Contacts of the helix formed by residues 148 - 164 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D GLU* 3.5 23.8 - - - +
110D HIS* 3.5 31.0 - - + +
115D PHE* 4.3 0.4 - - - -
147D GLN* 1.3 77.1 + - - +
149D GLN* 1.3 65.5 + - - +
150D GLU* 4.1 3.8 - - - +
151D ARG* 3.1 45.9 + - + +
152D LEU* 3.1 11.1 + - - +
824D 8DG 3.2 15.7 - - + +
89E PHE* 6.3 0.7 - - + -
92E GLU* 3.8 12.6 - - + +
129E ILE* 5.6 3.6 - - + -
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Residues in contact with GLN 149 (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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115D PHE* 3.9 21.6 - - + -
148D VAL* 1.3 71.1 - - - +
150D GLU* 1.3 64.0 + - - +
152D LEU* 3.5 3.9 + - + +
153D ALA 3.4 14.2 + - - -
173D VAL* 2.9 41.2 + - + +
175D GLY* 3.8 10.4 + - - -
177D HIS* 2.8 30.1 + - + -
192D THR* 2.8 37.4 + - + +
194D THR* 3.0 32.9 + - + +
824D 8DG 2.7 17.7 + - + +
132E LEU* 5.3 0.4 - - + -
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Residues in contact with GLU 150 (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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148D VAL* 3.2 4.3 - - + +
149D GLN* 1.3 76.7 + - - +
151D ARG* 1.3 61.0 + - - +
153D ALA* 3.8 3.8 + - - +
154D VAL* 3.3 23.9 + - - +
194D THR* 3.8 23.8 - - + -
195D SER 5.1 1.7 - - - +
824D 8DG 2.7 46.6 + - - -
92E GLU* 3.9 20.4 - - + +
93E GLY 5.2 2.0 + - - +
97E VAL* 3.9 26.0 - - + +
123E TYR* 4.7 0.7 + - - -
129E ILE* 4.1 18.3 - - + +
130E LEU 4.6 1.2 - - - +
132E LEU* 4.0 11.2 - - - +
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Residues in contact with ARG 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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109D GLU* 2.8 39.4 + - - -
146D LEU 4.0 10.1 + - - -
147D GLN* 3.3 21.2 + - - +
148D VAL* 3.1 28.0 + - + +
150D GLU* 1.3 78.5 - - - +
152D LEU* 1.3 64.9 + - - +
153D ALA 3.2 0.2 - - - -
154D VAL* 3.0 6.3 + - + +
155D GLN* 2.9 48.1 + - + +
92E GLU* 3.0 41.8 + - - +
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Residues in contact with LEU 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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104D PHE* 3.7 37.2 - - + -
106D SER* 4.8 1.1 - - - +
115D PHE* 4.2 13.0 - - + -
119D VAL* 5.4 0.2 - - + -
139D VAL* 6.2 0.2 - - + -
142D PHE* 3.6 41.1 - - + +
143D ALA* 3.7 9.9 - - + +
147D GLN* 3.6 13.2 + - + +
148D VAL 3.1 11.5 + - - +
149D GLN* 3.7 9.9 - - - +
150D GLU 3.5 0.2 - - - -
151D ARG* 1.3 76.8 - - - +
153D ALA* 1.3 62.4 + - - +
155D GLN* 3.5 1.7 + - - +
156D ILE* 3.2 45.4 + - + +
173D VAL* 4.3 13.0 - - + -
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Residues in contact with ALA 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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149D GLN 3.4 4.5 + - - +
150D GLU 4.0 4.9 - - - +
151D ARG 3.2 0.4 - - - -
152D LEU* 1.3 79.8 - - - +
154D VAL* 1.3 63.4 + - - +
156D ILE* 3.8 2.3 - - - +
157D ALA* 3.2 18.5 + - - +
171D VAL* 3.9 8.9 - - - +
173D VAL* 3.8 24.8 - - + +
194D THR* 3.8 14.8 - - - +
195D SER* 3.9 27.8 - - - +
196D ALA* 3.6 9.8 - - - +
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Residues in contact with VAL 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 GLU 3.3 16.6 + - - +
151D ARG* 3.0 9.5 + - + +
153D ALA* 1.3 75.3 - - - +
155D GLN* 1.3 60.3 + - + +
157D ALA* 3.4 2.8 + - - +
158D GLU* 3.0 53.8 + - + +
195D SER 4.8 4.7 - - - +
196D ALA* 3.7 18.6 - - + -
198D LEU* 6.5 0.7 - - + -
92E GLU 3.6 24.2 - - - +
93E GLY* 4.2 12.6 - - - -
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Residues in contact with GLN 155 (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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142D PHE* 3.7 35.2 - - + -
145D ARG* 4.1 13.8 + - - +
147D GLN* 2.8 33.9 - - - +
151D ARG* 2.9 42.9 + - + +
152D LEU 4.1 2.0 - - - +
154D VAL* 1.3 74.6 - - + +
156D ILE* 1.3 61.9 + - - +
158D GLU* 4.0 11.8 - - - +
159D ALA* 3.1 24.1 + - - +
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Residues in contact with ILE 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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119D VAL* 4.0 25.8 - - + -
