Contacts of the helix formed by residues 168 - 181 (chain C) in PDB entry 2QW4
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 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C TYR* 3.1 5.5 + - - -
166C LEU 3.3 6.6 + - - +
167C VAL* 1.3 77.3 - - - +
169C VAL* 1.3 57.2 + - - +
170C PRO* 2.8 14.2 - - + +
171C ALA* 2.6 29.3 + - - +
172C PHE 3.0 20.8 + - - -
207C HIS* 2.8 24.5 + - - -
208C VAL* 5.6 0.3 - - - +
211C VAL* 4.6 10.6 - - - +
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C VAL* 3.8 26.2 - - + -
41C HIS* 4.5 21.3 - - + +
42C LEU* 4.6 19.5 - - + -
122C TYR* 3.6 14.6 + - + +
168C ASP* 1.3 71.1 - - - +
170C PRO* 1.3 78.1 - - + +
172C PHE* 3.2 4.3 + - - +
173C ALA* 2.9 21.0 + - - +
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Residues in contact with PRO 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 3.9 21.4 - - + +
38C VAL* 3.6 20.9 - - + -
168C ASP* 2.8 19.3 - - + +
169C VAL* 1.3 90.3 - - + +
171C ALA* 1.3 60.4 + - - +
173C ALA* 3.1 11.1 + - - +
174C CYS* 3.1 19.9 + - - -
207C HIS* 3.5 30.5 - - + +
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Residues in contact with ALA 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C VAL* 3.8 15.3 - - + -
168C ASP* 2.6 27.6 + - - +
170C PRO* 1.3 69.0 - - - +
172C PHE* 1.3 67.5 + - - +
173C ALA 3.2 0.2 + - - -
174C CYS* 3.3 3.3 + - - +
175C LEU* 2.8 24.4 + - - +
204C LEU* 4.2 14.3 - - + +
207C HIS* 4.3 3.3 - - + -
208C VAL* 4.2 22.0 - - + -
224C LEU* 4.3 10.0 - - + +
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Residues in contact with PHE 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C HIS* 3.5 35.0 - + - -
118C LEU* 3.5 45.5 - - + -
119C ARG* 4.0 16.2 - - + -
122C TYR* 3.4 61.5 - + + -
162C LEU* 4.5 4.5 - - + -
167C VAL* 3.7 10.9 - - + +
168C ASP 3.0 11.4 + - - +
169C VAL 3.7 3.6 - - - +
171C ALA* 1.3 76.2 - - - +
173C ALA* 1.3 54.6 + - - +
175C LEU* 2.8 9.3 + - + -
176C SER* 2.8 47.4 + - - -
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Residues in contact with ALA 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 5.3 0.2 - - + -
37C LEU* 4.0 18.9 - - + +
38C VAL* 4.0 28.3 - - + +
41C HIS* 4.3 15.0 - - + +
89C TRP* 4.9 3.3 + - - -
169C VAL 2.9 14.0 + - - +
170C PRO* 3.2 12.3 - - + +
171C ALA 3.1 0.4 - - - -
172C PHE* 1.3 77.6 - - - +
174C CYS* 1.3 59.9 + - - +
176C SER* 3.3 14.9 + - - -
177C ALA* 3.5 12.6 - - - +
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Residues in contact with CYS 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.4 32.8 - - - -
37C LEU* 4.0 9.4 - - - -
170C PRO 3.1 8.8 + - - +
171C ALA 3.7 4.9 - - - +
173C ALA* 1.3 75.9 - - - +
175C LEU* 1.3 58.5 + - - +
176C SER 3.2 0.4 - - - -
177C ALA* 3.1 3.7 + - - +
178C LEU* 2.8 34.1 + - - +
200C ILE* 3.9 11.8 - - + +
203C CYS* 3.7 18.4 - - - -
204C LEU* 3.5 32.8 - - + -
207C HIS* 5.8 0.4 - - - -
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Residues in contact with LEU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 3.9 24.7 - - + -
162C LEU* 6.1 1.6 - - + -
