Contacts of the strand formed by residues 201 - 205 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ALA* 4.8 15.5 - - + +
125D ARG* 3.0 30.1 + - - -
154D GLY 3.0 14.0 + - - +
155D ALA* 3.2 13.0 - - + +
156D LEU 2.9 25.5 + - - -
193D ARG* 4.7 1.1 - - - +
199D GLU 4.6 5.2 - - - +
200D ILE* 1.3 78.5 - - - +
202D LEU* 1.3 59.7 + - - +
203D MSE 4.1 12.1 - - + +
228D CYS* 4.4 18.7 - - + -
329D MSE 5.6 1.3 - - - +
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Residues in contact with LEU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU* 3.4 19.1 - - + +
158D PHE* 4.5 11.7 - - + -
189D VAL 4.8 2.7 - - - +
192D VAL* 3.6 28.3 - - + -
193D ARG* 3.4 61.7 - - + +
196D ALA* 4.7 2.7 - - + -
200D ILE* 3.7 12.5 + - + +
201D GLU* 1.3 81.5 - - - +
203D MSE 1.3 64.6 + - - +
225D LEU 5.0 1.8 - - - +
226D ASP 4.8 0.2 + - - -
227D ILE* 3.4 19.6 - - + +
228D CYS* 2.8 33.0 + - - +
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Residues in contact with MSE 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D TYR* 4.3 12.3 - - + -
155D ALA* 3.9 22.7 - - + -
156D LEU 2.8 20.9 + - - +
157D LYS* 3.2 17.8 - - + +
158D PHE* 3.1 29.2 + - - -
201D GLU* 4.0 10.5 - - - +
202D LEU* 1.3 83.3 - - - +
204D VAL* 1.3 62.9 + - - +
205D ASP 4.1 0.2 - - - -
228D CYS* 3.9 24.0 - - + -
229D PHE* 3.4 44.0 - - + -
329D MSE 4.2 10.8 - - + -
330D ILE* 4.1 16.6 - - + -
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LYS* 5.2 0.4 - - - -
158D PHE* 3.6 26.9 - - + -
160D PRO* 3.3 32.1 - - + -
189D VAL* 4.3 11.0 - - + -
202D LEU 5.4 0.2 - - - -
203D MSE 1.3 77.0 - - - +
205D ASP* 1.3 53.9 + - - +
206D LEU* 3.4 17.5 - - + -
222D ILE* 4.6 11.7 - - + -
227D ILE* 4.2 23.8 - - + +
229D PHE 3.1 9.4 + - - +
230D VAL* 3.2 10.7 - - + +
231D GLU* 2.7 31.3 + - - -
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Residues in contact with ASP 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LYS* 3.5 17.6 + - - -
158D PHE 3.0 9.8 + - - +
159D TYR* 3.3 59.8 + - + +
160D PRO* 3.9 3.3 - - - +
161D LEU 5.3 0.7 + - - -
203D MSE 4.1 0.6 + - - -
204D VAL* 1.3 72.1 - - - +
206D LEU* 1.3 59.6 + - - +
207D SER* 2.8 34.1 + - - -
231D GLU* 2.7 42.4 - - + +
232D GLU* 4.3 2.2 - - - +
257D GLU* 4.0 4.3 - - - +
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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