Contacts of the helix formed by residues 226 - 239 (chain A) in PDB entry 2QMQ
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 226 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLY 2.9 28.3 + - - +
105A MET* 3.6 26.1 + - - +
106A GLU 5.0 1.3 + - - -
109A ALA* 4.5 14.0 - - + +
111A VAL* 4.2 8.5 - - + -
224A ALA* 3.6 14.4 - - - +
225A PRO* 1.3 77.9 - - - +
227A LEU* 1.3 63.3 + - - +
228A GLU 3.1 2.9 - - - -
229A ASN* 2.9 21.8 + - - +
230A ILE* 3.0 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE* 5.1 4.7 - - + -
194A PRO* 4.1 26.9 - - + -
197A ILE* 4.8 6.1 - - + -
221A ILE* 3.6 23.3 - - + +
222A GLN 3.9 19.7 - - - +
224A ALA* 3.1 20.7 + - + +
225A PRO 3.4 1.4 + - - -
226A ASN* 1.3 77.0 + - - +
228A GLU* 1.4 64.8 + - + +
230A ILE* 3.1 25.6 + - + +
231A GLU* 2.9 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A VAL* 3.8 24.2 - - + +
112A PHE 5.3 2.0 - - - +
114A LEU* 4.8 13.7 - - - +
225A PRO 5.3 0.2 + - - -
226A ASN 3.1 1.4 - - - -
227A LEU* 1.4 84.0 - - + +
229A ASN* 1.3 63.4 + - - +
231A GLU* 3.5 22.3 + - - +
232A LEU* 3.4 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLY* 3.0 34.3 + - - +
105A MET* 3.4 15.1 - - + +
109A ALA* 4.2 0.2 - - - +
110A PRO 2.9 25.7 + - - -
111A VAL* 3.5 9.0 - - - +
112A PHE* 2.9 40.1 + - + +
118A TYR* 4.7 0.5 - - - -
226A ASN* 2.9 15.3 + - + +
228A GLU* 1.3 74.7 - - - +
230A ILE* 1.3 64.5 + - - +
232A LEU* 3.0 21.2 + - - +
233A TYR 3.2 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.0 1.0 - - + +
72A GLY* 3.6 44.6 - - - +
73A LEU 5.6 0.4 - - - +
105A MET* 3.9 22.2 - - - -
197A ILE* 3.5 24.2 - - + -
221A ILE* 5.1 3.6 - - + -
224A ALA* 3.7 30.7 - - + -
226A ASN* 3.0 21.4 + - - +
227A LEU* 3.1 17.2 + - + +
229A ASN* 1.3 75.3 - - - +
231A GLU* 1.3 59.1 + - - +
233A TYR* 3.1 5.7 + - - +
234A TRP* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE* 3.6 48.6 - - + +
197A ILE* 4.7 0.2 - - - +
227A LEU* 2.9 18.4 + - + +
228A GLU* 3.6 26.2 - - - +
229A ASN 3.1 0.2 - - - -
230A ILE* 1.3 79.1 - - - +
232A LEU* 1.3 59.1 + - + +
234A TRP* 3.3 8.2 + - + +
235A ASN* 2.9 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 4.6 11.4 - - + +
113A PRO 5.8 0.2 - - - +
114A LEU* 6.2 4.7 - - + -
116A TYR* 3.9 38.6 - - + +
118A TYR* 3.6 31.9 - - + +
228A GLU 3.4 16.1 + - - +
229A ASN* 3.0 9.0 + - - +
231A GLU* 1.3 78.8 - - + +
233A TYR* 1.3 58.9 + - - +
235A ASN* 3.3 18.4 + - - +
236A SER* 3.0 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 3.7 6.8 - + - -
69A HIS* 2.8 42.3 + + - -
71A VAL* 3.7 31.6 - - + -
72A GLY 4.7 1.3 - - - -
102A ALA* 4.4 2.5 - - + -
105A MET* 3.6 29.4 - - + -
118A TYR* 3.8 13.8 - + + -
121A LEU* 3.9 8.1 - - + -
124A LEU* 3.8 30.1 - - + -
147A ALA* 3.4 28.3 - - + +
151A ILE* 3.6 12.6 - - + +
229A ASN 3.2 4.0 + - - -
230A ILE* 3.1 8.8 + - - +
232A LEU* 1.3 72.3 - - - +
234A TRP* 1.3 60.4 + - - +
236A SER* 3.2 2.1 + - - +
237A TYR* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 3.6 25.6 - - + +
176A LYS* 6.0 1.6 - - - -
184A HIS* 3.9 20.0 - + - -
193A ILE* 4.3 23.0 - - + +
196A MET* 3.9 28.4 - - + +
197A ILE* 3.7 24.7 - - + +
200A HIS* 3.5 41.3 - + + -
230A ILE 2.9 13.4 + - - +
231A GLU* 3.3 9.6 + - + +
233A TYR* 1.3 75.6 - - - +
235A ASN* 1.3 65.7 + - - +
237A TYR* 3.1 14.0 + + - +
238A ASN* 2.8 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE* 5.7 1.4 - - - +
231A GLU* 2.9 33.2 + - - +
232A LEU* 3.5 22.9 - - + +
233A TYR 3.3 0.4 - - - -
234A TRP* 1.3 87.5 - - - +
236A SER* 1.3 64.0 + - - +
238A ASN* 3.2 8.3 + - - +
239A ASN* 2.9 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 3.7 10.7 + - - +
119A PRO 2.7 30.9 + - - -
120A SER* 4.0 8.2 - - - +
121A LEU* 3.8 22.7 + - - +
232A LEU 3.0 14.3 + - - -
233A TYR* 3.7 7.6 - - - -
235A ASN* 1.3 77.0 - - - +
237A TYR* 1.3 61.1 + - - +
239A ASN* 3.2 7.0 + - - +
240A ARG* 3.2 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.0 13.0 - - + -
121A LEU* 3.9 11.8 - - + +
146A GLY 4.6 2.9 - - - -
147A ALA* 3.7 33.0 - - + -
150A TYR* 5.4 1.8 - - + -
170A ASN 5.3 1.4 + - - -
172A ASP* 3.8 12.1 + - + +
176A LYS* 5.5 3.6 - - - -
200A HIS* 3.6 26.8 - + - -
233A TYR 2.9 13.5 + - - +
234A TRP* 3.4 18.2 - + - +
236A SER* 1.3 76.8 - - - +
238A ASN* 1.3 78.7 + - - +
240A ARG* 3.0 74.6 + - - +
267A HIS* 3.7 21.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LYS* 3.3 43.3 + - - +
181A TRP* 3.4 27.2 - - + -
184A HIS* 3.4 16.3 + - - -
234A TRP* 2.8 62.1 + - - +
235A ASN* 3.2 9.0 + - - +
237A TYR* 1.3 89.5 - - - +
239A ASN* 1.3 59.8 + - - +
240A ARG* 3.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TRP* 3.5 22.7 - - - -
235A ASN* 2.9 34.3 + - - +
236A SER* 3.7 7.2 - - - +
237A TYR 3.1 0.6 - - - -
238A ASN* 1.3 76.9 - - - +
240A ARG* 1.3 65.3 - - - +
241A ARG* 3.6 1.4 + - - +
----------------------------------------------------------
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