Contacts of the helix formed by residues 148 - 165 (chain B) in PDB entry 1WUR
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 VAL 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLU* 3.4 24.5 - - - +
110B HIS* 3.7 26.5 - - + +
115B PHE* 4.2 2.2 - - - -
147B GLN* 1.3 77.1 + - - +
149B GLN* 1.3 66.3 + - - +
150B GLU* 4.0 8.1 - - - +
151B ARG* 3.1 52.0 + - + +
152B LEU* 3.2 10.6 + - - +
89C PHE* 6.0 1.1 - - + -
92C GLU* 3.8 12.8 - - + +
129C ILE* 5.4 4.9 - - + -
822C 8DG 3.1 13.2 - - + +
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Residues in contact with GLN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE* 3.9 22.1 - - + -
148B VAL* 1.3 71.9 - - - +
150B GLU* 1.3 62.4 + - - +
152B LEU* 3.3 12.0 + - + +
153B ALA 3.3 7.1 + - - -
173B VAL* 2.8 40.7 + - + -
175B GLY* 3.8 10.8 + - - +
177B HIS* 2.9 30.5 + - + -
192B THR* 2.7 36.9 + - + +
194B THR* 3.1 32.4 + - + +
822C 8DG 2.7 17.7 + - + +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 4.0 3.9 - - + +
149B GLN* 1.3 76.8 + - - +
151B ARG* 1.3 61.0 + - - +
153B ALA* 3.9 3.5 + - - +
154B VAL* 3.4 24.3 + - - +
194B THR* 3.9 23.9 - - + -
195B SER 5.1 1.6 - - - +
92C GLU* 3.8 22.7 - - + +
93C GLY 5.6 0.9 - - - +
97C VAL* 4.0 32.1 - - + +
123C TYR* 4.7 0.7 + - - -
129C ILE* 4.0 17.9 - - + +
130C LEU 4.6 0.7 - - - +
132C LEU* 4.1 3.8 - - - +
822C 8DG 2.6 46.6 + - - -
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLU* 2.7 42.2 + - - -
146B LEU 4.0 7.3 + - - -
147B GLN* 3.4 21.5 + - - +
148B VAL* 3.1 27.3 + - + +
150B GLU* 1.3 78.3 - - - +
152B LEU* 1.3 65.1 + - - +
154B VAL* 3.1 5.8 + - + +
155B GLN* 2.9 49.8 + - + +
92C GLU* 3.1 41.5 + - - +
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Residues in contact with LEU 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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104B PHE* 3.7 36.3 - - + -
106B SER* 4.7 4.9 - - - +
115B PHE* 4.2 13.5 - - + -
119B VAL* 5.3 1.1 - - + -
139B VAL* 6.3 0.2 - - + -
142B PHE* 3.6 42.4 - - + +
143B ALA* 3.8 6.1 - - + +
147B GLN* 3.7 12.3 + - + +
148B VAL 3.2 10.4 + - - +
149B GLN* 3.6 9.2 - - - +
151B ARG* 1.3 79.0 - - - +
153B ALA* 1.3 62.0 + - - +
155B GLN* 3.5 2.2 + - - +
156B ILE* 3.2 43.6 + - + +
173B VAL* 4.3 13.7 - - + -
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Residues in contact with ALA 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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149B GLN 3.3 3.7 + - - +
150B GLU 4.1 4.5 - - - +
151B ARG 3.2 0.8 - - - -
152B LEU* 1.3 78.4 - - - +
154B VAL* 1.3 62.0 + - - +
156B ILE* 3.5 0.7 + - - +
157B ALA* 3.1 23.7 + - - +
171B VAL* 3.8 10.9 - - - +
173B VAL* 3.7 26.4 - - + +
194B THR* 3.8 14.1 - - - +
195B SER* 3.8 28.0 - - - +
196B ALA* 3.5 4.5 - - - +
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Residues in contact with VAL 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 GLU 3.4 16.4 + - - +
151B ARG* 3.1 9.7 + - + +
153B ALA* 1.3 77.6 - - - +
155B GLN* 1.3 61.1 + - + +
157B ALA* 3.3 2.8 + - - +
158B GLU* 2.9 52.2 + - + +
195B SER 4.7 4.5 - - - +
196B ALA* 3.7 17.7 - - + -
92C GLU 3.6 26.7 - - - +
93C GLY* 4.4 8.5 - - - -
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Residues in contact with GLN 155 (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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142B PHE* 3.6 32.4 - - + -
145B ARG* 4.3 14.5 + - - +
147B GLN* 2.8 31.7 + - - -
151B ARG* 2.9 43.3 + - + +
152B LEU 4.1 1.8 - - - +
154B VAL* 1.3 71.4 - - + +
156B ILE* 1.3 61.9 + - - +
158B GLU* 4.0 12.6 - - - +
159B ALA* 2.9 30.1 + - - +
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Residues in contact with ILE 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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119B VAL* 4.1 18.2 - - + -
121B ILE* 4.2 11.7 - - + -
138B ILE* 4.2 16.1 - - + +
139B VAL* 4.0 28.7 - - + -
142B PHE* 4.4 11.2 - - + -
152B LEU* 3.2 43.7 + - + +
153B ALA 3.8 3.8 - - - +
155B GLN* 1.3 75.3 - - - +
157B ALA* 1.3 64.3 + - - +
159B ALA* 3.2 3.1 + - - +
