Contacts of the helix formed by residues 178 - 190 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 6.1 0.3 - - - +
176B GLY 3.2 5.4 - - - -
177B THR* 1.3 80.2 + - - +
179B LYS* 1.3 65.2 + - - +
180B SER* 3.2 4.3 - - - -
181B TYR* 3.1 21.7 + - - +
182B LEU* 3.3 9.2 + - - +
800B PO4 3.1 18.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 3.3 32.7 - - + +
172B TYR 3.7 2.9 - - - -
173B GLY* 2.8 25.8 + - - +
174B PRO 3.6 10.5 + - - -
175B PRO* 4.6 0.2 - - - +
177B THR* 3.6 11.9 + - - +
178B GLY* 1.3 73.1 - - - +
180B SER* 1.3 63.8 + - - +
182B LEU* 3.0 11.2 + - - +
183B ALA* 2.9 24.8 + - - +
230B PHE* 4.1 1.8 - - - -
275B ALA* 3.8 23.8 - - + -
276B THR 3.0 24.2 - - - +
277B ASN* 2.6 23.3 + - - +
296B ILE* 4.7 9.6 - - + -
800B PO4 3.0 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLY* 4.8 1.6 - - - -
179B LYS* 1.3 79.2 - - - +
181B TYR* 1.3 62.6 + - - +
183B ALA* 3.4 3.5 + - - +
184B LYS* 3.1 21.0 + - - +
194B PHE* 4.0 7.6 - - - -
196B SER* 5.2 2.1 + - - -
230B PHE* 3.4 27.3 - - - -
232B ASP* 4.2 6.3 + - - -
800B PO4 3.4 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 3.7 32.1 - - + +
134B ASP* 3.6 27.9 + - - +
135B VAL* 3.9 25.1 - - + -
136B ALA 5.8 0.2 - - - -
178B GLY* 3.1 13.9 + - - +
180B SER* 1.3 77.3 + - - +
182B LEU* 1.3 60.5 + - - +
184B LYS* 3.3 8.8 + - + +
185B ALA* 2.8 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B TRP* 3.6 19.5 - - + -
135B VAL* 4.6 13.2 - - + +
138B LEU* 3.9 20.0 - - + -
141B ALA* 4.3 5.2 - - + -
142B LYS* 4.6 7.4 - - + -
145B LEU* 3.5 28.9 - - + -
171B LEU* 4.7 8.1 - - + -
178B GLY 3.3 6.1 + - - +
179B LYS* 3.0 13.3 + - - +
181B TYR* 1.3 75.8 - - - +
183B ALA* 1.3 68.1 + - - +
185B ALA* 2.8 24.1 + - + +
186B VAL* 3.2 9.4 + - - +
296B ILE* 3.6 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 5.4 0.4 - - - -
171B LEU* 4.5 6.2 - - + +
179B LYS 2.9 7.3 + - - +
180B SER 3.5 9.0 - - - +
182B LEU* 1.3 74.1 - - - +
184B LYS* 1.3 63.6 + - - +
186B VAL* 3.1 22.8 + - - +
187B ALA* 3.2 4.7 + - - +
194B PHE* 3.4 8.5 - - + -
230B PHE* 3.5 41.1 - - + -
273B LEU* 3.8 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLU* 5.9 1.3 - - - +
128B PRO* 4.0 12.3 - - + -
130B VAL* 3.3 16.4 - - + -
180B SER 3.1 10.6 + - - +
181B TYR* 3.4 13.2 - - + +
182B LEU 3.1 0.6 - - - -
183B ALA* 1.3 73.5 - - - +
185B ALA* 1.3 53.6 - - - +
186B VAL 2.6 17.5 + - - -
187B ALA* 3.0 2.8 + - - +
188B THR* 2.9 24.6 + - - -
194B PHE* 3.2 23.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 3.1 27.8 - - + +
131B LYS 4.5 3.1 - - - +
132B TRP* 3.6 30.9 - - + -
135B VAL* 3.6 25.8 - - + -
181B TYR 2.8 13.2 + - - +
182B LEU* 2.8 17.9 + - - +
184B LYS* 1.3 69.6 - - - +
186B VAL* 1.3 59.8 + - - +
188B THR 4.1 0.2 - - - -
189B GLU* 3.6 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B TRP* 3.3 25.4 - - + -
145B LEU* 3.3 26.9 - - + -
149B VAL* 4.2 21.1 - - + -
150B ILE* 4.1 20.0 - - + -
182B LEU 3.4 9.0 - - - +
183B ALA* 3.1 10.8 - - - +
184B LYS 2.6 4.2 + - - -
185B ALA* 1.3 72.8 - - - +
187B ALA* 1.3 66.0 + - - +
188B THR 2.6 6.0 + - - -
189B GLU 3.1 12.6 + - - -
190B ALA* 3.1 14.4 + - + +
228B ILE* 3.9 14.4 - - + -
273B LEU* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PRO* 3.6 12.1 - - + -
183B ALA 3.2 0.4 + - - -
184B LYS 3.0 4.2 + - - +
186B VAL* 1.3 78.9 - - - +
188B THR* 1.3 59.3 + - - +
190B ALA* 3.7 1.2 + - - -
192B SER* 2.9 35.1 + - - +
193B THR 4.4 6.1 - - - +
194B PHE* 3.3 35.9 - - + -
228B ILE* 3.1 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PRO* 2.9 36.4 - - - +
129B ASN* 3.8 4.3 - - - -
130B VAL* 3.2 40.9 - - - +
131B LYS* 4.5 1.1 - - + +
184B LYS 2.9 13.6 + - - -
186B VAL 2.6 4.6 + - - -
187B ALA* 1.3 69.3 - - - +
189B GLU* 1.3 57.9 + - + +
190B ALA 2.5 17.9 + - - -
191B ASN* 2.8 16.5 + - - -
192B SER 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS* 2.9 33.7 - - - +
132B TRP* 3.1 50.7 + - + +
133B GLU* 4.7 0.7 + - - +
150B ILE* 4.0 12.4 - - - +
185B ALA 3.6 10.7 + - - +
186B VAL 3.1 5.5 + - - +
188B THR* 1.3 75.1 - - + +
190B ALA* 1.3 56.2 - - - +
191B ASN 3.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 4.9 7.4 - - + -
150B ILE* 3.9 22.4 - - + -
153B VAL* 5.5 9.3 - - + +
186B VAL* 3.3 18.4 - - + +
187B ALA* 4.0 1.1 - - - +
188B THR 2.5 7.3 + - - -
189B GLU* 1.3 74.5 - - - +
191B ASN* 1.3 53.8 + - - +
192B SER* 2.7 37.8 + - - +
226B PRO* 4.5 3.8 - - - +
228B ILE* 5.6 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