Contacts of the helix formed by residues 176 - 189 (chain m) in PDB entry 5M32
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 ARG 176 (chain m).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334h ARG* 3.0 36.8 - - - +
134m LEU 5.7 0.2 - - - -
135m GLY* 6.5 0.9 - - - -
138m LEU* 3.6 36.2 + - + +
139m ASP* 4.6 11.5 + - - +
142m PHE* 3.5 40.9 - - + -
167m LEU* 5.1 2.7 - - + +
173m ASP* 2.7 39.6 + - + +
175m ASP* 1.3 74.6 - - - +
177m ARG* 1.3 63.4 + - - +
178m ASN 3.2 0.9 - - - -
179m ARG* 3.4 24.6 + - - +
180m LEU* 3.1 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 177 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165m LYS* 6.3 3.1 - - - +
167m LEU* 3.9 41.7 + - + +
171m GLY 4.8 2.8 + - - -
172m GLY* 5.2 2.4 - - - -
173m ASP* 3.1 7.4 + - - +
174m TRP* 3.4 52.3 - - + +
176m ARG* 1.3 76.0 - - - +
178m ASN* 1.3 51.8 + - - +
180m LEU* 3.0 18.8 + - - +
181m LYS* 2.5 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 178 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337h ASN* 3.0 15.9 + - - +
377h HIS* 5.8 2.4 - - - -
174m TRP* 2.8 26.0 + - - +
175m ASP* 4.5 6.0 - - - -
176m ARG 3.2 1.8 - - - +
177m ARG* 1.3 75.6 - - - +
179m ARG* 1.3 63.1 - - - +
181m LYS* 3.7 23.5 - - - +
182m VAL* 2.9 33.3 + - - +
203m ASP 4.1 7.9 + - - -
204m THR* 3.6 32.0 - - + +
205m VAL* 5.5 2.3 - - + +
207m THR 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334h ARG* 5.2 5.5 - - - +
142m PHE* 3.9 19.5 - - + -
175m ASP* 2.8 41.4 + - - +
176m ARG* 3.4 37.2 + - - +
177m ARG 3.2 0.6 - - - -
178m ASN* 1.3 78.9 - - - +
180m LEU* 1.3 58.0 + - - +
182m VAL* 3.4 6.1 + - - +
183m TYR* 3.0 42.5 + - + +
207m THR* 3.0 32.4 + - - +
208m PHE* 3.9 21.4 - - + +
209m THR* 4.2 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138m LEU* 5.8 0.2 - - + -
142m PHE* 4.0 19.9 - - + -
145m LEU* 5.7 3.1 - - + -
161m THR* 6.3 0.2 - - - -
164m ALA* 3.3 43.7 - - + +
165m LYS* 4.2 18.8 - - + -
167m LEU* 4.4 11.2 - - + -
176m ARG 3.1 9.2 + - - +
177m ARG* 3.0 20.5 + - - +
179m ARG* 1.3 78.2 - - - +
181m LYS* 1.3 61.0 + - - +
183m TYR* 3.6 8.1 - - + +
184m GLN* 2.8 59.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177m ARG* 2.5 36.2 + - + +
178m ASN* 3.7 28.3 - - - +
179m ARG 3.2 0.2 - - - -
180m LEU* 1.3 74.2 - - - +
182m VAL* 1.3 60.0 + - - +
184m GLN* 3.3 7.1 + - - +
185m GLY* 2.9 24.8 + - - -
200m LEU* 3.6 46.6 - - + +
203m ASP* 4.2 17.3 + - - +
204m THR* 4.0 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 182 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178m ASN 2.9 21.2 + - - +
179m ARG* 3.7 4.7 - - - +
181m LYS* 1.3 74.1 - - - +
183m TYR* 1.3 65.6 + - + +
185m GLY 3.3 0.4 + - - +
186m LEU* 2.9 32.7 + - + +
201m PHE* 3.7 7.1 - - + -
204m THR* 3.4 23.8 - - + -
206m SER* 4.3 11.0 - - - -
207m THR 5.5 0.2 - - - +
208m PHE* 3.6 31.0 - - + -
213m LEU* 5.4 3.4 - - + -
