Contacts of the helix formed by residues 150 - 165 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B GLY* 1.3 71.6 - - - -
151B TRP* 1.3 54.2 + - - +
152B ILE 3.1 0.2 - - - -
153B ASP* 2.8 43.3 + - + +
154B SER* 3.3 9.8 + - - -
237B GLN* 4.8 3.6 - - - +
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Residues in contact with TRP 151 (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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75B PHE* 4.0 22.0 - + - -
79B LEU* 4.9 3.1 - - + -
113B LEU* 4.6 13.0 - - + -
116B PHE* 3.8 21.1 - + - -
117B ILE* 3.7 26.9 - - + +
148B PHE* 3.2 46.9 + + - +
149B GLY 2.9 0.6 + - - -
150B ASP* 1.3 78.9 - - - +
152B ILE* 1.3 56.8 + - - +
154B SER* 3.2 3.0 + - - -
155B ILE* 3.0 43.7 + - + +
234B LEU* 3.0 18.3 + - + +
237B GLN* 3.7 39.6 + - + +
238B GLY* 3.6 28.5 - - - -
241B ARG* 4.5 6.1 - - + -
242B ILE* 6.1 0.7 - - + -
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Residues in contact with ILE 152 (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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120B LEU* 4.8 2.2 - - + -
131B LEU* 3.3 43.1 - - + -
133B PHE* 4.5 4.9 - - + -
141B ARG* 4.2 12.3 - - + +
144B CYS* 3.9 21.5 - - + -
145B ALA* 4.4 8.7 - - + -
148B PHE* 3.8 36.4 - - + +
149B GLY 3.4 13.9 + - - +
150B ASP 2.9 1.4 + - - -
151B TRP* 1.3 76.8 - - - +
153B ASP* 1.3 76.3 + - - +
155B ILE* 3.5 12.4 + - + +
156B LEU* 3.2 24.5 + - + +
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Residues in contact with ASP 153 (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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141B ARG* 3.2 30.5 - - - +
145B ALA* 6.0 1.2 - - - +
150B ASP* 2.8 29.1 + - + +
152B ILE* 1.3 76.0 - - - +
154B SER* 1.3 59.4 + - - +
156B LEU* 3.3 7.9 + - - +
157B ALA* 2.8 29.1 + - - +
160B ARG* 5.4 0.2 + - - -
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Residues in contact with SER 154 (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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150B ASP 3.9 5.2 - - - -
151B TRP* 3.3 11.9 - - - -
153B ASP* 1.3 79.4 - - - +
155B ILE* 1.3 62.4 + - - +
157B ALA* 3.6 7.3 - - - +
158B PHE* 3.2 21.0 + - - +
234B LEU* 4.0 10.8 - - - +
237B GLN* 2.8 40.7 + - - -
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Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 4.6 2.5 - - + -
117B ILE* 4.3 22.2 - - + +
120B LEU* 4.0 35.9 - - + -
121B ALA* 4.5 13.5 - - + +
124B SER* 6.4 0.7 - - - -
131B LEU* 4.9 6.7 - - + -
148B PHE* 5.3 0.2 - - + -
151B TRP* 3.0 60.9 + - + +
152B ILE* 3.8 14.1 - - + +
153B ASP 3.2 0.2 - - - -
154B SER* 1.3 77.6 - - - +
156B LEU* 1.3 54.0 + - + +
158B PHE* 3.1 5.4 + - - +
159B SER* 2.7 32.0 + - - -
234B LEU* 4.3 7.9 - - + -
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Residues in contact with LEU 156 (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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124B SER* 4.7 6.7 - - - -
126B PRO* 3.8 30.0 - - + +
129B GLY* 5.3 3.1 - - - -
130B LYS 4.2 8.5 - - - +
131B LEU* 4.1 29.4 - - + -
141B ARG* 3.9 41.5 - - + +
152B ILE 3.2 20.3 + - - +
153B ASP* 3.3 6.7 + - - +
155B ILE* 1.3 74.0 - - + +
157B ALA* 1.3 65.3 + - - +
159B SER* 3.4 6.3 + - - +
160B ARG* 2.9 40.0 + - - +
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Residues in contact with ALA 157 (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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153B ASP 2.8 20.8 + - - +
154B SER* 3.6 9.9 - - - +
155B ILE 3.4 0.2 - - - -
156B LEU* 1.3 74.7 - - - +
158B PHE* 1.3 61.9 + - - +
160B ARG* 3.2 26.6 + - - +
161B SER* 3.1 18.4 + - - -
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Residues in contact with PHE 158 (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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117B ILE* 4.2 2.5 - - + -
