Contacts of the helix formed by residues 182 - 199 (chain C) in PDB entry 1PKD
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 THR 182 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C HIS* 3.6 34.5 + - + +
124C LEU* 3.7 8.7 - - + -
152C PHE* 3.6 33.4 - - + -
181C SER* 1.3 88.8 + - - +
183C ALA* 1.3 66.2 + - - +
185C ASP* 3.0 17.8 + - - +
186C ILE* 3.3 10.8 + - - +
175D VAL* 3.4 35.5 + - - +
178D TYR* 4.5 3.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C GLU* 4.1 5.4 - - - +
181C SER* 3.2 3.9 - - - +
182C THR* 1.3 83.2 + - - +
184C VAL* 1.3 56.1 + - - +
186C ILE* 3.1 11.8 + - - +
187C TRP 2.9 20.1 + - - -
271C PRO* 3.5 29.8 - - + +
274C ARG* 2.9 37.3 + - + +
275C ILE 5.7 0.7 - - - -
175D VAL* 5.4 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LEU* 5.2 0.9 - - + -
126C ARG* 4.6 14.4 - - + -
164C VAL* 4.8 9.2 - - + +
168C TYR 4.6 0.5 - - - +
170C ALA* 4.2 7.3 + - + +
172C GLU* 3.4 22.2 - - - +
173C ILE* 3.8 25.6 - - + -
180C TYR* 3.7 32.5 - - + -
181C SER 3.3 18.4 - - - +
182C THR 3.1 1.6 + - - -
183C ALA* 1.3 77.0 - - - +
185C ASP* 1.3 70.6 + - - +
187C TRP* 3.5 3.3 + - - +
188C SER* 3.0 27.1 + - - -
274C ARG* 4.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 3.7 13.2 - - + -
119C HIS* 2.9 29.0 - - + +
124C LEU* 3.8 5.4 - - - +
125C HIS* 2.9 32.0 + - - +
126C ARG* 2.9 28.4 + - - -
127C ASP 4.5 0.2 + - - -
128C LEU* 3.6 12.2 + - + +
182C THR 3.0 10.5 + - - +
184C VAL* 1.3 85.4 - - - +
186C ILE* 1.3 64.0 + - - +
188C SER* 3.5 7.5 + - - -
189C LEU* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C LEU* 4.6 8.5 - - + -
115C LEU* 3.9 13.0 - - + -
119C HIS* 4.7 4.9 - - + +
182C THR* 3.3 12.3 + - - +
183C ALA* 3.1 13.8 + - - +
185C ASP* 1.3 75.1 - - - +
187C TRP* 1.3 65.6 + - - +
189C LEU* 3.0 7.6 + - + +
190C GLY* 2.8 20.4 + - - -
266C MET* 3.9 24.0 - - + +
274C ARG* 3.9 15.7 - - + -
275C ILE* 3.4 25.1 - - + +
276C SER* 4.1 2.0 - - - -
277C ALA* 3.5 40.8 - - + +
175D VAL* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C TRP 5.2 0.4 + - - -
168C TYR* 3.5 20.5 + - - +
169C ARG 3.3 10.7 + - - -
170C ALA* 3.6 13.5 - - + -
171C PRO* 3.6 33.2 - - + -
183C ALA 2.9 12.4 + - - +
184C VAL 3.7 8.3 - - - +
185C ASP 3.4 0.2 - - - -
186C ILE* 1.3 74.5 - - - +
188C SER* 1.3 63.3 + - - +
190C GLY* 2.8 14.2 + - - -
191C CYS* 2.9 26.0 + - - -
203C PHE* 3.8 21.4 - + - -
211C GLN* 5.8 0.2 - - - +
215C ILE* 3.8 20.5 - - + +
219C LEU* 3.6 22.9 - - + -
266C MET 3.9 9.4 - - - -
267C LEU* 3.4 41.1 - - + +
268C HIS 4.1 4.7 - - - -
269C TYR* 4.8 2.2 - + - -
274C ARG* 3.8 23.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LEU* 3.7 31.8 + - - +
164C VAL* 3.8 11.8 - - - +
168C TYR* 2.8 29.1 + - - -
184C VAL 3.0 13.5 + - - -
185C ASP* 3.6 9.5 + - - -
187C TRP* 1.3 77.7 - - - +
189C LEU* 1.3 57.2 + - - +
191C CYS* 3.2 5.7 + - - +
192C ILE* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LEU* 3.9 9.0 - - + -
111C LEU* 3.8 39.5 - - + +
112C LEU* 3.8 30.5 - - + +
115C LEU* 4.4 11.0 - - + -
128C LEU* 4.2 15.5 - - + +
133C LEU* 5.3 1.1 - - + -
185C ASP 3.1 11.8 + - - +
186C ILE* 3.0 11.8 + - + +
188C SER* 1.3 74.1 - - - +
190C GLY* 1.3 59.2 + - - +
192C ILE* 3.1 16.6 + - + +
193C PHE* 2.8 30.9 + - - +
266C MET* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ILE 2.8 17.1 + - - -
187C TRP 2.8 5.1 + - - -
189C LEU* 1.3 71.1 - - - +
191C CYS* 1.3 62.7 + - - +
193C PHE* 3.3 2.0 + - - +
194C ALA* 3.1 18.4 + - - +
