Contacts of the strand formed by residues 154 - 159 (chain A) in PDB entry 1OIZ
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 ILE 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A SER* 4.1 0.4 - - - -
113A LYS* 3.3 12.6 - - + +
115A LEU* 4.2 3.4 - - + -
143A ILE* 3.8 20.9 - - + -
149A THR* 3.7 20.6 - - + -
153A GLY* 1.3 79.7 - - - +
155A LYS* 1.3 79.0 + - - +
156A ALA* 4.2 5.2 - - + +
189A LEU* 4.2 11.2 - - + -
190A LYS 2.9 16.2 + - - +
191A VAL* 4.2 18.4 - - + -
192A ARG* 2.9 29.0 + - - +
1275A TRT 3.7 39.5 - - + -
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Residues in contact with LYS 155 (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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108A ASP* 2.8 28.1 + - - +
110A THR* 3.1 16.6 + - - -
112A SER* 3.0 23.5 + - - +
113A LYS 2.9 9.6 + - - +
114A VAL* 3.4 5.0 - - + +
115A LEU* 2.9 27.7 + - - +
154A ILE* 1.3 77.1 - - - +
156A ALA* 1.3 60.9 + - - +
192A ARG* 3.6 24.7 - - - +
193A GLY* 3.3 22.7 - - - +
195A HIS* 4.4 4.3 - - + +
237A PHE* 3.8 31.9 - - + -
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Residues in contact with ALA 156 (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* 3.3 9.4 - - + +
117A TYR* 4.2 14.4 - - + -
154A ILE* 4.2 11.1 - - + +
155A LYS* 1.3 75.9 - - - +
157A ILE* 1.3 57.1 + - - +
158A PHE* 3.8 24.3 - - + -
191A VAL* 6.0 0.2 - - + -
193A GLY 3.0 8.7 + - - +
194A ILE* 3.6 5.9 - - + -
195A HIS* 2.8 35.0 + - - +
1275A TRT 4.7 6.5 - - + -
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Residues in contact with ILE 157 (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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114A VAL* 3.8 24.0 - - + -
115A LEU 2.7 12.4 + - - +
116A ILE* 3.4 20.5 - - + +
117A TYR* 2.8 33.6 + - - +
156A ALA* 1.3 76.9 - - - +
158A PHE* 1.3 66.3 + - - +
159A ASP* 4.0 1.5 + - + +
195A HIS* 3.3 11.2 - - + +
197A ILE* 4.5 21.3 - - + -
233A LEU* 4.3 15.3 - - + -
237A PHE* 3.9 28.7 - - + -
241A LEU* 3.9 22.7 - - + -
245A TYR* 5.7 2.0 - - + -
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Residues in contact with PHE 158 (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 TYR* 4.9 0.9 - - - -
117A TYR* 3.5 43.5 - + + -
119A ILE* 4.4 6.1 - - + -
156A ALA* 3.8 20.4 - - + -
157A ILE* 1.3 73.4 - - - +
159A ASP* 1.3 61.1 + - - +
160A LEU* 3.5 18.0 + - + +
183A LEU* 6.1 1.6 - - + -
194A ILE* 4.2 16.6 - - + -
195A HIS 2.7 14.7 + - - -
196A LEU* 3.5 20.3 - - + -
197A ILE* 3.0 27.1 + - - +
1275A TRT 3.8 67.5 - + - -
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Residues in contact with ASP 159 (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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116A ILE* 5.4 1.6 - - + -
117A TYR 2.7 15.3 + - - +
118A ARG* 4.2 8.5 - - - +
119A ILE* 2.9 28.1 + - - +
157A ILE* 4.0 2.2 - - + +
158A PHE* 1.3 69.4 - - - +
160A LEU* 1.3 60.7 + - - +
161A GLU* 3.1 23.7 + - - +
197A ILE* 3.7 16.6 - - + -
198A ASN* 3.0 25.2 - - - +
245A TYR* 2.7 36.4 + - + +
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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