Contacts of the helix formed by residues 161 - 175 (chain B) in PDB entry 2QU7
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 ASP 161 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B CL 4.3 4.0 - - - +
160B VAL* 1.3 71.4 - - - +
162B ASN* 1.3 57.8 + - - +
163B GLU* 3.4 10.0 + - - +
164B GLU* 3.0 49.1 + - - +
165B ALA* 3.1 26.7 + - - +
322B LYS* 3.7 17.9 - - + +
323B LEU 2.8 12.9 + - - +
324B SER* 4.9 1.7 - - - +
325B THR* 4.8 1.9 + - - +
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Residues in contact with ASN 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B CL 3.7 6.9 - - + +
147B ASP 4.5 4.6 + - - -
159B THR* 4.8 3.0 - - - -
160B VAL* 3.0 39.3 + - - +
161B ASP* 1.3 70.4 + - - +
163B GLU* 1.3 63.7 + - - +
165B ALA* 3.5 5.2 + - - +
166B ALA* 3.2 18.2 + - - +
191B SER 5.2 1.0 + - - +
192B THR* 3.7 25.0 - - - +
195B GLY* 3.6 27.0 - - - +
196B ARG* 2.7 47.7 + - - +
322B LYS* 5.1 1.6 - - - +
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B CL 4.2 1.8 - - - +
161B ASP* 3.3 8.1 + - - +
162B ASN* 1.3 75.2 - - - +
164B GLU* 1.3 60.1 + - - +
165B ALA 3.2 0.2 + - - -
166B ALA 3.2 0.9 + - - -
167B TYR* 2.8 31.5 + - - +
195B GLY* 3.2 16.7 + - - +
198B ASN* 3.6 22.3 + - + +
199B GLY* 3.2 21.6 - - - +
202B LYS* 3.7 25.8 - - + +
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Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ASP* 3.0 38.4 + - - +
163B GLU* 1.3 75.8 - - - +
165B ALA* 1.3 53.5 + - - +
167B TYR* 3.2 11.4 + - + +
168B ILE* 2.7 53.6 + - + +
202B LYS* 6.3 0.7 - - - +
324B SER* 3.6 27.3 + - - -
325B THR* 4.3 10.5 + - - +
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B VAL* 5.2 1.1 - - + -
161B ASP 3.1 16.7 + - - +
162B ASN* 3.6 9.0 - - - +
163B GLU 3.2 0.2 - - - -
164B GLU* 1.3 78.2 - - - +
166B ALA* 1.3 58.3 + - - +
168B ILE* 3.5 1.5 + - - -
169B ALA* 3.1 21.3 + - - +
196B ARG* 5.6 0.2 - - - +
278B PHE* 3.8 21.8 - - + -
294B ILE* 3.3 21.0 - - + +
325B THR* 3.3 31.9 - - + +
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ASN 3.2 5.2 + - - +
165B ALA* 1.3 76.9 - - - +
167B TYR* 1.3 60.5 + - - +
169B ALA* 4.3 2.7 - - - -
170B THR* 2.7 39.7 + - - +
183B LEU* 5.9 0.4 - - + -
196B ARG* 3.0 47.8 - - + +
199B GLY* 3.9 2.9 - - - -
200B TYR* 3.9 4.3 - - + +
248B VAL* 5.5 2.0 - - + -
250B THR* 5.3 3.4 - - + -
278B PHE* 3.7 13.7 - - + -
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Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLU 2.8 19.4 + - - +
164B GLU* 3.4 10.8 - - + +
166B ALA* 1.3 74.4 - - - +
168B ILE* 1.3 78.4 + - + +
171B LYS* 2.9 58.1 + - + +
199B GLY* 3.3 15.1 - - - +
202B LYS* 3.8 31.8 + - + -
203B ALA* 3.7 30.9 - - + +
206B GLU* 2.7 44.1 + - - -
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLU* 2.7 37.0 + - + +
165B ALA* 3.7 5.8 - - - +
167B TYR* 1.3 90.4 - - + +
169B ALA* 1.3 62.1 + - - +
