Contacts of the helix formed by residues 161 - 175 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A CL 4.2 5.1 - - - +
160A VAL* 1.3 71.6 - - - +
162A ASN* 1.3 58.2 + - - +
163A GLU* 3.5 9.9 + - - +
164A GLU* 3.1 34.1 + - + +
165A ALA* 3.0 26.0 + - - +
322A LYS* 3.8 18.7 - - + +
323A LEU 2.9 13.6 + - - +
324A SER* 4.9 8.0 - - - +
325A THR* 4.6 3.5 + - - +
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Residues in contact with ASN 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A CL 3.5 15.0 - - + +
147A ASP 4.7 3.2 + - - -
149A GLU* 4.9 6.1 + - - -
159A THR* 4.9 0.6 - - - -
160A VAL* 3.1 35.5 + - - +
161A ASP* 1.3 69.0 + - - +
163A GLU* 1.3 66.1 + - - +
165A ALA* 3.2 6.7 + - - +
166A ALA* 3.0 20.6 + - - +
191A SER* 5.2 1.2 + - - -
192A THR* 3.7 24.3 - - - +
195A GLY* 3.7 19.5 - - - +
196A ARG* 2.8 49.6 + - + +
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A CL 4.0 2.0 - - - +
161A ASP* 3.4 7.7 + - - +
162A ASN* 1.3 79.0 - - - +
164A GLU* 1.3 59.0 + - - +
167A TYR* 2.8 30.9 + - - +
195A GLY* 3.2 18.4 + - - +
198A ASN* 3.8 22.3 + - + +
199A GLY* 3.3 19.7 - - - +
202A LYS* 3.6 30.6 + - + +
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ASP* 3.1 32.3 + - + +
163A GLU* 1.3 79.1 - - - +
165A ALA* 1.3 62.6 + - - +
167A TYR* 3.6 23.4 - - - +
168A ILE* 3.1 51.6 + - + +
202A LYS* 4.4 11.4 + - - -
325A THR* 5.0 2.0 - - - +
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL* 5.1 1.1 - - + -
161A ASP 3.0 13.5 + - - +
162A ASN* 3.5 11.9 - - - +
163A GLU 3.2 0.4 - - - -
164A GLU* 1.3 78.6 - - - +
166A ALA* 1.3 62.0 + - - +
168A ILE* 4.9 0.9 - - - -
169A ALA 3.2 15.8 + - - -
278A PHE* 3.8 23.3 - - + -
294A ILE* 3.2 20.6 - - + +
325A THR* 3.4 30.6 + - + +
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASN 3.0 7.6 + - - +
163A GLU 4.2 0.9 - - - +
165A ALA* 1.3 73.0 - - - +
167A TYR* 1.3 59.6 + - - +
169A ALA* 3.9 3.6 - - - +
170A THR* 2.7 38.7 + - - +
183A LEU* 5.6 1.3 - - + -
196A ARG* 3.0 49.4 - - + +
199A GLY 4.0 1.8 - - - -
200A TYR* 4.1 4.3 - - + +
248A VAL* 5.7 1.1 - - + -
250A THR* 5.2 4.3 - - + -
278A PHE* 3.8 11.8 - - + -
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Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLU 2.8 19.6 + - - +
164A GLU* 3.6 26.0 - - - +
166A ALA* 1.3 76.9 - - - +
168A ILE* 1.3 73.5 + - + +
171A LYS* 3.0 50.3 + - + +
199A GLY* 3.3 14.9 - - - +
202A LYS* 3.5 42.0 - - + -
203A ALA* 3.7 20.4 - - + +
206A GLU* 2.6 43.1 + - - -
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLU* 3.1 43.5 + - + +
165A ALA* 3.8 4.7 - - - +
167A TYR* 1.3 87.7 - - + +
169A ALA* 1.3 65.3 + - - +
171A LYS* 3.6 17.9 + - - +
172A ARG* 3.1 23.0 + - - +
294A ILE* 4.0 6.3 - - + -