118B LEU* 4.3 8.1 - - + -
121B ALA* 3.4 28.5 - - + -
154B SER 3.2 4.1 + - - +
155B ILE 3.1 7.0 + - - +
157B ALA* 1.3 78.6 - - - +
159B SER* 1.3 55.7 + - - +
161B SER* 3.2 9.1 + - - -
162B LEU* 3.0 41.0 + - + +
227B LYS* 4.1 34.5 - - + -
230B GLU* 4.2 22.7 - - + -
231B LEU* 3.6 31.6 - - + -
234B LEU* 3.5 32.5 - - + -
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Residues in contact with SER 159 (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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121B ALA* 2.9 37.7 + - - -
124B SER* 4.0 4.9 + - - -
126B PRO* 3.6 21.8 - - - +
155B ILE* 2.7 17.5 + - - -
156B LEU* 3.4 13.9 - - - -
157B ALA 3.1 0.2 - - - -
158B PHE* 1.3 74.4 - - - +
160B ARG* 1.3 63.6 + - - +
161B SER 3.1 1.6 - - - -
162B LEU* 3.5 2.8 - - - +
163B HIS* 3.0 30.7 + - - -
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Residues in contact with ARG 160 (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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164A SER* 6.0 2.2 - - - -
126B PRO* 3.9 32.7 + - + +
127B GLY* 6.3 0.2 - - - -
153B ASP 5.4 0.4 + - - -
156B LEU* 2.9 29.6 + - - +
157B ALA* 3.4 36.3 - - - +
159B SER* 1.3 76.5 + - - +
161B SER* 1.3 60.6 + - - +
163B HIS* 3.8 7.1 - - + +
164B SER* 3.1 25.8 + - - -
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Residues in contact with SER 161 (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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157B ALA 3.1 12.5 + - - -
158B PHE* 3.3 14.5 + - - -
159B SER 3.1 0.6 - - - -
160B ARG* 1.3 77.0 - - - +
162B LEU* 1.3 66.9 + - - +
164B SER* 3.1 20.8 + - - -
165B LEU* 3.5 10.1 + - - +
227B LYS* 3.2 27.5 + - - +
230B GLU* 4.6 3.1 + - - -
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Residues in contact with LEU 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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118B LEU* 4.0 26.7 - - + +
121B ALA* 4.1 9.9 - - + -
122B TYR* 4.0 39.7 - - + +
158B PHE* 3.0 22.7 + - + +
159B SER 3.5 8.1 - - - +
161B SER* 1.3 75.8 + - - +
163B HIS* 1.3 66.9 + - - +
164B SER 3.2 0.7 + - - -
165B LEU* 3.2 19.3 + - + +
166B LEU 3.5 5.2 + - - -
167B VAL* 3.9 29.4 + - + +
172B PHE* 4.5 3.6 - - + -
175B LEU* 5.5 5.4 - - + -
227B LYS* 4.1 24.3 - - + +
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Residues in contact with HIS 163 (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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121B ALA 3.3 18.2 - - - -
122B TYR* 3.1 35.0 + + - -
123B ARG 4.9 0.2 - - - -
124B SER 3.0 21.2 + - - -
125B LYS* 5.6 1.9 - - + +
126B PRO* 4.1 12.8 - - + +
159B SER* 3.0 21.6 + - - +
160B ARG* 4.0 8.1 - - + +
161B SER 3.2 0.6 - - - -
162B LEU* 1.3 82.3 - - - +
164B SER* 1.3 56.8 + - - +
166B LEU* 2.8 34.0 + - + +
167B VAL 5.5 0.2 - - - +
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Residues in contact with SER 164 (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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160A ARG* 5.9 2.9 - - - -
160B ARG 3.1 14.4 + - - -
161B SER* 3.1 12.6 + - - -
163B HIS* 1.3 72.6 - - - +
165B LEU* 1.3 59.9 + - - +
166B LEU* 2.9 17.3 + - - +
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Residues in contact with LEU 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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161B SER* 3.5 10.3 + - - +
162B LEU* 3.2 11.4 + - - +
164B SER* 1.3 78.8 - - - +
166B LEU* 1.3 68.3 + - - +
167B VAL* 3.3 15.6 + - + +
223B ARG* 4.1 44.9 - - + +
224B LEU* 4.7 6.7 - - + +
227B LYS* 3.6 44.4 - - + +
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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