Contacts of the strand formed by residues 148 - 152 (chain A) in PDB entry 2PU1
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 148 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PRO* 3.5 39.7 - - + -
147A CYS* 1.3 71.0 - - - +
149A ASN* 1.3 59.7 + - - +
150A VAL* 3.0 25.1 + - + +
167A MET* 3.1 3.4 - - - +
168A ILE* 2.8 51.3 + - + +
170A PRO* 3.8 11.9 - - + -
179A ALA 4.1 4.0 - - - -
180A LEU* 3.9 17.5 - - + -
183A GLY* 3.6 30.3 - - - -
396A GLY 3.2 22.0 - - - +
398A PRO* 3.5 19.7 - - + -
407A LEU* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A CYS 3.7 4.6 + - - +
148A PHE* 1.3 69.0 - - - +
150A VAL* 1.3 60.3 + - - +
151A ILE 3.4 20.3 - - - +
152A ASN* 4.3 10.6 - - - +
164A GLN 4.4 3.0 + - - -
165A GLU* 3.5 28.2 - - + +
166A PHE 3.5 8.4 + - - -
167A MET* 3.6 15.4 - - + +
208A GLU* 3.0 37.9 + - + +
210A GLY* 3.4 17.5 + - - -
371A HIS* 5.7 0.7 - - + +
394A LYS* 6.5 0.2 - - + -
396A GLY* 3.8 2.6 - - - +
397A ALA* 3.4 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PHE* 3.0 29.5 + - + +
149A ASN* 1.3 75.3 - - - +
151A ILE* 1.4 62.7 - - - +
166A PHE 3.1 8.2 + - - +
168A ILE* 4.0 25.8 - - + -
187A TYR* 3.9 22.4 - - + -
190A LEU* 3.7 14.6 - - + -
210A GLY* 3.4 4.8 - - - -
211A PHE* 2.7 35.2 + - - -
225A LEU* 3.6 27.6 - - + -
397A ALA* 4.2 3.1 - - + -
398A PRO* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ASN* 3.4 1.9 - - - +
150A VAL* 1.4 83.1 - - - +
152A ASN* 1.3 64.3 + - - +
161A LEU* 4.2 6.5 - - + -
166A PHE* 2.8 44.7 + - + +
190A LEU* 3.9 10.5 - - + -
194A ILE* 4.4 10.8 - - + -
211A PHE 3.4 4.3 - - - +
213A PRO* 4.1 21.8 - - + -
215A ILE* 4.6 0.7 - - + -
221A PRO* 3.7 36.1 - - + +
224A ILE* 4.0 26.5 - - + -
225A LEU* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ASN* 4.3 14.0 - - - +
150A VAL 4.3 0.2 - - - -
151A ILE* 1.3 78.9 + - - +
153A GLY* 1.3 55.5 + - - +
154A GLY 5.0 0.4 - - - +
157A ALA* 4.2 16.0 - - + +
159A ASN* 3.0 18.5 + - - -
161A LEU* 2.5 26.7 - - - +
164A GLN 3.1 16.8 - - - +
166A PHE* 4.7 0.2 - - - -
206A GLY* 3.8 27.5 - - - +
207A ASP 4.7 2.0 - - - +
208A GLU* 5.3 2.4 - - - +
210A GLY* 3.7 12.3 + - - +
211A PHE 2.7 23.5 + - - +
212A ALA* 4.3 3.5 - - - +
----------------------------------------------------------
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