Contacts of the strand formed by residues 167 - 173 (chain A) in PDB entry 2O07
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 PHE 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A LYS* 3.8 9.9 - - + +
97A VAL 3.9 12.1 - - - -
98A LEU* 3.7 47.6 - - + -
121A VAL* 4.0 25.4 - - + -
159A PHE* 4.8 2.9 - + - -
163A ASN* 3.7 36.3 - - + -
165A ASP 4.0 0.2 - - - -
166A ALA* 1.3 88.8 - - + +
168A ASP* 1.3 58.4 + - - +
169A VAL 3.9 13.7 - - - +
170A ILE* 4.0 12.3 - - + -
196A ALA* 3.1 17.7 + - + +
197A LEU* 3.2 10.4 - - + +
198A LYS* 2.8 29.6 + - - -
201A GLY* 4.4 0.3 - - - -
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Residues in contact with ASP 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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91A HIS* 3.5 24.7 + - - +
93A ASN 4.3 4.3 - - - +
94A PRO* 4.0 13.5 - - + -
95A ARG* 3.0 16.1 + - - +
96A LYS* 2.8 37.9 + - - +
167A PHE* 1.3 72.6 - - - +
169A VAL* 1.3 63.1 + - + +
197A LEU* 3.9 0.9 - - - -
198A LYS* 3.7 25.0 - - - +
200A ASP* 4.8 2.9 - - - +
201A GLY* 3.2 6.6 - - - -
202A VAL 2.9 25.5 + - - -
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Residues in contact with VAL 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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87A PRO* 3.8 27.4 - - + +
88A LEU* 4.2 9.2 - - + -
91A HIS* 4.3 5.4 - - + -
94A PRO* 3.7 26.9 - - + -
96A LYS 3.4 2.5 + - - +
97A VAL* 3.3 17.3 - - + -
98A LEU 2.9 24.1 + - - +
167A PHE* 3.9 1.2 - - - +
168A ASP* 1.3 84.7 - - - +
170A ILE* 1.3 67.6 + - - +
171A ILE* 4.1 22.4 - - + -
202A VAL* 3.2 20.6 - - + +
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Residues in contact with ILE 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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98A LEU* 3.2 28.5 - - + +
100A ILE* 4.5 2.9 - - + -
160A MET* 4.0 14.8 - - + -
167A PHE* 4.0 11.2 - - + -
169A VAL* 1.3 78.2 - - - +
171A ILE* 1.3 70.9 + - - +
172A THR 4.2 0.2 + - - -
193A MET* 3.7 47.7 - - + +
196A ALA* 3.9 19.1 - - + -
197A LEU* 3.7 18.2 - - + +
202A VAL 3.1 6.9 + - - -
203A LEU* 3.2 11.0 - - + +
204A CYS 2.9 25.5 + - - +
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Residues in contact with ILE 171 (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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83A ILE* 3.8 47.3 - - + +
84A ALA* 4.1 7.6 - - - +
87A PRO* 3.9 12.6 - - + -
88A LEU* 5.1 1.1 - - + -
97A VAL* 4.3 7.6 - - + -
98A LEU 2.8 10.0 + - - +
99A ILE* 3.2 8.1 - - + +
100A ILE* 2.8 32.1 + - - +
107A VAL* 4.0 17.9 - - + -
111A VAL* 3.8 29.6 - - + -
169A VAL* 4.1 14.8 - - + -
170A ILE* 1.3 78.1 - - - +
172A THR* 1.3 60.1 + - - +
173A ASP* 3.7 3.7 + - + +
204A CYS 3.2 4.5 - - - +
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Residues in contact with THR 172 (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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83A ILE* 3.5 4.7 - - - +
100A ILE* 3.7 16.2 - - + +
170A ILE* 4.1 0.9 - - - +
171A ILE* 1.3 72.5 - - - +
173A ASP* 1.3 59.8 + - - +
174A SER* 3.5 25.3 + - - +
189A TYR* 2.7 42.7 + - + +
193A MET* 3.7 5.5 - - - -
204A CYS 3.0 9.3 + - - -
205A CYS* 3.5 22.4 - - + -
206A GLN* 3.3 23.2 + - - +
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Residues in contact with ASP 173 (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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79A TYR* 3.1 22.4 + - - -
80A GLN* 3.9 0.5 - - - +
83A ILE* 4.2 1.6 - - + -
99A ILE* 4.5 3.4 - - + -
100A ILE 2.8 14.4 + - - +
101A GLY* 3.5 0.9 - - - -
102A GLY* 3.0 41.7 + - - +
104A ASP* 4.3 2.3 - - - +
107A VAL* 3.4 28.5 - - + +
171A ILE* 3.7 9.0 + - + -
172A THR* 1.3 71.5 - - - +
174A SER* 1.3 55.4 + - - +
501A MTA 3.3 7.4 - - - +
601A SPD 3.1 31.9 + - - +
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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