Contacts of the helix formed by residues 171 - 196 (chain P) in PDB entry 6QY3
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 171 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169P SER* 3.3 12.9 - - - -
170P ASP* 1.3 82.2 - - - +
172P ASP* 1.3 63.7 + - - +
173P ILE* 3.0 14.1 + - + +
174P ASN* 3.1 6.3 + - - +
175P ALA* 3.1 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 172 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170P ASP 3.8 0.4 + - - -
171P ASN* 1.3 74.0 - - - +
173P ILE* 1.3 56.7 + - - +
174P ASN 3.5 0.2 - - - -
175P ALA* 3.7 11.6 - - + +
176P ALA* 2.9 29.8 + - - +
238P PHE* 4.4 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161P PHE* 6.2 4.5 - - + -
171P ASN* 3.0 8.9 + - + +
172P ASP* 1.3 77.2 - - - +
174P ASN* 1.3 57.6 + - - +
176P ALA* 3.3 5.3 + - - +
177P LEU* 2.9 27.4 + - - +
230P VAL* 5.5 6.5 - - + +
234P ARG* 5.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 174 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166P THR 4.9 5.4 - - - +
167P ARG* 4.2 17.0 - - - +
169P SER* 3.4 27.8 - - - +
171P ASN* 3.1 6.6 + - + +
173P ILE* 1.3 75.3 - - - +
175P ALA* 1.3 61.2 + - - +
177P LEU* 3.6 8.7 - - - +
178P ASP* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170P ASP 5.1 3.8 - - - +
171P ASN 3.1 13.2 + - - +
172P ASP* 3.7 14.4 - - + +
173P ILE 3.2 0.2 - - - -
174P ASN* 1.3 77.2 - - - +
176P ALA* 1.3 57.3 + - - +
178P ASP* 3.4 5.6 + - - +
179P TYR* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172P ASP 2.9 18.3 + - - +
173P ILE* 3.8 5.4 - - - +
175P ALA* 1.3 73.8 - - - +
177P LEU* 1.3 60.1 + - - +
179P TYR* 3.6 7.1 - - - +
180P GLY* 2.9 26.3 + - - -
226P ILE* 6.1 0.2 - - - +
230P VAL* 5.3 11.9 - - + -
238P PHE* 6.2 2.0 - - + +
241P ILE* 4.9 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173P ILE 2.9 17.4 + - - +
174P ASN* 3.6 9.6 - - - +
176P ALA* 1.3 78.0 - - - +
178P ASP* 1.3 56.3 + - - +
180P GLY* 3.5 1.0 + - - -
181P TYR* 2.9 30.6 + - - +
226P ILE* 5.9 4.6 - - - +
230P VAL* 5.7 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 178 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174P ASN 2.9 17.4 + - - +
175P ALA* 3.9 6.1 - - - +
177P LEU* 1.3 75.7 - - - +
179P TYR* 1.3 57.7 + - - +
181P TYR* 3.8 6.7 - - - +
182P THR* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175P ALA 2.9 19.0 + - - +
176P ALA* 3.6 9.2 - - - +
177P LEU 3.2 0.2 - - - -
178P ASP* 1.3 75.0 - - - +
180P GLY* 1.3 60.2 + - - +
182P THR* 3.1 7.2 + - - -
183P LEU* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 180 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176P ALA 2.9 16.3 + - - -
177P LEU* 4.0 1.1 - - - -
179P TYR* 1.3 75.7 - - - +
181P TYR* 1.3 57.4 + - - +
183P LEU* 3.9 6.0 - - - +
184P LEU* 2.9 33.0 + - - +
226P ILE* 5.0 16.2 - - - -
245P LEU* 5.7 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 181 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177P LEU 2.9 19.2 + - - +
178P ASP* 3.9 7.6 - - - +
180P GLY* 1.3 76.2 - - - +
182P THR* 1.3 57.2 + - - +
184P LEU* 4.4 4.7 - - - +
185P LEU* 2.8 31.5 + - - +
226P ILE* 5.7 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81O TYR* 6.2 3.6 - - - -
74P PRO* 5.2 13.7 - - - -
178P ASP 2.9 19.1 + - - -
179P TYR* 3.1 7.6 + - - -
181P TYR* 1.3 76.3 - - - +
183P LEU* 1.3 59.9 + - - +
185P LEU* 3.7 5.2 - - - +
186P SER* 2.9 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179P TYR 2.9 14.5 + - - +
180P GLY* 3.9 6.7 - - - +
182P THR* 1.3 75.0 - - - +
184P LEU* 1.3 60.6 + - - +
186P SER* 3.0 8.5 + - - -
187P MET* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180P GLY 2.9 17.0 + - - +
181P TYR* 4.4 3.6 - - - +
183P LEU* 1.3 76.6 - - - +
185P LEU* 1.3 57.2 + - - +
187P MET* 3.9 5.9 - - - +
188P PHE* 2.9 32.4 + - - +
219P MET* 4.5 12.6 - - + +
