Contacts of the strand formed by residues 201 - 205 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA* 4.2 22.6 + - + +
125B ARG* 2.5 34.8 + - - -
154B GLY 3.0 11.5 + - - +
155B ALA* 3.1 18.5 - - + +
156B LEU 2.8 27.4 + - - +
193B ARG* 4.8 1.1 - - - +
199B GLU 4.4 6.5 - - - +
200B ILE* 1.3 75.3 - - - +
202B LEU* 1.3 59.8 + - - +
203B MSE 4.1 8.9 - - - +
228B CYS* 4.4 20.8 - - + -
329B MSE 5.6 2.4 - - - +
330B ILE* 4.6 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 3.3 26.0 - - + +
158B PHE* 4.5 11.9 - - + -
189B VAL* 4.6 3.1 - - + +
192B VAL* 3.7 35.2 - - + -
193B ARG* 3.6 54.5 - - + +
196B ALA* 4.7 3.1 - - + -
200B ILE* 3.6 7.5 + - + +
201B GLU* 1.3 81.4 - - - +
203B MSE 1.3 61.9 + - - +
204B VAL* 5.6 0.2 - - + -
225B LEU 5.0 1.3 - - - +
227B ILE* 3.6 18.6 - - + +
228B CYS* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TYR* 4.0 22.9 - - + -
155B ALA* 3.9 21.1 - - + -
156B LEU 2.7 18.7 + - - +
157B LYS* 3.0 42.2 - - + -
158B PHE* 3.1 11.0 + - - -
201B GLU* 3.9 14.4 - - - +
202B LEU* 1.3 79.9 - - - +
204B VAL* 1.3 61.6 + - - +
228B CYS* 4.0 19.1 - - + -
229B PHE* 3.3 51.1 - - + -
329B MSE 4.4 2.7 - - + -
330B ILE* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LYS* 4.8 0.7 - - - -
158B PHE* 3.6 26.9 - - + -
160B PRO* 3.3 30.1 - - + -
189B VAL* 4.4 9.2 - - + -
202B LEU 4.3 0.2 + - - -
203B MSE 1.3 77.1 - - - +
205B ASP* 1.3 53.6 + - - +
206B LEU* 3.6 16.4 - - + -
222B ILE* 4.6 13.0 - - + -
227B ILE* 4.3 26.7 - - + -
229B PHE 3.1 9.0 + - - +
230B VAL* 3.1 9.7 - - + +
231B GLU* 2.7 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LYS* 3.7 13.4 + - + -
158B PHE 3.0 10.7 + - - +
159B TYR* 3.3 59.3 + - + +
160B PRO* 3.8 2.8 - - - +
161B LEU* 5.3 0.9 + - - +
203B MSE 4.1 1.0 - - - -
204B VAL* 1.3 70.8 - - - +
206B LEU* 1.3 61.4 + - - +
207B SER* 2.8 34.7 + - - -
231B GLU* 2.7 45.6 - - + +
232B GLU* 4.2 2.1 - - - +
257B GLU* 4.0 4.9 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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