160B ILE* 3.0 40.0 + - + +
171B VAL* 3.9 14.8 - - + -
173B VAL* 4.8 1.1 - - + -
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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 ALA 3.1 18.2 + - - +
154B VAL 3.6 4.0 - - - +
156B ILE* 1.3 79.0 - - - +
158B GLU* 1.3 57.2 + - - +
160B ILE* 3.3 6.7 + - - +
161B GLN* 3.0 28.1 + - - +
169B VAL* 3.8 8.5 - - + +
171B VAL* 3.7 17.2 - - + +
196B ALA* 3.7 22.7 - - + +
198B LEU* 3.5 17.8 - - + +
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 2.9 39.3 + - + +
155B GLN* 4.0 11.7 - - - +
157B ALA* 1.3 75.7 - - - +
159B ALA* 1.3 58.2 + - - +
161B GLN* 3.3 4.0 + - - +
162B GLU* 2.9 30.2 + - - +
198B LEU* 4.1 18.6 - - + +
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Residues in contact with ALA 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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80B LEU* 3.8 20.6 - - + +
138B ILE* 3.8 12.1 - - + -
142B PHE* 3.7 24.0 - - + -
155B GLN 2.9 19.5 + - - +
156B ILE 3.5 4.9 - - - +
157B ALA 3.2 0.2 - - - -
158B GLU* 1.3 77.0 - - - +
160B ILE* 1.3 62.0 + - - +
162B GLU* 3.3 4.1 + - - +
163B VAL* 3.0 29.3 + - - +
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Residues in contact with ILE 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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121B ILE* 3.5 30.7 - - + -
123B TYR* 5.0 2.7 - - + -
130B LEU* 5.2 0.9 - - + -
135B PHE* 3.8 23.3 - - + -
138B ILE* 4.2 15.5 - - + -
156B ILE* 3.0 32.7 + - + +
157B ALA 3.7 5.4 - - - +
159B ALA* 1.3 74.8 - - - +
161B GLN* 1.3 63.7 + - - +
163B VAL* 3.3 5.5 + - - +
164B LEU* 2.9 46.5 + - + +
166B PRO* 5.0 3.1 - - + -
169B VAL* 3.8 24.7 - - + -
171B VAL* 4.3 1.6 - - + -
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Residues in contact with GLN 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 3.0 14.1 + - - +
158B GLU* 3.5 9.6 - - - +
160B ILE* 1.3 77.5 - - - +
162B GLU* 1.3 57.2 + - - +
165B GLU* 2.7 47.5 + - - +
166B PRO* 3.4 32.2 + - - +
168B GLY* 5.0 3.4 - - - -
169B VAL* 3.9 11.2 - - + +
198B LEU* 3.9 23.3 - - + +
199B GLY* 5.3 1.8 - - - +
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Residues in contact with GLU 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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80B LEU* 3.8 22.1 - - + +
81B GLU* 5.9 3.5 - - - +
158B GLU 2.9 16.5 + - - +
159B ALA* 3.7 5.8 - - - +
160B ILE 3.3 0.4 - - - -
161B GLN* 1.3 78.1 - - - +
163B VAL* 1.3 62.8 + - - +
165B GLU* 4.1 14.5 - - - +
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Residues in contact with VAL 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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80B LEU* 3.7 20.9 - - + -
84B VAL* 3.6 46.7 - - + -
88B VAL* 4.1 17.4 - - + +
128B LYS* 4.3 9.4 + - - -
130B LEU* 4.1 11.0 - - + -
138B ILE* 4.8 3.4 - - + -
159B ALA 3.0 18.4 + - - +
160B ILE* 3.8 5.2 - - - +
162B GLU* 1.3 78.6 - - + +
164B LEU* 1.3 64.9 + - + +
165B GLU* 5.4 0.2 - - - -
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Residues in contact with LEU 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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88B VAL* 3.9 20.2 - - + -
123B TYR* 3.6 35.0 - - + -
126B ASP 5.0 1.7 + - - +
128B LYS* 3.3 31.7 - - - +
129B ILE 3.9 7.0 - - - -
130B LEU* 3.7 40.4 - - + +
135B PHE* 4.5 1.3 - - + -
160B ILE* 2.9 27.5 + - + +
163B VAL* 1.3 89.8 - - + +
165B GLU* 1.3 74.5 + - - +
166B PRO* 3.2 10.6 - - + +
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Residues in contact with GLU 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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126B ASP* 3.5 18.4 - - - +
128B LYS* 4.5 15.0 + - - +
161B GLN* 2.7 34.4 + - - +
162B GLU* 4.1 12.5 - - - +
164B LEU* 1.3 75.6 - - - +
166B PRO* 1.3 69.8 - - - +
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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
------------------------------------------------------------
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