Contacts of the strand formed by residues 167 - 173 (chain B) in PDB entry 2O06
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B LYS* 3.8 10.3 - - + -
97B VAL 3.7 7.6 - - - -
98B LEU* 3.7 53.4 - - + -
119B SER* 6.0 0.7 - - - -
121B VAL* 3.9 26.0 - - + -
159B PHE* 4.7 2.2 - + - -
163B ASN* 3.8 28.3 - - + -
166B ALA* 1.3 99.9 - - + +
168B ASP* 1.3 63.4 + - - +
169B VAL 3.8 13.9 - - - +
170B ILE* 4.0 13.0 - - + -
196B ALA* 3.1 14.6 + - + +
197B LEU* 3.3 7.6 - - - +
198B LYS* 2.9 30.0 + - - +
201B GLY* 4.3 0.5 - - - -
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Residues in contact with ASP 168 (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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91B HIS* 3.6 29.9 + - - +
93B ASN 4.2 2.5 - - - +
94B PRO* 3.9 14.1 - - + -
95B ARG* 2.9 13.1 + - - +
96B LYS 2.8 33.8 + - - +
167B PHE* 1.3 73.0 - - - +
169B VAL* 1.3 63.7 + - - +
197B LEU* 4.1 0.2 - - - -
198B LYS* 3.1 36.4 + - - +
200B ASP* 4.9 2.3 - - - +
201B GLY* 3.3 6.1 - - - -
202B VAL 2.9 25.3 + - - -
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Residues in contact with VAL 169 (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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87B PRO* 3.9 23.8 - - + +
88B LEU* 4.0 9.9 - - + -
91B HIS* 4.3 4.9 - - + -
94B PRO* 3.7 26.2 - - + -
96B LYS 3.2 2.3 + - - +
97B VAL* 3.2 16.7 - - + +
98B LEU 2.9 24.8 + - - -
167B PHE* 3.8 2.2 - - - +
168B ASP* 1.3 85.8 - - - +
170B ILE* 1.3 76.3 + - - +
171B ILE* 4.0 13.9 - - + -
197B LEU* 4.2 0.2 - - - -
202B VAL* 3.2 24.7 - - + +
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Residues in contact with ILE 170 (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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98B LEU* 3.4 18.8 - - + +
100B ILE* 4.6 0.7 - - + -
160B MET* 4.0 20.2 - - + -
167B PHE* 4.0 9.9 - - + -
169B VAL* 1.3 77.6 - - - +
171B ILE* 1.3 67.1 + - - +
172B THR* 4.3 6.7 - - - +
193B MET* 3.7 48.6 - - + +
196B ALA* 3.8 20.9 - - + -
197B LEU* 3.7 19.7 - - + +
202B VAL 3.1 7.1 + - - -
203B LEU* 3.2 9.0 - - + +
204B CYS 2.9 25.3 + - - +
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Residues in contact with ILE 171 (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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83B ILE* 3.7 48.7 - - + +
84B ALA* 4.1 6.5 - - - +
87B PRO* 4.0 15.0 - - + -
88B LEU* 5.3 1.1 - - + -
97B VAL* 4.3 7.4 - - + -
98B LEU 2.8 12.2 + - - +
99B ILE* 3.3 7.2 - - + -
100B ILE* 2.8 32.6 + - - +
107B VAL* 4.0 17.5 - - + -
111B VAL* 3.8 28.5 - - + -
169B VAL* 4.0 10.1 - - + -
170B ILE* 1.3 77.0 - - - +
172B THR* 1.3 57.4 + - - +
173B ASP* 3.8 6.7 + - + +
204B CYS 3.2 5.6 - - - +
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Residues in contact with THR 172 (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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83B ILE* 3.7 2.1 - - - +
100B ILE* 3.7 9.2 - - + +
170B ILE* 4.2 2.0 + - - +
171B ILE* 1.3 72.8 + - - +
173B ASP* 1.3 59.4 + - - +
174B SER* 3.5 10.3 + - - +
184B LEU* 4.0 30.3 - - + +
189B TYR* 2.7 37.1 + - + +
193B MET* 3.6 6.2 - - - -
204B CYS 3.0 9.7 + - - -
205B CYS* 3.5 25.9 - - + -
206B GLN* 3.1 25.5 + - - +
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Residues in contact with ASP 173 (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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79B TYR* 2.6 42.5 + - - -
80B GLN* 3.8 8.0 + - - -
83B ILE* 3.9 8.1 - - + -
99B ILE* 4.6 2.2 - - + -
100B ILE 2.8 13.2 + - - +
101B GLY* 3.6 1.4 - - - -
102B GLY* 3.1 43.1 + - - +
104B ASP* 4.4 0.7 - - - +
107B VAL* 3.3 23.1 + - + +
171B ILE* 3.8 5.7 + - + -
172B THR* 1.3 68.5 - - - +
174B SER* 1.3 58.0 + - - +
501B MTA 3.2 14.7 - - - +
601B PUT 3.7 7.4 + - - -
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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