 49.1 - - + +
270C LYS* 2.9 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C SER 2.7 24.1 + - - -
175C VAL 3.1 4.7 + - - -
177C LEU* 1.3 79.2 - - - +
179C LEU* 1.3 59.9 + - - +
180C SER 3.6 0.2 + - - -
184C TRP* 3.4 16.9 - - - -
186C GLY 5.1 0.2 - - - -
187C PRO* 3.7 18.7 - - - +
259C ILE* 3.9 10.5 - - - -
263C VAL* 3.7 23.8 - - - +
268C VAL* 3.7 14.0 - - - +
270C LYS* 3.7 12.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
41C SER* 5.1 11.2 + - - -
60C SER* 3.4 37.0 - - - +
68C ASP 4.5 1.9 - - - +
69C GLY* 5.1 1.1 - - - -
70C SER 4.1 4.7 - - - +
175C VAL* 2.8 38.2 + - + +
176C ALA* 3.9 3.8 - - - +
178C SER* 1.3 71.2 - - - +
180C SER* 1.3 65.0 + - - +
259C ILE* 5.9 0.4 - - + -
262C LEU* 3.7 31.2 - - + +
263C VAL* 3.9 14.4 - - + +
266C THR* 3.6 33.8 - - + +
268C VAL* 3.8 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ASP 3.3 29.6 - - - -
69C GLY* 3.8 1.6 - - - -
84C ALA* 5.1 0.2 - - - -
176C ALA 3.0 15.6 + - - -
177C LEU 2.7 16.5 + - - -
179C LEU* 1.3 82.1 - - - +
181C ASP* 1.3 59.5 + - - +
182C ILE* 2.9 33.4 + - - +
268C VAL* 3.2 9.3 - - - +
270C LYS* 2.9 19.1 + - - -
----------------------------------------------------------
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