Contacts of the helix formed by residues 178 - 190 (chain A) in PDB entry 2QPA
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 GLY 178 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLY 3.1 5.5 + - - -
177A THR* 1.3 80.5 - - - +
179A LYS* 1.3 64.5 + - - +
181A TYR* 3.1 22.9 + - - +
182A LEU* 3.5 4.4 + - - +
800A ADP 3.0 47.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.3 32.8 - - + +
172A TYR 3.4 4.3 - - - -
173A GLY* 3.1 38.3 + - - +
177A THR* 3.5 18.9 + - - +
178A GLY* 1.3 73.7 - - - +
180A SER* 1.3 61.5 + - - +
182A LEU* 3.0 19.5 + - - +
183A ALA* 3.0 12.6 + - - +
230A PHE* 4.4 1.8 - - - -
275A ALA* 3.8 12.6 - - + -
276A THR 3.2 8.8 + - - -
277A ASN* 2.7 15.8 + - - -
296A ILE* 4.0 18.8 - - + -
800A ADP 2.6 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LYS* 1.3 77.8 - - - +
181A TYR* 1.3 67.7 + - - +
183A ALA* 3.2 2.1 + - - +
184A LYS* 3.0 36.0 + - - +
194A PHE* 4.1 2.5 - - - -
230A PHE* 3.4 34.9 - - - -
232A ASP* 4.4 4.9 - - - -
800A ADP 3.2 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.8 28.8 - - + +
134A ASP* 3.0 44.1 + - + +
135A VAL* 3.6 20.0 - - + -
178A GLY* 3.1 15.1 + - - +
180A SER* 1.3 82.3 + - - +
182A LEU* 1.3 56.6 + - - +
184A LYS* 3.0 20.2 + - + +
185A ALA* 2.9 25.5 + - - +
800A ADP 4.1 40.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TRP* 3.6 25.8 - - + -
135A VAL* 4.3 15.7 - - + +
138A LEU* 3.8 21.8 - - + -
141A ALA* 4.6 4.7 - - + -
142A LYS* 4.8 6.3 - - + -
145A LEU* 3.6 23.3 - - + -
171A LEU* 4.5 7.9 - - + -
178A GLY 3.5 4.0 + - - +
179A LYS* 3.0 12.7 + - - +
181A TYR* 1.3 81.3 - - - +
183A ALA* 1.3 56.7 + - - +
185A ALA* 2.9 19.9 - - + +
186A VAL* 3.0 9.7 + - - +
296A ILE* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 4.3 5.6 - - + +
179A LYS 3.0 8.3 + - - +
180A SER 3.6 7.2 - - - +
182A LEU* 1.3 72.2 - - - +
184A LYS* 1.3 62.3 + - - +
185A ALA 3.0 1.3 - - - -
186A VAL* 2.9 7.3 + - - +
187A ALA* 2.8 26.9 + - - +
194A PHE* 3.6 7.5 - - + -
228A ILE* 4.6 0.5 - - - +
230A PHE* 3.6 36.6 - - + -
273A LEU* 3.6 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 4.5 8.0 - - - +
126A GLU* 4.1 27.0 + - - +
128A PRO* 3.5 6.8 - - + +
130A VAL* 3.2 16.8 - - + -
180A SER* 3.0 26.8 + - - +
181A TYR* 3.0 21.9 + - + +
183A ALA* 1.3 77.1 - - - +
185A ALA* 1.3 52.1 + - - +
187A ALA* 3.2 2.4 - - - +
188A THR* 2.8 38.3 + - - -
194A PHE* 3.3 38.6 - - + -
196A SER* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.1 22.4 - - + +
131A LYS 4.8 1.8 - - - -
132A TRP* 3.6 22.4 - - + -
135A VAL* 4.2 11.4 - - + -
181A TYR 2.9 9.3 + - - +
182A LEU* 2.9 22.4 - - + +
183A ALA 3.0 0.2 - - - -
184A LYS* 1.3 74.8 - - - +
186A VAL* 1.3 65.4 + - - +
188A THR* 3.3 1.0 + - - -
189A GLU* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TRP* 3.6 15.7 - - + -
145A LEU* 3.1 43.1 - - + -
149A VAL* 3.7 30.7 - - + -
150A ILE* 4.6 3.8 - - + +
182A LEU 3.0 11.8 + - - +
183A ALA* 2.9 12.4 + - - +
185A ALA* 1.3 77.8 - - - +
187A ALA* 1.3 70.6 + - - +
188A THR 3.0 0.2 + - - -
189A GLU* 3.1 8.8 + - - +
190A ALA* 3.1 10.5 + - + +
228A ILE* 3.5 18.8 - - + -
273A LEU* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PRO* 3.2 20.4 - - + -
183A ALA 2.8 12.3 + - - +
184A LYS 3.2 9.2 - - - +
186A VAL* 1.3 77.4 - - - +
188A THR* 1.3 67.2 + - - +
190A ALA 3.2 5.7 - - - +
192A SER* 3.2 28.2 + - - +
194A PHE* 3.6 17.0 - - + -
228A ILE* 3.5 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PRO* 3.0 24.0 + - - +
129A ASN* 4.0 4.5 - - - -
130A VAL 2.9 46.8 + - - +
131A LYS* 4.4 12.3 - - + -
184A LYS 2.8 21.1 + - - -
185A ALA 3.5 0.7 - - - -
186A VAL 3.0 0.4 + - - -
187A ALA* 1.3 66.9 - - - +
189A GLU* 1.3 54.7 + - - +
190A ALA 2.3 20.6 + - - -
191A ASN* 2.6 18.9 + - - +
192A SER 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LYS* 3.1 38.0 - - - +
132A TRP* 3.1 61.2 + - + +
150A ILE* 4.0 15.1 - - + +
185A ALA 2.9 17.8 + - - +
186A VAL 3.6 4.0 - - - +
188A THR* 1.3 75.0 - - - +
190A ALA* 1.3 57.1 + - - +
191A ASN 3.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A VAL* 4.6 8.7 - - + -
150A ILE* 3.9 20.4 - - + -
153A VAL* 4.1 24.0 - - + +
186A VAL* 3.1 10.8 + - + +
187A ALA* 3.2 3.1 - - - +
188A THR 2.3 16.2 + - - -
189A GLU* 1.3 72.3 - - - +
191A ASN* 1.3 71.5 + - - +
192A SER* 3.1 11.4 + - - +
226A PRO* 5.0 0.2 - - - +
----------------------------------------------------------
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