121D ILE* 4.1 11.2 - - + -
138D ILE* 4.3 8.2 - - + +
139D VAL* 4.0 25.8 - - + -
142D PHE* 4.4 13.0 - - + -
152D LEU* 3.2 41.9 + - + +
153D ALA 3.8 3.8 - - - +
154D VAL 3.3 0.2 - - - -
155D GLN* 1.3 75.5 - - - +
157D ALA* 1.3 64.0 + - - +
159D ALA* 3.3 3.6 + - - +
160D ILE* 3.1 33.1 + - + +
171D VAL* 3.9 22.0 - - + -
173D VAL* 4.7 1.3 - - + -
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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 ALA 3.2 15.7 + - - +
154D VAL 3.7 3.8 - - - +
156D ILE* 1.3 81.1 - - - +
158D GLU* 1.3 56.6 + - - +
160D ILE* 3.3 2.9 + - - +
161D GLN* 2.9 28.9 + - - +
169D VAL* 4.4 11.4 - - + +
171D VAL* 3.7 20.8 - - + +
196D ALA* 3.9 18.8 - - + +
198D LEU* 3.5 19.5 - - + +
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Residues in contact with GLU 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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154D VAL* 3.0 42.4 + - + +
155D GLN* 4.0 11.0 - - - +
157D ALA* 1.3 73.6 - - - +
159D ALA* 1.3 62.4 + - - +
161D GLN* 3.4 4.4 + - - +
162D GLU* 3.0 28.5 + - - +
198D LEU* 4.1 20.2 - - + +
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Residues in contact with ALA 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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80D LEU* 3.8 21.0 - - + +
138D ILE* 3.7 12.6 - - + -
142D PHE* 3.6 23.8 - - + -
155D GLN 3.1 18.8 + - - +
156D ILE 3.5 5.2 - - - +
157D ALA 3.2 0.2 - - - -
158D GLU* 1.3 75.5 - - - +
160D ILE* 1.3 58.6 + - - +
162D GLU* 3.2 4.3 + - - +
163D VAL* 3.0 35.4 + - - +
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Residues in contact with ILE 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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121D ILE* 3.5 38.6 - - + -
123D TYR* 5.1 3.6 - - + -
130D LEU* 5.4 1.6 - - + -
135D PHE* 3.6 30.3 - - + -
138D ILE* 4.2 15.0 - - + -
156D ILE* 3.1 21.4 + - + +
157D ALA 3.7 5.6 - - - +
159D ALA* 1.3 76.6 - - - +
161D GLN* 1.3 58.0 + - - +
163D VAL* 4.7 4.0 - - - -
164D LEU* 3.0 44.5 + - + +
166D PRO* 4.2 1.0 - - + +
169D VAL* 3.8 26.0 - - + -
171D VAL* 4.2 1.8 - - + -
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Residues in contact with GLN 161 (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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157D ALA 2.9 16.4 + - - +
158D GLU* 3.5 7.2 - - - +
160D ILE* 1.3 78.4 - - - +
162D GLU* 1.3 53.1 + - - +
164D LEU 2.4 19.5 - - - +
165D GLU* 3.3 11.8 - - - +
166D PRO* 3.2 33.4 + - - +
168D GLY* 4.9 0.2 - - - -
169D VAL* 4.1 11.2 - - + +
198D LEU* 3.6 36.5 - - + +
199D GLY* 4.3 9.7 - - - +
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Residues in contact with GLU 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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80D LEU* 3.8 21.5 - - + +
158D GLU 3.0 16.7 + - - +
159D ALA* 3.2 5.3 + - - +
161D GLN* 1.3 75.6 - - - +
163D VAL* 1.3 66.8 + - - +
164D LEU 3.4 3.5 - - - +
165D GLU* 3.9 9.8 - - - +
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Residues in contact with VAL 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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80D LEU* 3.7 21.1 - - + -
81D GLU* 6.4 0.2 - - - -
84D VAL* 3.5 47.6 - - + -
88D VAL* 3.9 17.4 - - + +
128D LYS* 4.9 6.6 - - - +
130D LEU* 4.0 10.8 - - + -
138D ILE* 4.6 4.3 - - + -
159D ALA 3.0 18.2 + - - +
160D ILE* 4.1 4.5 - - - +
162D GLU* 1.3 78.0 - - - +
164D LEU* 1.3 62.4 + - + +
165D GLU* 5.0 2.1 - - - +
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Residues in contact with LEU 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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88D VAL* 3.7 33.0 - - + -
123D TYR* 3.6 36.8 - - + -
128D LYS* 3.9 14.6 - - + +
129D ILE 3.7 16.2 - - - -
130D LEU* 3.7 24.9 - - + +
135D PHE* 4.6 0.2 - - + -
160D ILE* 3.0 25.4 + - + +
161D GLN 2.4 31.4 - - - +
163D VAL* 1.3 84.6 - - + +
165D GLU* 1.3 60.0 + - - +
166D PRO* 3.1 10.1 - - + -
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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