Contacts of the helix formed by residues 177 - 188 (chain X) in PDB entry 2QW0
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 ALA 177 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173X ILE* 3.8 17.3 - - + -
174X PRO* 3.1 22.1 + - + +
175X GLN 3.0 0.8 + - - -
176X ARG* 1.3 78.1 - - - +
178X ALA* 1.3 66.9 + - - +
179X GLU 3.2 1.9 + - - -
180X SER* 3.4 6.2 + - - -
181X ARG* 3.1 26.5 + - - +
359X ASP 3.3 17.5 - - - +
360X SER* 3.6 19.7 - - - +
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Residues in contact with ALA 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X GLN 4.3 2.5 - - - +
4X VAL* 3.5 38.1 - - + +
7X MET* 3.8 11.0 - - + -
157X PHE* 5.6 1.3 - - + -
173X ILE* 5.3 0.2 - - - +
174X PRO 4.3 1.6 + - - +
175X GLN 3.5 13.4 + - - +
177X ALA* 1.3 77.9 - - - +
179X GLU* 1.3 62.7 + - - +
181X ARG* 3.3 2.4 + - - +
182X VAL* 3.0 26.9 + - - +
212X PHE* 4.0 16.0 - - + -
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Residues in contact with GLU 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X MET* 4.8 3.5 - - - +
2X GLN* 2.9 59.2 + - + +
7X MET* 4.1 11.4 - - - +
176X ARG 4.5 7.1 + - - +
177X ALA 3.2 1.2 + - - -
178X ALA* 1.3 77.0 - - - +
180X SER* 1.3 52.2 + - - +
182X VAL* 3.0 4.5 + - - +
183X LEU* 2.7 62.6 + - + +
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Residues in contact with SER 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176X ARG 4.9 1.3 + - - -
177X ALA 3.4 5.9 + - - -
179X GLU* 1.3 75.1 - - - +
181X ARG* 1.3 62.0 + - - +
182X VAL 3.1 5.3 + - - -
183X LEU 3.9 0.2 - - - -
184X PHE* 3.4 25.6 + - - +
310X MET* 5.2 0.7 - - - +
329X PHE* 3.6 45.9 - - - -
359X ASP* 4.5 7.8 - - - +
360X SER* 3.2 31.4 + - - -
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Residues in contact with ARG 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173X ILE* 3.7 18.1 - - - +
177X ALA* 3.1 27.3 + - - +
178X ALA 3.6 5.4 - - - +
179X GLU 3.2 0.2 - - - -
180X SER* 1.3 81.8 + - - +
182X VAL* 1.3 56.5 + - - +
184X PHE* 3.3 21.4 - - - -
208X VAL* 3.5 23.2 - - - +
212X PHE* 3.7 43.5 - - + +
213X ALA 4.0 2.4 + - - -
307X THR 2.8 29.9 + - - -
308X GLU 2.9 19.0 + - - -
309X ALA 3.6 2.0 - - - +
310X MET* 3.5 38.8 - - + +
360X SER* 2.8 31.1 + - - -
362X PHE 4.2 0.6 - - - +
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Residues in contact with VAL 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X MET* 3.8 17.5 - - + -
178X ALA 3.0 14.1 + - - +
179X GLU 3.0 8.1 + - - +
181X ARG* 1.3 79.6 - - - +
183X LEU* 1.3 69.0 + - + +
184X PHE 3.2 4.5 - - - -
185X MET* 3.0 31.2 + - - +
186X SER* 4.1 0.7 + - - -
212X PHE* 3.6 18.4 - - + +
213X ALA* 5.1 0.2 - - - +
216X VAL* 3.6 31.0 - - + -
217X ALA* 3.8 21.2 - - + +
220X ALA* 4.7 6.7 - - + -
221X LEU* 5.5 7.0 - - + -
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Residues in contact with LEU 183 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X GLN* 5.7 0.9 - - - +
7X MET* 6.0 1.3 - - - -
179X GLU* 2.7 48.9 + - + +
180X SER 3.7 0.4 + - - -
182X VAL* 1.3 79.7 - - + +
184X PHE* 1.3 60.6 + - - +
185X MET 3.0 1.6 - - - -
186X SER* 3.0 19.3 + - - +
187X THR* 2.8 30.8 + - + +
221X LEU* 5.1 11.2 - - + -
329X PHE* 4.0 21.1 - - + -
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Residues in contact with PHE 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180X SER 3.4 15.9 + - - +
181X ARG 3.3 28.0 - - - -
182X VAL 3.2 0.8 + - - -
183X LEU* 1.3 77.2 - - - +
185X MET* 1.3 84.2 + - + +
186X SER 3.0 2.2 - - - -
187X THR* 3.5 9.6 - - - -
188X GLN* 2.8 47.3 + - + +
189X VAL* 3.4 6.6 + - + -
213X ALA* 3.8 12.3 - - + -
249X PHE* 4.3 7.9 - + - -
303X ALA* 5.2 3.8 - - + -
310X MET* 3.8 20.9 - - + -
311X ASN* 3.4 36.6 - - + -
329X PHE* 3.9 7.8 - - + -
505X 34Z 3.6 18.4 - - + -
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Residues in contact with MET 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182X VAL 3.0 16.3 + - - +
184X PHE* 1.3 103.0 - - + +
186X SER* 1.3 56.8 + - - +
189X VAL* 3.2 39.2 - - + +
190X GLY 3.2 0.5 + - - -
191X LEU* 3.1 47.8 + - + +
213X ALA* 3.4 37.5 - - + +
214X VAL* 5.8 0.2 - - + -
217X ALA* 4.6 4.7 - - + -
221X LEU* 5.8 1.3 - - + -
247X SER* 5.5 4.3 - - - +
248X LEU 6.5 0.2 - - - -
249X PHE* 3.9 29.6 - - + -
278X THR* 4.4 3.4 - - - +
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Residues in contact with SER 186 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182X VAL 4.1 0.6 + - - -
183X LEU* 3.3 27.6 - - - +
184X PHE 3.0 0.2 - - - -
185X MET* 1.3 80.2 - - - +
187X THR* 1.3 63.3 + - - +
188X GLN 3.4 0.2 - - - -
190X GLY* 3.0 25.5 + - - -
191X LEU* 2.5 25.7 + - - +
192X ARG* 4.4 2.9 - - - -
221X LEU* 5.3 7.7 - - - +
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Residues in contact with THR 187 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183X LEU* 2.8 23.8 + - + +
184X PHE* 3.5 5.9 - - - -
186X SER* 1.3 74.3 - - - +
188X GLN* 1.3 86.4 + - - +
190X GLY* 5.6 0.3 - - - -
314X TYR* 4.8 5.0 + - - -
328X PHE* 3.5 38.1 - - + +
329X PHE* 4.2 4.5 - - + -
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Residues in contact with GLN 188 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184X PHE* 2.8 26.4 + - + +
187X THR* 1.3 101.2 + - - +
189X VAL* 1.3 68.0 + - + +
190X GLY 3.5 0.6 + - - -
301X VAL* 4.7 2.4 - - - +
311X ASN* 2.8 34.8 - - - +
314X TYR* 3.5 54.2 - - + -
316X ARG* 4.4 10.9 - - - -
327X GLY* 3.7 5.9 - - - -
328X PHE* 3.0 41.4 + - - +
330X SER* 4.7 0.2 + - - -
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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