171B LYS* 3.8 16.7 - - - +
172B ARG* 3.1 22.2 + - - +
294B ILE* 4.1 5.6 - - + -
325B THR* 5.9 0.4 - - - +
326B LYS* 6.6 0.2 - - - -
327B LEU* 3.6 39.3 - - + +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA 3.1 17.9 + - - +
166B ALA 3.9 3.6 - - - +
168B ILE* 1.3 77.3 - - - +
170B THR* 1.3 63.4 + - - +
172B ARG* 3.4 10.0 + - - +
173B VAL* 3.4 19.1 + - - +
248B VAL* 4.1 9.2 - - + -
276B VAL* 3.7 28.3 - - + +
278B PHE* 4.0 13.0 - - + -
294B ILE* 3.9 11.0 - - + -
327B LEU* 4.6 7.0 - - - -
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Residues in contact with THR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ALA* 2.7 24.8 + - - +
169B ALA* 1.3 74.9 - - - +
171B LYS* 1.3 64.9 + - - +
173B VAL* 3.1 6.2 + - - +
174B LEU* 3.0 32.4 + - + +
181B VAL* 4.8 6.7 - - + -
200B TYR* 3.4 47.4 - - + +
203B ALA* 3.8 19.5 - - + -
204B ILE* 4.3 4.5 - - + -
248B VAL* 4.0 16.7 - - - +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B TYR* 2.9 59.1 + - + +
168B ILE* 3.8 16.7 - - - +
170B THR* 1.3 76.3 - - - +
172B ARG* 1.3 56.3 + - - +
174B LEU* 3.2 8.7 + - - +
175B GLU* 2.9 54.1 + - - +
203B ALA* 3.8 9.5 - - + +
206B GLU* 3.8 11.4 + - - +
207B PHE* 3.9 18.2 - - + -
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Residues in contact with ARG 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ILE 3.1 18.0 + - - +
169B ALA* 3.6 7.6 - - - +
170B THR 3.2 0.4 - - - -
171B LYS* 1.3 76.9 - - - +
173B VAL* 1.3 63.2 + - - +
175B GLU* 3.5 30.8 + - - +
176B SER* 3.8 4.2 + - - -
276B VAL* 4.4 6.3 - - + -
327B LEU* 4.2 26.2 - - + -
329B ILE* 4.0 27.5 - - - +
333B CYS* 3.4 48.6 + - + +
334B SER* 4.2 18.0 + - - -
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ALA 3.4 7.2 + - - +
170B THR 3.1 7.0 + - - +
172B ARG* 1.3 75.7 - - - +
174B LEU* 1.3 59.0 + - - +
176B SER* 2.5 27.5 + - - -
178B CYS* 3.5 6.8 - - + +
181B VAL* 3.8 28.7 - - + -
246B GLY* 3.8 15.9 - - - -
247B ILE 4.5 6.7 - - - +
248B VAL* 3.8 14.6 - - + -
274B ILE* 3.7 23.8 - - + -
275B ILE 5.1 1.1 - - - -
276B VAL* 3.5 29.6 - - + +
333B CYS* 5.1 0.4 - - + -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B THR* 3.0 26.4 + - + +
171B LYS 3.2 7.6 + - - +
173B VAL* 1.3 72.9 - - - +
175B GLU* 1.3 51.9 + - - +
176B SER 2.7 27.3 - - - +
178B CYS 3.4 16.4 - - - +
179B LYS* 3.6 22.2 - - + +
181B VAL* 3.6 19.5 - - + -
203B ALA* 3.7 33.9 - - + +
204B ILE* 4.1 8.5 - - + +
207B PHE* 3.8 28.5 - - + -
209B LEU* 3.7 24.0 - - + -
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Residues in contact with GLU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LYS* 2.9 42.0 + - - +
172B ARG* 3.7 28.5 + - - +
173B VAL 3.3 0.4 - - - -
174B LEU* 1.3 74.9 - - - +
176B SER* 1.3 56.6 + - - +
207B PHE* 4.1 16.6 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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