325A THR* 6.2 0.2 - - - +
327A LEU* 3.6 36.5 - - + +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ALA 3.2 15.7 + - - +
166A ALA 3.9 3.8 - - - +
168A ILE* 1.3 80.3 - - - +
170A THR* 1.3 62.1 + - - +
172A ARG* 3.4 6.3 + - - +
173A VAL* 3.3 26.0 + - - +
248A VAL* 4.0 16.2 - - + -
276A VAL* 3.6 28.2 - - + +
278A PHE* 4.2 3.6 - - + -
294A ILE* 3.8 14.1 - - + -
327A LEU* 4.7 1.8 - - - -
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Residues in contact with THR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ALA* 2.7 23.4 + - - +
169A ALA* 1.3 73.1 - - - +
171A LYS* 1.3 61.6 + - - +
173A VAL* 3.1 5.5 + - - +
174A LEU* 2.9 41.6 + - + +
181A VAL* 4.5 7.6 - - + -
200A TYR* 3.5 45.4 - - + +
203A ALA* 3.7 20.6 - - + -
204A ILE* 4.1 5.2 - - + -
248A VAL* 4.0 15.6 - - - +
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A TYR* 3.0 45.8 + - + +
168A ILE* 3.7 23.8 + - - +
170A THR* 1.3 76.4 - - - +
172A ARG* 1.3 56.2 + - - +
174A LEU* 3.1 13.8 + - - +
175A GLU* 2.9 45.9 + - - +
203A ALA* 3.8 4.8 - - + +
206A GLU* 3.9 17.5 - - - +
207A PHE* 4.0 17.0 - - + -
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Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE 3.1 17.4 + - - +
169A ALA* 3.5 7.9 - - - +
170A THR 3.2 0.2 - - - -
171A LYS* 1.3 76.3 - - - +
173A VAL* 1.3 61.3 + - - +
175A GLU* 3.3 43.5 + - - +
176A SER 4.0 1.7 + - - -
276A VAL* 4.2 6.1 - - + -
292A THR* 4.9 0.4 - - + -
327A LEU* 3.9 18.6 - - + -
329A ILE* 4.0 33.2 - - - +
330A ARG 5.7 0.2 + - - -
333A CYS* 3.3 49.0 + - + +
334A SER* 3.8 20.6 + - - -
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ALA 3.4 13.9 - - - +
170A THR 3.1 7.7 + - - +
172A ARG* 1.3 76.0 - - - +
174A LEU* 1.3 57.8 + - - +
176A SER* 2.6 29.8 + - - -
178A CYS* 4.2 4.4 - - - +
181A VAL* 3.8 21.3 - - + -
246A GLY* 3.8 28.7 - - - -
247A ILE 4.2 7.9 - - - +
248A VAL* 3.8 16.4 - - + -
274A ILE* 4.0 17.0 - - + -
275A ILE 5.2 1.1 - - - -
276A VAL* 3.7 21.3 - - + +
333A CYS 5.2 0.7 - - - -
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A THR* 2.9 28.0 + - + +
171A LYS 3.1 7.8 + - - +
173A VAL* 1.3 71.0 - - - +
175A GLU* 1.3 59.9 + - - +
176A SER 3.0 15.4 - - - +
178A CYS 3.9 14.7 - - - +
179A LYS* 4.6 0.7 - - - -
181A VAL* 3.7 24.9 - - + -
203A ALA* 3.6 35.2 - - + +
204A ILE* 4.0 7.6 - - + -
207A PHE* 3.6 38.3 - - + -
209A LEU* 3.8 25.1 - - + -
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LYS* 2.9 35.9 + - - +
172A ARG* 3.4 42.6 + - - +
173A VAL 3.2 0.4 - - - -
174A LEU* 1.3 73.1 - - - +
176A SER* 1.3 63.0 + - - +
207A PHE* 4.6 11.9 - - + -
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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