Contacts of the strand formed by residues 165 - 170 (chain A) in PDB entry 1O94
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 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.0 29.8 - - + -
25A TYR* 4.0 11.7 - - + +
55A ALA* 3.8 28.7 - - + -
57A ASN* 5.1 0.4 - - - +
99A LEU* 4.0 14.6 - - + -
100A ALA 3.1 4.8 + - - +
101A GLY* 3.2 11.9 - - - -
102A VAL* 2.9 27.4 + - - +
163A PHE* 3.9 1.9 - - - +
164A ASP* 1.3 86.6 - - + +
166A VAL* 1.3 69.0 + - - +
167A TYR* 4.1 16.6 - - + -
218A ALA* 3.5 9.6 - - + +
220A ALA* 3.9 26.5 - - + -
253A MET* 6.3 0.2 - - - -
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Residues in contact with VAL 166 (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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102A VAL* 3.8 5.4 - - + -
104A LEU* 3.6 32.3 - - + -
155A ALA* 4.2 5.6 - - + +
158A SER* 3.9 24.5 - - - -
163A PHE* 4.7 2.5 - - + -
165A ILE* 1.3 79.3 - - - +
167A TYR* 1.3 62.5 + - - +
209A VAL* 4.1 17.7 - - + -
213A VAL* 4.5 6.1 - - + -
217A CYS* 4.3 20.9 - - + -
218A ALA 2.9 11.5 + - - +
219A ILE* 3.4 15.7 - - + +
220A ALA 2.9 24.1 + - - +
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Residues in contact with TYR 167 (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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25A TYR* 2.7 30.9 + - - -
28A PRO* 3.8 14.2 - - + +
57A ASN* 3.3 25.6 - - - -
102A VAL 3.1 22.5 + - - +
103A GLU* 3.9 15.3 - - + -
104A LEU* 3.2 31.7 + - - +
165A ILE* 4.1 12.3 - - + -
166A VAL* 1.3 75.8 - - - +
168A VAL* 1.3 64.4 + - - +
220A ALA* 3.2 17.3 - - + -
221A THR 3.8 2.7 - - - -
222A ARG* 3.6 27.8 - - + -
253A MET* 5.2 0.9 - - - -
255A ASP* 2.7 43.9 + - + +
295A LEU* 5.1 0.2 - - - +
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Residues in contact with VAL 168 (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* 4.5 1.8 - - + -
151A TYR* 4.4 8.7 - - + -
166A VAL 4.1 0.6 + - - -
167A TYR* 1.3 76.1 - - - +
169A TYR* 1.3 61.2 + - - +
176A PRO* 3.9 18.4 - - + -
202A TRP* 3.7 24.5 - - + +
205A THR* 4.0 28.0 - - + -
206A LEU* 3.9 24.2 - - + -
209A VAL* 4.3 21.1 - - + -
219A ILE* 5.3 1.1 - - + -
220A ALA 3.1 7.7 + - - -
221A THR* 2.6 30.7 + - - +
222A ARG 3.4 7.6 + - - -
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Residues in contact with TYR 169 (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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60A TYR* 3.7 13.7 - - + -
103A GLU* 3.3 37.5 - - + -
104A LEU 3.2 21.2 + - - +
105A TRP* 3.7 22.2 - + + -
106A TYR 5.5 1.4 + - - +
151A TYR* 4.7 1.4 + - - -
167A TYR* 3.8 1.0 - - - -
168A VAL* 1.3 71.4 - - - +
170A GLY* 1.3 61.3 + - - +
171A ALA* 3.5 24.7 - - + -
172A HIS* 2.6 30.5 + - - -
174A TYR* 3.4 31.6 - + - +
176A PRO* 3.3 21.9 - - - +
222A ARG* 4.1 9.9 - - + +
1730A FMN 3.1 28.2 + - - -
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Residues in contact with GLY 170 (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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168A VAL 3.5 2.4 + - - -
169A TYR* 1.3 72.8 - - - +
171A ALA* 1.3 57.2 + - - +
174A TYR 5.1 0.7 - - - -
176A PRO* 4.2 11.4 - - - -
177A LEU* 3.7 20.4 - - - +
202A TRP* 3.3 24.8 - - - -
222A ARG 2.8 22.9 + - - +
224A GLY 3.3 12.8 + - - -
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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