Contacts of the helix formed by residues 152 - 168 (chain B) in PDB entry 1W45
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 SER 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ASP 4.4 0.4 + - - -
151B THR* 1.3 80.6 + - - +
153B GLY* 1.3 68.0 + - - +
154B TYR 4.0 0.2 + - - -
155B LEU* 4.0 5.9 - - - +
156B GLU* 3.5 14.0 + - - -
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Residues in contact with GLY 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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152B SER* 1.3 83.0 - - - +
154B TYR* 1.3 63.8 + - - -
155B LEU* 5.5 0.2 - - - -
156B GLU* 3.5 13.7 - - - +
157B ARG* 4.0 5.0 + - - +
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Residues in contact with TYR 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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153B GLY* 1.3 71.5 - - - -
155B LEU* 1.3 64.5 + - - +
156B GLU 3.2 0.2 - - - -
157B ARG* 3.0 23.4 + - + +
158B ILE* 3.0 19.9 + - - +
195B GLY 5.0 2.4 + - - -
198B GLU* 3.6 45.2 + - + +
199B MET* 3.9 29.7 + - + +
202B ILE* 4.6 7.6 - - + +
240B LEU* 3.5 29.4 - - + +
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Residues in contact with LEU 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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113B GLU* 3.7 24.7 - - + +
117B ILE* 4.0 11.2 - - + -
151B THR* 3.7 18.2 - - + -
152B SER 4.0 7.6 - - - +
153B GLY 3.2 0.2 - - - -
154B TYR* 1.3 73.9 - - - +
156B GLU* 1.3 66.3 + - - +
157B ARG 3.2 0.2 + - - -
158B ILE* 3.3 8.1 + - + +
159B LEU* 3.1 39.5 + - + +
239B SER* 3.3 37.5 - - - +
240B LEU* 3.8 11.1 - - + +
243B ALA* 3.7 29.8 - - + -
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Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 4.4 1.0 - - - +
148B GLN* 2.9 47.6 + - + +
151B THR* 3.3 46.7 - - - +
152B SER* 3.5 6.0 + - - -
153B GLY 3.5 11.9 - - - +
154B TYR 3.2 0.2 - - - -
155B LEU* 1.3 81.4 - - - +
157B ARG* 1.3 81.9 + - - +
159B LEU* 3.5 3.9 + - - +
160B VAL* 3.2 32.2 + - + +
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Residues in contact with ARG 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 GLY 4.4 6.7 - - - +
154B TYR* 3.0 27.9 + - + +
156B GLU* 1.3 90.2 - - - +
158B ILE* 1.3 59.8 + - - +
160B VAL* 3.4 5.0 + - - +
161B CYS* 3.0 28.9 + - - +
199B MET* 4.0 34.7 - - - +
202B ILE* 4.3 10.0 - - + +
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Residues in contact with ILE 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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154B TYR 3.0 11.4 + - - +
155B LEU* 3.3 15.7 - - + +
157B ARG* 1.3 75.8 - - - +
159B LEU* 1.3 62.9 + - + +
161B CYS* 3.6 1.9 - - - +
162B LEU* 3.2 35.5 + - + +
202B ILE* 3.6 43.9 - - + +
205B LEU* 5.5 6.5 - - + -
206B CYS* 5.1 7.0 - - + -
240B LEU* 3.9 11.9 - - + -
243B ALA* 4.0 29.6 - - + +
244B MET* 4.1 21.8 - - + -
247B VAL* 4.7 11.0 - - + -
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Residues in contact with LEU 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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116B ILE* 3.9 28.0 - - + -
117B ILE* 4.2 26.5 - - + -
120B LEU* 3.7 19.5 - - + +
147B ILE* 3.9 26.7 - - + -
151B THR* 4.2 10.8 - - + +
155B LEU* 3.1 40.5 + - + +
156B GLU 3.8 3.1 - - - +
158B ILE* 1.3 79.0 - - + +
160B VAL* 1.3 62.9 + - - +
162B LEU* 3.4 9.7 + - + +
163B LEU* 3.3 27.2 + - - +
243B ALA* 5.3 1.6 - - + -
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Residues in contact with VAL 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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144B GLU* 3.9 19.5 - - + +
147B ILE* 5.0 7.2 - - + -
148B GLN* 4.0 19.1 - - + +
156B GLU* 3.2 37.1 + - + +
157B ARG* 3.8 5.4 - - - +
