Contacts of the helix formed by residues 253 - 261 (chain B) in PDB entry 2PJ7
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 GLY 253 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ASN* 3.4 18.6 - - - -
147B PHE* 4.0 1.1 - - - -
149B ALA* 3.8 5.3 - - - +
250B ALA 4.3 4.2 + - - -
251B ALA 3.4 3.6 - - - -
252B GLY* 1.3 81.2 - - - +
254B SER* 1.3 60.3 + - - -
255B ASP* 3.3 11.4 - - - -
256B ASP* 3.4 5.7 + - - +
257B TRP* 3.1 26.2 + - - +
501B 235 4.6 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.4 15.7 - - - -
144B ASN* 3.2 9.4 + - - -
147B PHE* 3.6 41.5 - - - -
179B LEU* 5.4 0.9 - - - -
192B TYR* 2.7 31.3 + - - -
194B THR* 4.1 6.8 + - - +
253B GLY* 1.3 71.2 - - - -
255B ASP* 1.3 62.5 + - - +
257B TRP* 3.6 3.6 - - - +
258B ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B TYR* 3.6 13.2 - - + -
194B THR* 4.3 2.9 - - + -
203B LEU 4.9 0.5 - - - +
204B TYR* 4.8 10.4 - - - -
205B PRO* 4.2 2.6 - - + +
207B SER* 4.6 0.5 + - - -
253B GLY 3.8 5.4 - - - -
254B SER* 1.3 78.0 + - - +
256B ASP* 1.3 84.2 + - - +
258B ALA 3.5 0.2 + - - -
259B TYR* 3.1 16.1 + - - +
266B SER* 2.8 30.7 + - - +
267B PHE 4.7 6.1 - - - +
268B THR* 2.8 28.1 + - - +
501B 235 2.8 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ALA* 3.8 8.1 - - + -
205B PRO* 3.3 29.6 - - - +
206B TYR* 3.8 8.9 - - + -
207B SER* 2.6 32.3 + - - -
208B TYR* 3.1 32.1 + - + +
250B ALA 4.6 1.2 - - - +
253B GLY* 3.8 6.5 + - - +
254B SER 3.3 0.4 - - - -
255B ASP* 1.3 93.1 + - - +
257B TRP* 1.3 64.1 + - - +
259B TYR* 3.3 6.0 + - - +
260B ASP* 3.0 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PHE* 3.9 26.7 - + + -
148B ASP* 3.5 38.8 + - + +
149B ALA* 3.7 8.9 - - + +
171B GLU* 4.4 3.9 + - - -
179B LEU* 4.7 1.6 - - + -
180B ALA* 3.4 35.4 - - + -
183B ILE* 3.9 37.9 - - + -
184B ARG* 3.6 29.4 - - + +
192B TYR* 6.5 0.2 - + - -
253B GLY 3.1 17.6 + - - +
254B SER* 3.6 6.3 - - - +
256B ASP* 1.3 76.8 - - - +
258B ALA* 1.3 76.7 + - + +
260B ASP* 3.1 7.8 + - + +
261B GLN* 3.1 59.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ILE* 5.0 2.0 - - + -
192B TYR* 3.7 36.3 - - + -
254B SER 2.9 17.6 + - - +
255B ASP 3.9 3.6 - - - +
256B ASP 3.3 0.2 - - - -
257B TRP* 1.3 87.8 - - + +
259B TYR* 1.3 63.7 + - - +
261B GLN* 3.0 15.9 + - - +
263B ILE* 3.2 32.3 + - + +
266B SER* 4.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PRO* 3.6 21.5 - - + -
206B TYR* 3.4 35.7 - + - -
213B PRO* 3.5 16.9 - - + +
214B GLU* 3.5 10.9 + - + +
215B ASN* 2.6 27.9 + - - -
219B LEU* 4.4 2.9 - - + -
255B ASP 3.1 17.3 + - - +
256B ASP 3.6 4.0 - - - +
257B TRP 3.2 0.2 - - - -
258B ALA* 1.3 77.7 - - - +
260B ASP* 1.3 58.1 + - - +
262B GLY* 2.8 22.3 + - - -
263B ILE 3.3 20.6 + - - +
264B LYS* 3.5 49.4 + - - -
266B SER* 4.2 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ASP 5.1 2.9 - - - +
149B ALA* 4.6 5.5 - - - +
206B TYR* 2.9 30.1 + - - -
208B TYR* 2.7 34.3 + - - -
211B LYS* 5.3 0.2 + - - -
256B ASP 3.0 17.2 + - - +
257B TRP* 3.1 9.4 + - + +
259B TYR* 1.3 77.1 - - - +
261B GLN* 1.3 67.0 + - - +
262B GLY 3.2 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ARG* 4.2 11.8 - - - +
187B LEU* 3.6 47.7 - - + +
257B TRP* 3.2 59.4 + - + +
258B ALA* 3.0 13.4 + - - +
260B ASP* 1.3 83.7 + - - +
262B GLY* 1.3 57.1 + - - +
263B ILE* 3.6 1.1 - - + -
----------------------------------------------------------
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