Contacts of the strand formed by residues 201 - 205 (chain F) in PDB entry 2POZ
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 GLU 201 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125F ARG* 2.6 45.2 + - - +
154F GLY 3.1 6.0 + - - +
155F ALA* 3.2 12.6 - - + +
156F LEU 2.9 26.0 + - - -
193F ARG* 4.9 0.7 - - - +
199F GLU 5.0 3.8 - - - +
200F ILE* 1.3 76.2 - - - +
202F LEU* 1.3 60.2 + - - +
203F MSE 4.0 12.2 - - - +
226F ASP* 5.7 0.7 - - - -
228F CYS* 4.7 16.9 - - + -
329F MSE 5.7 2.3 - - - +
330F ILE* 4.6 0.2 - - - +
179H ALA* 4.2 20.2 - - + +
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Residues in contact with LEU 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F LEU* 3.4 16.2 - - + +
158F PHE* 4.2 12.8 - - + -
189F VAL 4.7 2.5 - - - +
192F VAL* 3.8 25.1 - - + -
193F ARG* 3.6 65.3 - - + +
196F ALA* 4.7 2.9 - - + -
200F ILE* 3.6 14.6 + - + -
201F GLU* 1.3 81.0 - - - +
203F MSE 1.3 65.8 + - - +
225F LEU 4.8 2.2 - - - +
226F ASP 4.8 0.2 + - - -
227F ILE* 3.7 17.4 - - + +
228F CYS* 2.8 33.4 + - - +
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Residues in contact with MSE 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F TYR* 3.6 40.6 - - + -
155F ALA* 3.7 10.8 - - + -
156F LEU 2.8 13.4 + - - +
157F LYS* 3.2 22.1 - - + -
158F PHE* 3.0 30.1 + - - -
201F GLU* 3.9 19.3 - - - +
202F LEU* 1.3 81.9 - - - +
204F VAL* 1.3 62.3 + - - +
228F CYS* 4.0 8.7 - - + -
229F PHE* 3.5 43.7 - - + -
329F MSE 4.9 4.9 - - + -
330F ILE* 3.8 15.3 - - + -
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Residues in contact with VAL 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F LYS* 4.9 0.7 - - - -
158F PHE* 3.5 19.7 - - + -
160F PRO* 3.6 29.8 - - + -
189F VAL* 4.4 4.3 - - + -
203F MSE 1.3 74.9 - - - +
205F ASP* 1.3 57.3 + - - +
206F LEU* 3.8 15.9 - - + -
218F PHE* 4.9 0.2 - - + -
222F ILE* 4.3 18.4 - - + -
227F ILE* 3.8 35.2 - - + -
229F PHE 3.1 7.9 + - - +
230F VAL* 3.1 8.9 - - + +
231F GLU* 2.8 30.5 + - - -
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Residues in contact with ASP 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F ASN* 5.5 1.7 + - - -
132F TYR* 5.4 2.0 + - - +
157F LYS* 4.2 20.1 + - + -
158F PHE 2.9 15.5 + - - +
159F TYR* 3.0 34.9 - - - +
160F PRO* 3.4 4.7 - - - +
203F MSE 4.0 0.6 + - - -
204F VAL* 1.3 72.0 - - - +
206F LEU* 1.3 60.4 + - - +
207F SER* 3.0 31.8 + - - -
231F GLU* 3.6 36.5 - - + +
232F GLU* 4.3 2.3 - - - +
257F GLU* 5.2 2.8 - - - +
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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