Contacts of the helix formed by residues 150 - 165 (chain D) 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 150 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLY* 1.3 69.1 - - - -
151D TRP* 1.3 56.2 + - - +
152D ILE* 3.1 0.7 - - - -
153D ASP* 2.8 30.5 + - - +
154D SER* 3.3 11.1 + - - -
237D GLN* 4.5 4.7 - - - +
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Residues in contact with TRP 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D PHE* 3.9 26.9 - + - -
79D LEU* 5.5 1.6 - - + -
113D LEU* 4.3 17.9 - - + -
116D PHE* 4.3 13.2 - + - -
117D ILE* 4.1 20.9 - - + -
148D PHE* 3.6 32.7 + + + +
149D GLY 2.8 5.9 + - - -
150D ASP* 1.3 73.9 - - - +
152D ILE* 1.3 55.2 + - - +
154D SER* 3.4 3.1 + - - -
155D ILE* 3.0 46.2 + - + +
234D LEU* 3.1 18.3 + - + +
237D GLN* 3.3 40.7 + - + +
238D GLY* 3.4 29.2 - - - -
241D ARG* 4.2 11.9 - - + -
242D ILE* 5.4 1.8 - - + -
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Residues in contact with ILE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU* 4.6 2.9 - - + -
131D LEU* 3.6 42.2 - - + -
133D PHE* 4.8 1.1 - - + -
141D ARG* 4.0 7.6 - - + +
144D CYS* 3.9 9.9 - - + -
145D ALA* 4.0 23.8 - - + +
148D PHE* 3.7 38.9 - - + +
149D GLY 3.1 17.8 + - - +
150D ASP* 5.3 0.2 - - - -
151D TRP* 1.3 76.6 - - - +
153D ASP* 1.3 75.7 + - - +
155D ILE* 4.3 10.8 - - + -
156D LEU* 3.0 23.3 + - + +
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Residues in contact with ASP 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ARG* 2.8 53.5 + - - +
150D ASP* 2.8 20.8 + - - +
152D ILE* 1.3 86.0 - - - +
154D SER* 1.3 53.2 + - - +
156D LEU* 3.2 6.7 + - - +
157D ALA* 2.8 35.6 + - - +
160D ARG* 5.8 0.2 + - - -
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Residues in contact with SER 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ASP* 3.3 6.8 + - - +
151D TRP 3.5 9.6 - - - -
153D ASP* 1.3 77.5 - - - +
155D ILE* 1.3 61.0 + - - +
157D ALA* 3.3 8.9 + - - +
158D PHE* 3.1 22.2 + - - +
230D GLU* 5.1 1.2 - - - +
234D LEU* 3.5 14.8 - - - +
237D GLN* 2.6 40.2 + - - -
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Residues in contact with ILE 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D PHE* 5.3 1.6 - - + -
117D ILE* 4.2 27.4 - - + -
120D LEU* 3.8 28.7 - - + -
121D ALA* 4.4 11.3 - - + +
131D LEU* 5.0 3.6 - - + -
148D PHE* 4.9 2.9 - - + -
151D TRP* 3.0 60.8 + - + +
152D ILE* 4.0 17.7 - - + +
154D SER* 1.3 72.0 - - - +
156D LEU* 1.3 68.0 + - + +
158D PHE* 3.2 8.3 + - - +
159D SER* 2.9 20.8 + - - -
234D LEU* 4.5 4.5 - - + -
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D SER* 4.8 5.4 - - - -
125D LYS 4.9 0.7 - - - +
126D PRO* 4.1 31.7 - - + +
129D GLY* 4.7 8.5 - - - +
130D LYS 4.7 5.8 - - - +
131D LEU* 4.1 31.2 - - + -
141D ARG* 3.5 43.1 - - + +
152D ILE 3.0 21.1 + - - +
153D ASP* 3.2 8.5 + - - +
155D ILE* 1.3 76.0 - - + +
157D ALA* 1.3 56.7 + - - +
159D SER* 3.2 7.4 + - - -
160D ARG* 2.8 40.9 + - - +
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Residues in contact with ALA 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ASP 2.8 20.4 + - - +
154D SER* 3.5 9.0 - - - +
156D LEU* 1.3 72.0 - - - +
158D PHE* 1.3 57.3 + - - +
160D ARG* 3.3 25.3 + - - +
161D SER* 3.1 23.7 + - - -
