Contacts of the helix formed by residues 161 - 170 (chain D) in PDB entry 1WOI
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 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147D ASP 4.0 2.0 - - - -
149D THR* 2.6 29.6 + - - +
150D ASP 3.4 10.0 + - - -
151D THR* 4.8 1.7 - - - -
155D THR 4.9 0.5 + - - -
156D LYS 3.5 24.4 + - - -
158D SER* 3.1 15.4 + - - -
160D SER* 1.3 81.5 - - - +
162D PRO* 1.3 67.8 - - - +
163D PHE 3.4 2.0 - - - -
164D ARG* 3.0 4.8 + - - +
165D ARG* 2.9 26.2 + - - +
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Residues in contact with PRO 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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121D HIS* 3.3 30.3 - - + +
122D SER* 4.1 5.6 - - - +
124D SER* 4.3 4.9 - - - -
125D TYR* 3.5 29.0 - - + +
147D ASP* 4.0 11.4 - - + +
158D SER 3.5 5.9 - - - +
159D ASN* 3.2 24.2 - - - +
160D SER 3.5 2.0 - - - -
161D SER 1.3 90.3 - - - +
163D PHE* 1.3 66.7 + - + +
165D ARG* 3.3 1.9 + - + -
166D ALA* 2.9 27.6 + - - +
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Residues in contact with PHE 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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121D HIS* 3.4 32.5 - + - -
124D SER* 4.3 7.6 - - - -
128D LEU* 4.0 25.6 - - + -
139D VAL* 4.0 20.0 - - + -
141D GLN* 3.2 37.9 - - + -
146D LEU 4.1 1.6 - - - +
147D ASP* 3.5 19.9 + - + +
148D PHE* 3.3 23.0 - - + -
161D SER 3.4 0.6 - - - -
162D PRO* 1.3 77.4 - - + +
164D ARG* 1.3 60.7 + - - +
166D ALA* 3.7 3.7 - - + +
167D CYS* 3.0 25.5 + - - -
176D ILE* 3.8 22.0 - - + -
225D TYR* 5.5 0.4 - + - -
227D SER* 3.4 17.9 - - - -
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Residues in contact with ARG 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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147D ASP 4.1 0.6 + - - -
148D PHE* 2.9 55.4 + - - +
149D THR 3.4 19.5 - - - +
150D ASP* 3.5 19.1 + - - +
161D SER 3.0 5.4 + - - +
163D PHE* 1.3 76.1 - - - +
165D ARG* 1.3 80.2 + - - +
167D CYS* 4.0 2.0 - - - +
168D GLU* 3.0 34.0 + - - +
189D GLU* 2.8 42.4 + - - -
193D ALA* 3.8 18.2 - - - +
197D ARG* 5.9 0.6 - - - +
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Residues in contact with ARG 165 (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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125D TYR* 3.5 31.3 - - + -
150D ASP* 2.8 46.5 + - - -
156D LYS* 2.9 45.5 + - - +
157D TRP* 3.6 27.6 - - + -
161D SER* 2.9 19.7 + - - +
162D PRO* 3.6 7.6 - - + +
164D ARG* 1.3 89.8 - - - +
166D ALA* 1.3 65.1 + - - +
168D GLU* 2.7 52.5 + - - +
169D ALA* 3.4 8.3 + - - +
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Residues in contact with ALA 166 (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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125D TYR* 3.6 15.9 - - + -
128D LEU* 3.6 35.2 - - + -
162D PRO 2.9 17.5 + - - +
163D PHE* 3.8 6.1 - - - +
165D ARG* 1.3 77.6 - - - +
167D CYS* 1.3 57.8 + - - +
169D ALA 3.1 1.7 + - - -
170D LEU* 2.8 36.4 + - + +
173D LEU* 3.8 9.4 - - + -
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Residues in contact with CYS 167 (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 PHE* 3.8 7.2 - - + -
163D PHE 3.0 22.5 + - - +
164D ARG* 4.0 3.8 - - - +
165D ARG 3.4 0.2 - - - -
166D ALA* 1.3 77.2 - - - +
168D GLU* 1.3 60.7 + - - +
169D ALA 3.2 1.2 + - - -
170D LEU 3.5 20.5 + - - +
171D PRO* 4.4 1.9 - - - +
173D LEU* 4.0 18.8 - - - -
176D ILE* 3.9 10.8 - - - -
197D ARG* 3.5 35.4 + - - +
199D HIS* 3.7 29.2 - - - -
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Residues in contact with GLU 168 (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 ASP* 4.9 0.2 - - - +
156D LYS* 5.2 3.3 + - - +
164D ARG* 3.0 21.1 + - - +
165D ARG* 2.7 54.0 + - - +
167D CYS* 1.3 77.7 - - - +
169D ALA* 1.3 57.6 + - + +
170D LEU 3.7 0.2 - - - -
171D PRO* 5.8 0.4 - - - -
197D ARG* 5.3 2.0 - - - +
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Residues in contact with ALA 169 (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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125D TYR* 4.1 21.8 - - + +
129D ARG* 5.1 5.4 - - - -
165D ARG 3.4 14.5 + - - +
166D ALA 3.1 3.5 + - - +
167D CYS 3.1 0.4 - - - -
168D GLU* 1.3 78.7 - - + +
170D LEU* 1.3 73.4 + - + +
171D PRO* 3.7 9.5 - - - +
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Residues in contact with LEU 170 (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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128D LEU* 3.3 41.1 - - + +
129D ARG* 4.0 19.5 - - + +
131D PHE 5.4 0.2 - - - -
132D ALA* 3.7 32.3 - - + +
137D LEU* 5.4 3.6 - - + -
166D ALA* 2.8 23.0 + - + +
167D CYS 3.5 9.9 + - - +
169D ALA* 1.3 90.7 - - + +
171D PRO* 1.3 62.9 - - + +
172D ASN* 3.0 11.0 - - - +
173D LEU* 2.9 36.0 + - + +
197D ARG* 5.4 0.2 + - - -
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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