214m MET* 5.3 2.0 - - - -
219m PHE* 4.2 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 183 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142m PHE* 3.8 45.0 - + + +
145m LEU* 3.7 32.7 - - + +
146m ARG* 3.6 26.2 - - + -
149m LEU* 4.9 11.5 - - + +
179m ARG* 3.0 30.1 + - + +
180m LEU* 3.3 7.4 + - + +
182m VAL* 1.3 83.4 - - + +
184m GLN* 1.3 58.3 + - + +
186m LEU* 3.8 3.6 - - + +
187m TYR* 3.0 30.1 + - - +
208m PHE* 5.3 11.1 - + + +
213m LEU* 3.6 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 184 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145m LEU* 5.5 5.1 - - - +
161m THR* 3.3 37.3 - - - +
165m LYS* 4.9 8.1 - - - +
180m LEU* 2.8 44.7 + - + +
181m LYS* 3.7 6.3 - - - +
182m VAL 3.3 0.2 - - - -
183m TYR* 1.3 74.7 - - - +
185m GLY* 1.3 60.9 + - - +
187m TYR* 4.7 6.1 - - - -
188m CYS* 2.8 49.0 + - - +
200m LEU* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 185 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181m LYS 2.9 14.4 + - - -
182m VAL 3.3 0.2 + - - -
184m GLN* 1.3 76.8 - - - +
186m LEU* 1.3 60.8 + - - +
189m VAL* 3.2 20.3 + - - +
197m ALA* 3.9 15.9 - - - +
200m LEU* 4.2 5.1 - - - +
201m PHE* 2.9 35.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149m LEU* 3.8 32.0 - - + +
182m VAL* 2.9 21.4 + - + +
183m TYR* 4.1 4.7 - - - +
185m GLY* 1.3 75.1 - - - +
187m TYR* 1.3 58.7 + - - +
189m VAL* 3.3 22.0 - - + +
190m ALA* 4.4 4.7 + - - +
201m PHE* 3.1 13.7 - - + -
213m LEU* 4.6 18.6 - - + +
222m TYR* 5.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 187 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145m LEU* 6.2 0.7 - - + -
149m LEU* 4.0 17.9 - - + -
152m MET* 6.3 0.2 - - - -
154m ASN* 2.8 44.8 + - - +
157m ILE* 3.6 47.1 - - + -
158m THR* 4.6 11.2 - - + +
161m THR* 6.0 0.7 - - + -
183m TYR 3.0 18.9 + - - +
184m GLN* 4.1 7.4 - - - +
186m LEU* 1.3 77.1 - - - +
188m CYS* 1.3 65.5 + - - +
189m VAL 3.1 4.9 - - - -
190m ALA* 2.8 34.1 + - + +
191m ILE* 3.6 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 188 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184m GLN* 2.8 44.0 + - - +
185m GLY 4.4 1.6 - - - +
187m TYR* 1.3 78.7 - - - +
189m VAL* 1.3 60.4 - - - +
190m ALA 3.2 0.4 + - - -
191m ILE* 3.6 13.2 + - - -
193m ASP* 2.9 54.6 + - + +
196m GLN* 4.3 20.2 - - + -
197m ALA* 4.5 3.8 - - - +
200m LEU* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain m).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185m GLY 3.2 14.3 + - - +
186m LEU* 3.3 30.7 - - + +
188m CYS* 1.3 77.5 - - - +
190m ALA* 1.3 61.7 + - + +
191m ILE 3.4 0.4 + - - -
192m ARG 4.1 1.4 + - - -
194m PHE* 3.2 41.9 - - + -
197m ALA* 4.1 6.7 - - + +
201m PHE* 4.7 6.7 - - + -
226m VAL* 3.9 19.7 - - + -
287m LEU* 4.8 10.8 - - + +
291m HIS* 5.0 5.9 - - - +
----------------------------------------------------------
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