230D GLU* 5.1 3.3 - - - +
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Residues in contact with PHE 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ILE* 4.8 4.0 - - + -
118D LEU* 4.5 10.5 - - + -
121D ALA* 3.6 17.3 - - + -
154D SER 3.1 12.6 + - - +
155D ILE* 3.4 9.0 - - - +
157D ALA* 1.3 73.2 - - - +
159D SER* 1.3 66.6 + - - +
160D ARG 3.2 0.4 - - - -
161D SER* 3.1 7.3 + - - -
162D LEU* 3.0 46.3 + - + +
227D LYS* 3.7 28.9 - - + -
230D GLU* 3.6 24.5 + - + +
231D LEU* 3.6 45.3 - - + -
234D LEU* 3.5 25.4 - - + -
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Residues in contact with SER 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ALA* 2.5 42.4 + - - -
124D SER* 4.6 3.2 + - - -
126D PRO* 3.4 13.7 - - - +
155D ILE* 2.9 13.8 + - - -
156D LEU* 3.3 16.2 - - - -
158D PHE* 1.3 73.7 - - - +
160D ARG* 1.3 67.9 + - - +
162D LEU* 3.8 3.2 - - - +
163D HIS* 3.0 38.6 + - - -
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Residues in contact with ARG 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PRO* 3.6 30.0 + - + +
127D GLY* 6.2 0.2 - - - -
153D ASP 5.8 0.4 + - - -
156D LEU* 2.8 26.6 + - - +
157D ALA* 3.3 40.8 + - - +
158D PHE 3.2 0.4 - - - -
159D SER* 1.3 78.6 - - - +
161D SER* 1.3 62.5 + - - +
163D HIS* 3.3 3.7 + - - +
164D SER* 3.2 20.3 + - - -
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Residues in contact with SER 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D ALA 3.1 9.6 + - - -
158D PHE* 3.1 13.9 + - - -
160D ARG* 1.3 78.4 - - - +
162D LEU* 1.3 62.1 + - - +
164D SER* 3.3 22.9 + - - -
165D LEU* 3.6 10.0 + - - +
227D LYS* 2.4 34.8 + - - -
230D GLU* 4.3 7.4 + - - -
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Residues in contact with LEU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LEU* 4.3 18.4 - - + -
121D ALA* 4.1 16.6 - - + -
122D TYR* 4.2 27.4 - - + +
158D PHE* 3.0 40.4 + - + +
159D SER 3.8 6.5 - - - +
160D ARG 3.4 0.2 - - - -
161D SER* 1.3 69.4 - - - +
163D HIS* 1.3 65.9 + - - +
165D LEU* 2.8 32.7 + - + +
166D LEU 3.7 1.9 + - - -
167D VAL* 4.2 26.4 + - + +
172D PHE* 5.4 0.7 - - + -
175D LEU* 5.0 4.7 - - + -
224D LEU* 5.0 6.7 - - + -
227D LYS* 4.1 19.0 - - + +
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Residues in contact with HIS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ALA 3.4 7.0 + - - -
122D TYR* 3.1 40.6 - + - -
124D SER 3.5 13.5 + - - -
125D LYS* 6.0 1.1 - - - -
126D PRO* 3.4 22.9 - - + -
159D SER* 3.0 33.7 + - - +
160D ARG* 3.9 3.1 - - - +
162D LEU* 1.3 78.6 - - + +
164D SER* 1.3 55.8 + - - +
166D LEU* 2.7 36.6 + - - +
167D VAL 5.6 0.4 - - - +
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Residues in contact with SER 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ARG 3.2 11.8 + - - -
161D SER* 3.3 16.0 + - - -
163D HIS* 1.3 75.6 - - - +
165D LEU* 1.3 69.2 + - - +
166D LEU* 3.3 12.8 + - - +
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D SER 3.8 11.7 - - - +
162D LEU* 2.8 20.3 + - + +
164D SER* 1.3 79.1 + - - +
166D LEU* 1.3 72.2 + - - +
167D VAL* 3.5 22.4 - - + +
223D ARG* 3.7 56.0 + - + +
224D LEU* 4.0 13.2 - - + -
227D LYS* 3.8 26.2 - - + +
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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