Contacts of the strand formed by residues 159 - 164 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A LEU* 3.8 10.1 - - - -
115A LEU* 3.3 39.9 - - + -
155A VAL 3.1 14.4 + - - +
156A TRP 3.3 10.5 + - - +
157A ARG 4.4 2.8 - - - +
158A GLU* 1.3 81.0 - - - +
160A LYS* 1.3 58.6 + - - +
161A VAL 4.7 0.7 - - - +
190A HIS 4.8 0.5 - - - +
191A GLY 5.0 0.7 - - - +
192A LEU* 3.0 25.2 - - + +
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU 5.6 1.8 - - - +
108A THR* 5.3 2.0 - - + -
112A ASP* 4.4 24.0 - - + +
113A LEU 3.0 13.6 + - - +
158A GLU 4.8 1.3 - - - +
159A ALA* 1.3 74.6 - - - +
161A VAL* 1.3 72.6 + - + +
191A GLY 5.2 1.8 - - - -
192A LEU* 3.6 8.5 - - - +
193A TRP* 3.0 29.0 + - + -
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU* 4.4 2.5 - - + -
107A LEU* 4.7 4.5 - - + +
108A THR* 3.9 28.9 - - + -
113A LEU 3.5 4.1 + - - +
114A LEU* 3.4 25.5 - - + +
115A LEU* 2.9 30.7 + - - +
133A LEU* 6.1 0.2 - - + -
160A LYS* 1.3 89.8 - - + +
162A LEU* 1.3 68.7 + - - +
192A LEU* 4.5 4.2 - - - +
193A TRP* 3.6 24.2 - - + +
195A ILE* 3.8 29.4 - - + -
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU* 3.6 26.0 - - + +
138A ILE* 3.9 17.0 - - + -
148A LEU* 5.1 4.7 - - + -
156A TRP* 4.5 19.3 - - + -
161A VAL* 1.3 76.9 - - - +
163A LEU* 1.3 71.1 + - - +
164A LEU* 4.0 27.4 - - + -
183A ALA* 4.4 21.5 - - + +
187A ALA* 5.0 4.0 - - + -
192A LEU* 4.4 11.9 - - + +
193A TRP 3.0 12.4 + - - +
194A LEU* 3.7 12.7 - - + +
195A ILE* 2.9 26.5 + - - +
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 3.7 23.6 - - + -
104A LEU* 5.3 4.5 - - + -
114A LEU* 4.3 18.4 - - + -
115A LEU 2.8 16.3 + - - +
116A LEU* 3.8 15.1 - - + -
117A PRO* 3.6 15.6 - - - +
124A TYR* 3.6 44.0 - - + -
162A LEU* 1.3 74.5 - - - +
164A LEU* 1.3 79.2 + - - +
195A ILE* 3.5 38.4 - - + +
197A ASP* 5.0 3.4 - - + +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PRO* 4.3 8.5 - - + -
124A TYR* 5.3 0.7 - - - -
138A ILE* 5.2 1.3 - - + -
146A ALA* 4.2 20.0 - - + -
148A LEU* 4.7 4.0 - - + -
162A LEU* 4.0 32.1 - - + -
163A LEU* 1.3 88.2 - - - +
165A ASN* 1.3 61.7 - - - +
166A TYR* 3.9 19.7 - - + -
179A TYR* 4.2 15.0 - - + +
180A PHE* 5.1 5.2 - - + -
183A ALA* 4.0 20.2 - - + -
194A LEU* 4.7 7.9 - - + -
195A ILE 3.0 8.5 + - - +
196A HIS* 3.4 17.2 - - + -
197A ASP* 3.0 26.2 + - - +
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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