Contacts of the strand formed by residues 159 - 164 (chain B) in PDB entry 2DOU
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 ALA 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 3.7 12.3 - - - +
115B LEU* 3.6 37.2 - - + -
155B VAL 2.7 20.1 + - - +
156B TRP 3.5 11.1 + - - +
157B ARG 4.1 3.3 - - - +
158B GLU* 1.3 78.9 - - - +
160B LYS* 1.3 60.6 + - - +
161B VAL 4.6 0.4 - - - +
190B HIS 4.9 1.0 - - - +
191B GLY 5.0 1.0 - - - +
192B LEU* 3.7 22.4 - - + +
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU 5.6 1.8 - - - +
108B THR* 5.2 2.2 - - + -
112B ASP* 4.4 25.8 - - + +
113B LEU 3.0 12.8 + - - +
158B GLU 4.7 2.2 - - - +
159B ALA* 1.3 75.2 - - - +
161B VAL* 1.3 72.7 + - + +
191B GLY 4.7 3.2 - - - +
192B LEU* 3.7 9.7 - - - +
193B TRP* 3.1 25.1 + - + -
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 4.3 4.9 - - + -
107B LEU* 4.7 5.4 - - + +
108B THR* 3.8 28.0 - - + -
113B LEU 3.6 4.3 + - - +
114B LEU* 3.6 24.3 - - + -
115B LEU* 2.9 31.2 + - - +
160B LYS* 1.3 88.2 - - + +
162B LEU* 1.3 65.1 + - - +
192B LEU* 4.2 4.2 - - - +
193B TRP* 3.5 26.5 - - + +
195B ILE* 3.7 31.6 - - + -
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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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115B LEU* 3.6 23.8 - - + +
138B ILE* 4.0 15.9 - - + -
148B LEU* 4.7 6.3 - - + -
156B TRP* 4.5 18.2 - - + -
161B VAL* 1.3 75.4 - - - +
163B LEU* 1.3 64.4 + - - +
164B LEU* 4.2 30.3 - - + -
183B ALA* 4.2 24.7 - - + +
187B ALA* 5.0 4.3 - - + -
192B LEU* 4.1 13.7 - - + -
193B TRP 3.0 11.9 + - - +
194B LEU* 3.5 12.2 - - + +
195B ILE 2.9 26.7 + - - +
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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
----------------------------------------------------------
100B LEU* 3.8 32.5 - - + -
104B LEU* 5.0 4.3 - - + -
114B LEU* 4.1 18.6 - - + +
115B LEU 2.9 15.5 + - - +
116B LEU* 3.9 11.8 - - + -
117B PRO* 3.6 15.9 - - - +
124B TYR* 3.7 46.4 - - + +
161B VAL* 5.1 1.1 - - + -
162B LEU* 1.3 73.6 - - - +
164B LEU* 1.3 81.9 + - - +
195B ILE* 3.5 26.7 - - + +
197B ASP* 4.8 4.3 - - + -
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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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117B PRO* 4.0 22.7 - - + -
124B TYR* 5.3 1.3 - - - -
138B ILE* 5.1 1.1 - - + -
146B ALA* 4.3 4.7 - - + -
148B LEU* 4.5 4.7 - - + -
162B LEU* 4.2 23.8 + - + -
163B LEU* 1.3 86.6 - - - +
165B ASN* 1.3 64.0 + - - +
166B TYR* 4.1 15.7 - - + -
179B TYR* 4.0 25.8 - - + +
180B PHE* 5.4 4.9 - - + -
183B ALA* 3.9 27.1 - - + -
194B LEU* 5.1 7.6 - - + -
195B ILE 3.1 8.8 + - - +
196B HIS* 3.4 13.9 - - + -
197B ASP* 3.0 25.6 + - - +
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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