Contacts of the strand formed by residues 166 - 169 (chain B) in PDB entry 2C1H
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 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B CYS* 4.4 13.9 - - - -
120B ILE 3.0 6.2 + - - +
121B MET* 3.3 30.7 - - + -
122B THR* 2.9 25.7 + - - -
164B ALA* 4.0 2.8 - - - +
165B ASP* 1.3 84.7 - - + +
167B VAL* 1.3 62.7 + - - +
192B VAL* 4.6 0.9 - - - -
193B GLY* 3.5 28.3 - - - -
194B ILE 3.3 25.1 - - - -
195B LEU* 3.5 20.9 - - + -
248B ASP* 3.9 14.1 - - + -
249B ILE* 3.9 27.1 - - + -
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B THR* 3.4 19.3 - - - +
124B VAL* 3.9 15.9 - - + -
156B ALA* 4.0 23.8 - - + +
159B HIS* 4.2 6.5 - - + -
160B ALA 5.1 0.2 - - - +
164B ALA* 4.9 1.8 - - + -
166B PHE* 1.3 76.7 - - - +
168B SER* 1.3 60.4 + - - +
169B PRO* 3.3 6.7 - - + +
180B ILE* 4.4 9.6 - - + -
184B LEU* 3.9 12.6 - - + -
192B VAL* 4.5 9.6 - - + -
193B GLY 3.1 15.7 + - - +
194B ILE* 3.8 17.3 - - + -
195B LEU 2.9 23.0 + - - -
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ASP* 2.9 28.0 + - - -
121B MET* 4.3 4.7 - - - +
122B THR 2.7 18.8 + - - -
123B ASP* 3.5 7.4 + - - +
124B VAL 3.1 16.7 + - - -
166B PHE 4.2 0.2 - - - -
167B VAL* 1.3 73.4 - - - +
169B PRO* 1.4 63.9 - - - +
170B SER 3.3 2.3 + - - -
195B LEU* 3.2 25.6 - - - -
197B TYR* 3.6 17.4 - - - -
316B PHE* 4.9 3.6 - - - -
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Residues in contact with PRO 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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124B VAL* 3.4 19.3 - - + +
167B VAL* 3.3 15.9 - - + +
168B SER* 1.4 81.1 - - - +
170B SER* 1.3 58.0 + - - +
171B ASP* 3.3 19.1 - - - +
176B ARG* 3.0 22.8 + - - +
177B ILE* 3.8 15.5 - - + -
180B ILE* 3.8 24.0 - - + -
194B ILE* 3.9 11.9 - - + -
195B LEU 3.3 11.9 - - - +
196B SER* 4.3 1.1 - - - -
197B TYR* 3.3 14.4 + - - -
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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
------------------------------------------------------------
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