222P PHE* 5.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181P TYR 2.8 23.9 + - - +
182P THR* 3.8 6.3 - - - +
183P LEU 3.2 0.2 - - - -
184P LEU* 1.3 76.7 - - - +
186P SER* 1.3 57.3 + - - +
188P PHE* 4.6 3.8 - - - -
189P ALA* 2.9 30.8 + - - +
212P PHE* 5.5 10.9 - - + +
215P ALA* 4.1 10.2 - - + +
216P SER* 5.8 4.3 - - - +
219P MET* 5.1 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 186 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P LEU* 5.5 1.0 - - - +
77P PHE* 5.4 12.3 - - - -
182P THR 2.9 18.1 + - - -
183P LEU* 3.0 8.3 + - - -
185P LEU* 1.3 75.9 - - - +
187P MET* 1.3 59.6 + - - +
189P ALA* 3.4 5.3 + - - +
190P ARG* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 187 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183P LEU 2.9 14.5 + - - +
184P LEU* 4.0 6.3 - - - +
186P SER* 1.3 76.8 - - - +
188P PHE* 1.3 57.2 + - - +
190P ARG* 3.2 7.7 + - - +
191P GLU* 2.9 27.4 + - - +
266P VAL* 5.8 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 188 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184P LEU 2.9 17.9 + - - +
185P LEU 4.2 0.7 - - - +
187P MET* 1.3 76.4 - - - +
189P ALA* 1.3 58.1 + - - +
191P GLU* 3.3 9.0 + - - +
192P VAL* 2.9 27.4 + - - +
215P ALA* 3.8 28.1 - - + +
218P ILE* 5.1 6.9 - - + +
219P MET* 4.2 10.5 - - + +
266P VAL* 5.8 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185P LEU 2.9 22.1 + - - +
186P SER* 3.7 5.8 - - - +
188P PHE* 1.3 75.8 - - - +
190P ARG* 1.3 59.5 + - - +
192P VAL* 3.3 6.0 + - - +
193P VAL* 2.9 26.9 + - - +
211P GLN 6.1 1.3 - - - +
212P PHE* 6.1 2.9 - - + -
215P ALA* 3.7 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P LEU* 4.3 22.2 - - + -
186P SER 2.9 19.3 + - - +
187P MET* 3.5 7.2 - - - +
189P ALA* 1.3 71.5 - - - +
191P GLU* 1.3 61.8 + - - +
193P VAL* 3.2 9.4 + - - +
194P VAL* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187P MET 2.9 13.6 + - - +
188P PHE* 3.3 12.1 + - - +
190P ARG* 1.3 77.2 - - - +
192P VAL* 1.3 56.5 + - - +
194P VAL* 3.1 10.4 + - - +
195P CYS* 2.9 26.7 + - - +
266P VAL* 4.7 10.1 - - + +
267P SER* 5.0 8.7 - - - -
270P THR* 4.2 24.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188P PHE 2.9 17.1 + - - +
189P ALA* 3.3 8.7 + - - +
191P GLU* 1.3 76.1 - - - +
193P VAL* 1.3 57.8 + - - +
195P CYS* 3.3 9.2 + - - +
196P GLY 3.0 21.5 + - - -
197P CYS* 3.7 17.0 + - + +
199P THR* 4.9 16.8 - - - -
214P LEU* 5.8 3.8 - - + -
215P ALA* 5.2 8.1 - - + +
270P THR* 5.4 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79P THR* 6.0 5.4 - - - -
80P PRO* 5.3 15.0 - - + +
83P ALA* 3.3 20.7 - - + +
189P ALA 2.9 14.2 + - - +
190P ARG* 3.2 13.4 + - - +
192P VAL* 1.3 75.0 - - - +
194P VAL* 1.3 62.0 + - - +
196P GLY* 3.4 12.1 + - - +
197P CYS 5.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62P ASN* 6.5 0.9 - - + -
83P ALA* 4.2 13.3 - - + +
84P ARG* 4.9 9.9 - - - +
190P ARG 2.9 12.7 + - - +
191P GLU* 3.1 13.0 + - - +
193P VAL* 1.3 76.7 - - - +
195P CYS* 1.3 64.0 + - - +
196P GLY* 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 195 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86P ASP* 4.9 4.5 - - - +
87P SER* 4.7 3.5 + - - -
90P GLN* 4.5 11.1 - - - +
191P GLU 2.9 12.1 + - - +
192P VAL* 3.6 11.2 - - - +
193P VAL 3.3 0.2 - - - -
194P VAL* 1.3 78.2 - - - +
196P GLY* 1.3 58.3 + - - +
197P CYS* 3.4 10.1 + - + +
270P THR* 5.6 5.8 - - - +
271P LYS* 6.4 0.7 - - - -
274P ILE* 4.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 196 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P ALA* 6.0 0.7 - - - -
87P SER* 3.6 38.9 - - - +
90P GLN* 4.8 1.3 - - - -
91P ILE* 5.4 2.1 + - - +
192P VAL 3.0 6.8 + - - -
193P VAL* 3.4 11.2 + - - -
194P VAL 3.3 3.0 - - - -
195P CYS* 1.3 76.8 - - - +
197P CYS* 1.3 65.3 + - - +
198P MET 3.8 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