Contacts of the strand formed by residues 177 - 182 (chain A) in PDB entry 2PZI
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 PRO 177 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PRO* 3.8 31.9 - - + -
167A LEU* 4.0 13.2 - - + -
168A ALA 3.4 7.6 - - - +
169A LEU* 4.0 11.0 - - + -
175A GLY 3.4 4.7 - - - +
176A ARG* 1.4 90.0 - - + +
178A VAL* 1.3 62.9 + - - +
214A PHE* 5.1 1.4 - - - -
234A TYR* 3.9 22.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TYR* 3.7 18.8 - - + -
167A LEU* 3.6 7.0 - - - +
168A ALA* 2.8 38.9 + - + +
170A ASP* 3.8 24.2 - - + +
176A ARG* 3.9 16.2 - - - +
177A PRO* 1.3 79.1 - - - +
179A VAL* 1.3 65.6 + - - +
180A LEU* 3.8 9.6 - - + -
214A PHE* 3.9 14.1 - - + -
231A VAL* 3.6 23.1 - - + -
232A MET 3.4 10.5 - - - +
234A TYR 4.5 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 3.5 25.8 - - + -
165A ILE* 3.2 32.3 - - + -
166A TYR 3.2 3.4 - - - +
167A LEU* 4.6 1.1 - - + -
178A VAL* 1.3 79.0 - - - +
180A LEU* 1.3 65.7 + - - +
230A ILE 3.4 0.9 - - - +
231A VAL* 3.3 5.4 - - - -
232A MET* 2.7 55.7 + - + +
234A TYR* 3.9 16.2 - - + -
753A AXX 3.8 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 4.1 9.2 - - + -
147A VAL* 4.1 35.0 - - + -
151A TYR* 4.3 7.6 - - + -
153A VAL* 5.5 0.4 - - + -
165A ILE* 3.8 2.6 - - - +
166A TYR* 2.9 50.0 + - + +
168A ALA* 3.8 28.7 - - + -
178A VAL* 3.8 13.0 - - + -
179A VAL* 1.3 79.9 - - - +
181A LYS* 1.3 62.8 + - - +
217A VAL* 4.7 0.2 - - + -
229A TYR* 4.1 18.8 - - + -
230A ILE 3.2 4.3 - - - +
231A VAL* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLY* 5.8 2.2 - - - -
161A GLY 5.6 1.6 - - - +
162A LEU* 3.6 44.5 - - + +
163A GLY 5.8 0.2 - - - -
164A TRP 4.5 6.3 - - - +
165A ILE* 3.7 28.9 - - + +
166A TYR* 4.9 0.4 - - - -
180A LEU* 1.3 75.6 - - - +
182A GLY* 1.3 69.0 + - - +
229A TYR* 3.4 7.1 - - - -
230A ILE* 2.9 37.5 + - + +
232A MET* 4.0 16.8 - - + +
280A GLU* 5.1 7.5 + - - -
293A ASP* 2.7 32.5 + - - +
295A GLY* 6.4 0.4 - - - -
753A AXX 4.2 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 3.9 25.4 + - - +
164A TRP 5.0 2.6 + - - -
166A TYR* 5.2 0.8 - - - -
181A LYS* 1.3 90.0 - - - +
183A LEU* 1.3 64.9 + - - +
184A VAL 3.7 3.8 - - - -
227A VAL* 5.7 2.0 - - - -
228A GLY 3.7 9.4 - - - -
229A TYR* 3.6 15.2 - - - -
230A ILE* 5.0 1.0 - - - +
----------------------------------------------------------
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