Contacts of the helix formed by residues 160 - 170 (chain B) in PDB entry 2WOE
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 HIS 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B TYR* 3.8 16.2 + + - -
120B SER 3.4 11.0 - - - -
121B GLU* 3.2 31.0 + - - +
123B ASP 3.4 20.4 - - - +
124B ALA* 3.9 15.4 - - + +
158B HIS 3.9 1.4 - - - -
159B ASN* 1.3 77.5 + - - +
161B PRO* 1.3 75.6 - - + +
162B LEU* 3.1 51.1 + - + +
163B SER* 3.2 4.7 + - - -
164B ASP* 2.9 34.5 + - - -
401B AR6 4.0 4.9 + - - -
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Residues in contact with PRO 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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119B TYR* 3.9 18.2 - - + -
159B ASN* 5.3 1.1 - - - +
160B HIS* 1.3 101.2 - - + +
162B LEU* 1.3 57.5 + - + +
164B ASP* 3.5 11.6 + - + +
165B ALA* 3.0 30.1 + - - +
197B HIS* 4.1 17.6 + - + +
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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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124B ALA* 4.7 0.2 - - + -
160B HIS* 3.1 25.3 + - + +
161B PRO* 1.3 73.9 - - + +
163B SER* 1.3 65.9 + - - +
165B ALA* 3.5 1.5 + - - +
166B ALA* 3.1 25.3 + - - +
197B HIS* 3.9 33.4 - - + +
199B ASP* 5.7 7.0 - - + +
200B PHE* 3.5 20.4 - - + -
212B TYR* 3.4 30.3 - - + +
213B ILE* 3.8 14.3 - - + +
214B VAL* 3.8 11.9 - - + -
401B AR6 5.8 0.7 - - - +
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Residues in contact with SER 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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123B ASP 3.8 22.0 - - - -
124B ALA* 4.7 1.1 - - - -
125B GLY 4.3 11.2 + - - -
128B ALA* 3.9 13.7 - - - +
129B ALA* 4.9 1.6 + - - +
154B ALA* 5.1 1.2 - - - +
158B HIS* 3.8 19.0 + - - +
160B HIS* 3.2 12.5 + - - -
162B LEU* 1.3 76.1 - - - +
164B ASP* 1.3 67.4 + - - +
166B ALA* 3.3 2.1 + - - +
167B CYS* 2.9 29.0 + - - -
213B ILE* 4.0 13.1 - - - +
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Residues in contact with ASP 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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151B LEU* 3.7 20.3 - - + +
154B ALA* 5.5 3.0 - - - +
155B ARG* 2.9 47.1 + - - +
158B HIS 4.2 3.8 - - - +
159B ASN* 4.6 1.0 - - - +
160B HIS 2.9 32.9 + - - +
161B PRO* 3.6 10.5 - - + +
163B SER* 1.3 77.4 + - - +
165B ALA* 1.3 63.1 + - - +
167B CYS* 3.4 4.2 + - - +
168B LEU* 3.1 31.6 + - + +
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Residues in contact with ALA 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 PRO 3.0 18.6 + - - +
162B LEU 3.9 3.4 - - - +
164B ASP* 1.3 76.6 - - - +
166B ALA* 1.3 57.4 + - - +
168B LEU* 3.3 8.3 + - - +
169B THR* 3.0 33.9 + - - -
193B LEU* 3.6 21.3 - - + -
196B GLN* 4.0 12.3 + - - +
197B HIS* 3.6 20.0 - - + +
200B PHE* 4.5 0.4 - - + -
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Residues in contact with ALA 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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129B ALA* 4.8 0.7 - - + -
162B LEU 3.1 18.9 + - - +
163B SER 3.7 2.0 - - - +
165B ALA* 1.3 77.5 - - - +
167B CYS* 1.3 56.6 + - - +
169B THR* 3.3 4.5 + - - -
170B LEU* 2.9 36.9 + - - +
193B LEU* 4.3 4.2 - - - +
200B PHE* 4.1 3.6 - - + -
213B ILE* 3.4 32.1 - - + -
217B MET* 3.8 22.3 - - + +
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Residues in contact with CYS 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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128B ALA* 3.8 7.0 - - - -
129B ALA* 3.5 24.2 - - - -
132B CYS* 3.4 30.3 - - - -
150B VAL* 3.7 19.3 - - + +
151B LEU* 4.8 1.3 - - + -
154B ALA* 3.8 18.8 - - + -
163B SER* 2.9 24.6 + - - +
164B ASP* 3.6 7.0 - - - +
165B ALA 3.3 0.2 - - - -
166B ALA* 1.3 77.7 - - - +
168B LEU* 1.3 62.9 + - - +
170B LEU* 3.4 5.6 + - - +
171B GLY 3.0 18.2 + - - -
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Residues in contact with LEU 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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146B LEU* 5.0 2.9 - - + +
147B GLU* 3.5 62.8 - - + +
150B VAL* 4.0 11.0 - - + +
151B LEU* 3.7 19.5 - - + -
164B ASP* 3.1 20.8 + - + +
165B ALA* 3.3 6.7 + - - +
167B CYS* 1.3 75.7 - - - +
169B THR* 1.3 57.9 - - - +
171B GLY* 3.3 1.7 + - - -
172B ARG* 2.9 54.9 - - - +
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Residues in contact with THR 169 (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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165B ALA 3.0 18.0 + - - -
166B ALA 3.3 4.5 + - - -
168B LEU* 1.3 77.2 + - - +
170B LEU* 1.3 61.6 + - - +
172B ARG* 3.4 10.0 + - - +
173B MET* 3.0 45.4 + - - +
189B GLU* 4.0 21.1 + - + +
190B ALA* 4.4 5.4 - - + -
193B LEU* 3.5 42.1 - - + +
196B GLN* 5.6 1.0 + - - -
217B MET* 4.4 5.4 - - + -
221B LEU* 5.6 0.2 - - + -
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Residues in contact with LEU 170 (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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129B ALA* 3.8 39.0 - - + +
132B CYS* 4.9 6.1 - - + -
166B ALA 2.9 21.0 + - - +
167B CYS* 3.8 4.5 - - - +
169B THR* 1.3 75.2 - - - +
171B GLY* 1.3 63.4 - - - +
173B MET* 3.3 9.7 + - - +
174B VAL* 3.0 29.5 + - - +
217B MET* 3.9 30.7 - - + -
220B VAL* 5.1 2.0 - - + -
221B LEU* 5.6 0.4 - - + -
250B LEU* 4.0 16.8 - - + -
253B MET* 4.1 22.8 - - + +
254B LEU* 4.5 18.2 - - + -
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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