159B LEU* 1.3 74.2 - - - +
161B CYS* 1.3 61.8 + - - +
163B LEU* 3.1 9.5 + - + +
164B GLN* 2.8 58.6 + - - +
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Residues in contact with CYS 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 ARG 3.0 18.2 + - - +
158B ILE* 3.6 7.4 - - - +
159B LEU 3.3 0.2 - - - -
160B VAL* 1.3 77.3 - - - +
162B LEU* 1.3 54.3 + - - +
164B GLN* 4.8 5.2 - - - +
165B GLY* 2.6 37.4 + - - +
202B ILE* 4.3 5.6 - - + -
203B THR* 5.6 0.2 - - - -
206B CYS* 2.0 48.7 - - - -
207B THR* 4.0 13.5 - - - -
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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
----------------------------------------------------------
117B ILE* 6.4 0.2 - - - -
120B LEU* 4.3 39.5 - - + +
121B ALA* 4.4 5.2 - - + +
128B LEU* 3.8 8.6 - - - +
158B ILE* 3.2 24.5 + - + +
159B LEU* 3.7 14.6 - - + +
160B VAL 3.3 0.4 - - - -
161B CYS* 1.3 80.7 - - - +
163B LEU* 1.3 58.0 + - - +
165B GLY* 4.0 1.1 - - - -
166B SER* 3.2 22.9 + - - -
206B CYS* 3.5 29.6 - - + +
243B ALA* 6.2 2.2 - - + -
247B VAL* 4.3 28.3 - - + -
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Residues in contact with LEU 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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120B LEU* 3.9 15.0 - - + -
128B LEU* 4.8 14.6 - - + -
132B MET* 4.0 26.8 - - + +
143B LEU* 3.7 25.1 - - + -
144B GLU* 4.2 29.6 - - + +
147B ILE* 3.7 29.4 - - + -
159B LEU 3.3 14.6 + - - +
160B VAL* 3.1 10.1 + - + +
162B LEU* 1.3 75.0 - - - +
164B GLN* 1.3 63.2 + - - +
165B GLY 3.2 1.3 - - - -
166B SER* 2.6 26.0 + - - -
167B ARG* 3.6 2.6 + - - +
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Residues in contact with GLN 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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144B GLU* 2.8 35.2 - - - +
160B VAL* 2.8 33.5 + - - +
161B CYS* 4.2 3.6 - - - +
163B LEU* 1.3 73.0 - - - +
165B GLY* 1.3 58.5 - - - +
167B ARG* 3.0 29.3 + - + +
168B ASP* 3.7 4.3 + - - +
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Residues in contact with GLY 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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125B LYS* 5.0 0.9 - - - +
161B CYS* 2.6 27.4 + - - -
162B LEU* 4.0 2.7 - - - -
164B GLN* 1.3 70.2 - - - +
166B SER* 1.3 57.5 + - - +
167B ARG 3.2 0.2 - - - -
168B ASP* 3.0 30.2 + - - +
206B CYS 5.2 8.7 - - - -
207B THR* 6.1 4.3 - - - -
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Residues in contact with SER 166 (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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125B LYS* 2.6 65.1 + - - +
128B LEU* 4.0 16.4 - - - +
129B ARG* 4.4 9.6 - - - +
132B MET* 4.5 8.1 - - - -
162B LEU 3.2 15.2 + - - -
163B LEU* 2.6 20.1 + - - -
165B GLY* 1.3 78.7 - - - +
167B ARG* 1.3 57.3 + - - +
168B ASP 3.3 0.2 - - - -
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Residues in contact with ARG 167 (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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125B LYS* 4.3 9.4 + - - +
129B ARG* 5.2 13.6 - - + +
132B MET* 6.6 0.7 - - + -
163B LEU 4.7 2.5 - - - +
164B GLN* 3.0 18.5 + - + +
166B SER* 1.3 82.8 + - - +
168B ASP* 1.3 74.0 + - - +
169B ASP 4.0 1.0 + - - -
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Residues in contact with ASP 168 (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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125B LYS* 3.8 10.3 - - - +
164B GLN 3.7 5.3 + - - +
165B GLY* 3.0 23.2 + - - +
166B SER 3.3 0.2 - - - -
167B ARG* 1.3 94.7 + - - +
169B ASP* 1.3 80.2 + - - +
170B VAL* 3.6 17.7 + - + +
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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