263C LEU* 3.3 15.5 - - - +
266C MET* 3.5 21.2 - - - +
267C LEU* 3.9 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C TRP 4.0 15.7 - - - +
168C TYR* 3.7 21.8 - - + -
187C TRP* 2.9 42.1 + - - -
188C SER 3.3 8.7 - - - +
190C GLY* 1.3 74.6 - - - +
192C ILE* 1.3 57.9 + - - +
194C ALA* 3.4 4.7 + - - +
195C GLU* 2.9 28.5 + - - +
202C LEU* 4.1 17.7 + - + +
203C PHE* 4.1 18.8 - - - -
267C LEU* 3.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 4.0 16.8 - - + -
91C MET* 5.8 0.4 - - - -
111C LEU* 4.7 0.4 - - + -
128C LEU* 3.8 13.9 - - + +
129C LYS* 3.7 28.9 - - - +
130C PRO* 4.0 11.9 - - + -
133C LEU* 3.9 24.9 - - + -
168C TYR* 4.0 16.2 - - + -
188C SER 2.9 25.8 + - - +
189C LEU* 3.1 16.1 + - + +
191C CYS* 1.3 71.9 - - - +
193C PHE* 1.3 57.0 + - - +
195C GLU* 3.2 8.2 + - + +
196C MET* 2.8 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ILE* 4.0 25.1 - - + -
108C LEU* 3.6 33.9 - - + -
189C LEU* 2.8 17.0 + - - +
190C GLY* 3.3 9.4 - - - +
192C ILE* 1.3 71.7 - - - +
194C ALA* 1.3 63.2 + - - +
196C MET* 2.9 22.8 + - + +
197C VAL* 3.2 21.1 + - + +
255C LEU* 3.9 17.5 - - + -
259C GLY* 3.7 22.2 - - - -
262C LEU* 4.3 4.9 - - + -
263C LEU* 3.8 27.6 - - + -
266C MET* 4.4 6.1 - - + -
285C PHE* 4.0 24.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C GLY 3.1 6.4 + - - +
191C CYS 3.5 8.1 - - - +
193C PHE* 1.3 78.9 - - - +
195C GLU* 1.3 61.6 - - - +
197C VAL* 3.2 16.1 + - - +
198C THR* 3.2 19.2 + - - +
200C ARG 4.9 0.2 - - - -
202C LEU* 3.8 30.1 - - + -
252C VAL* 4.0 22.0 - - + -
255C LEU* 6.2 0.4 - - - -
263C LEU* 4.2 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LYS* 5.3 2.8 - - - +
91C MET* 3.4 31.5 - - + +
130C PRO* 4.0 5.5 - - - +
167C TRP* 5.7 1.0 - - - -
168C TYR* 2.7 38.7 + - - -
191C CYS 2.9 15.8 + - - +
192C ILE* 3.6 7.4 - - + +
193C PHE 3.2 0.2 - - - -
194C ALA* 1.3 74.4 - - - +
196C MET* 1.3 61.6 + - - +
199C ARG* 2.8 33.0 + - - -
200C ARG* 3.6 26.4 - - - +
201C ALA* 3.8 22.0 + - - +
202C LEU* 4.9 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 4.0 24.5 - - + -
91C MET* 4.1 13.5 - - + -
98C GLY 4.3 0.9 - - - +
99C ILE* 3.9 16.0 - - + +
104C ILE* 3.5 44.1 - - + +
107C TYR* 3.9 30.3 - - + -
108C LEU* 4.1 28.0 - - + +
111C LEU* 4.3 14.4 - - + -
192C ILE* 2.8 16.0 + - + +
193C PHE* 2.9 26.2 + - - +
195C GLU* 1.3 77.4 - - - +
197C VAL* 1.3 62.4 + - - +
199C ARG* 4.1 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLY 4.2 4.3 - - - +
101C LEU* 5.1 2.2 - - + -
104C ILE* 4.4 14.9 - - + +
193C PHE* 3.2 23.5 + - + +
194C ALA* 3.2 8.6 + - - +
196C MET* 1.3 80.9 - - - +
198C THR* 1.3 59.7 + - + +
199C ARG* 3.7 14.9 + - - -
252C VAL* 3.2 28.9 - - + -
254C PRO* 3.5 30.9 - - + +
255C LEU* 3.9 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ALA 3.2 14.1 + - - +
197C VAL* 1.3 80.9 - - + +
199C ARG* 1.3 73.6 + - - +
200C ARG* 3.0 45.9 + - - +
251C VAL 4.9 1.8 - - - +
252C VAL* 3.6 28.5 - - + -
253C PRO* 4.7 9.0 - - + -
254C PRO* 5.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C MET* 4.2 24.4 - - + +
92C ASP* 5.3 5.0 - - - +
94C SER 3.2 21.7 + - - -
95C ALA* 2.3 41.7 + - + +
96C LEU 3.8 6.9 + - - -
98C GLY* 3.2 36.3 + - - +
99C ILE* 4.0 21.3 - - + -
195C GLU* 2.8 19.9 + - - -
196C MET 4.2 2.7 - - - +
197C VAL 3.8 14.5 + - - -
198C THR* 1.3 83.3 + - - +
200C ARG* 1.3 58.1 + - - +
254C PRO* 5.9 3.4 - - - +
----------------------------------------------------------
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