171C ALA 2.8 18.5 + - - +
172C PHE* 2.8 13.2 + - + +
174C CYS* 1.3 77.9 - - - +
176C SER* 1.3 61.3 + - - +
178C LEU* 3.5 12.6 - - + +
179C VAL* 3.3 23.9 + - - +
204C LEU* 4.8 4.7 - - + -
224C LEU* 3.6 38.1 - - + +
225C LEU* 4.0 25.4 - - + -
227C LYS* 5.3 5.2 - - + -
228C LEU* 3.8 29.2 - - + -
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Residues in contact with SER 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C HIS* 5.2 2.1 + - - -
89C TRP* 3.4 19.3 + - - -
115C LEU* 3.5 12.5 - - - +
118C LEU* 4.0 17.9 - - - -
119C ARG* 5.1 4.9 - - - -
172C PHE* 2.8 32.6 + - - -
173C ALA* 3.3 12.5 + - - -
175C LEU* 1.3 76.2 - - - +
177C ALA* 1.3 64.4 + - - +
178C LEU 3.1 0.2 - - - -
179C VAL* 2.9 20.0 + - - +
180C LEU 3.2 8.5 + - - -
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Residues in contact with ALA 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 4.4 3.8 - - + -
89C TRP* 4.0 11.4 - - + -
93C ILE* 3.7 23.8 - - + -
173C ALA 3.5 12.7 + - - +
174C CYS* 3.1 9.1 + - - +
176C SER* 1.3 81.2 + - - +
178C LEU* 1.3 57.8 - - - +
180C LEU* 3.1 4.3 + - - +
181C ILE* 2.9 32.8 + - - +
200C ILE* 3.9 22.4 - - + -
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Residues in contact with LEU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C CYS 2.8 17.2 + - - +
175C LEU* 3.5 12.6 - - + +
177C ALA* 1.3 77.6 - - - +
179C VAL* 1.3 60.1 + - + +
181C ILE* 3.5 17.6 - - + +
182C THR* 3.9 7.4 - - - -
197C GLN* 3.8 43.4 - - + +
200C ILE* 4.0 9.9 - - + -
201C ALA* 4.0 18.8 - - + +
204C LEU* 3.7 29.6 - - + -
225C LEU* 4.2 17.3 - - + -
228C LEU* 5.7 6.7 - - + +
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Residues in contact with VAL 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ALA* 3.8 9.5 - - - +
114C GLU* 3.6 36.6 - - + +
115C LEU* 3.7 22.2 - - + +
118C LEU* 3.9 15.3 - - + -
175C LEU 3.3 15.0 + - - +
176C SER 2.9 10.8 + - - +
178C LEU* 1.3 78.3 - - - +
180C LEU* 1.3 58.0 + - - +
182C THR* 3.8 12.4 - - - +
184C ARG* 4.0 4.3 + - - -
228C LEU* 3.7 26.2 - - + -
231C LEU* 4.4 6.5 - - + -
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C TRP* 3.7 34.1 - - + -
90C ALA* 3.8 14.6 - - + -
93C ILE* 4.9 3.8 - - + -
96C PHE* 3.6 31.2 - - + -
107C LEU* 3.6 52.3 - - + +
108C LEU* 3.8 16.6 - - + +
111C ALA* 4.0 9.3 - - + +
115C LEU* 4.3 6.0 - - + +
176C SER 3.2 3.6 + - - -
177C ALA 3.1 8.5 + - - +
179C VAL* 1.3 77.4 - - - +
181C ILE* 1.3 67.5 + - + +
182C THR* 3.3 9.1 + - - +
184C ARG* 5.2 0.7 + - - -
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Residues in contact with ILE 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ILE* 3.8 29.6 - - + -
96C PHE* 4.3 14.1 - - + -
99C LEU* 5.7 1.1 - - + -
107C LEU* 4.6 4.5 - - + -
177C ALA 2.9 12.8 + - - +
178C LEU* 3.5 6.0 - - - +
179C VAL 3.6 0.2 - - - -
180C LEU* 1.3 88.7 - - + +
182C THR* 1.3 59.4 + - - +
193C VAL* 3.5 35.2 - - + +
196C LEU* 3.8 25.8 - - + -
197C GLN* 2.9 37.7 - - + +
200C ILE* 4.1 9.4 - - + -
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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