Contacts of the helix formed by residues 235 - 247 (chain B) in PDB entry 1P45
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 ALA 235 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 4.9 10.5 - - + -
24B HIS* 3.2 41.9 + - + -
194B ILE* 3.6 27.9 - - + +
233B LYS 4.2 1.0 + - - -
234B ASP* 1.3 71.0 + - - +
236B THR* 1.3 69.0 + - - +
237B PRO* 3.3 1.8 - - - -
238B VAL* 2.9 12.6 + - - -
239B ALA* 3.0 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B HIS* 5.5 0.4 - - + +
27B ARG* 3.6 32.8 - - - +
28B VAL* 4.7 7.0 - - - -
234B ASP* 3.0 18.6 + - - +
235B ALA* 1.3 76.6 - - - +
237B PRO* 1.3 64.4 - - - +
239B ALA* 3.1 6.6 + - - +
240B LYS* 2.8 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B TRP* 4.9 17.0 - - + -
231B ASN* 6.4 0.9 - - + -
234B ASP* 3.1 35.4 - - + +
235B ALA 3.3 1.3 - - - -
236B THR* 1.3 93.0 - - - +
238B VAL* 1.3 61.1 + - - +
240B LYS* 4.2 8.2 - - + +
241B THR* 2.9 28.2 + - - -
260B ALA* 4.3 2.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 3.6 31.2 - - + -
147B MET* 4.0 18.2 - - + -
189B VAL* 4.7 1.8 - - + +
191B ALA* 4.1 14.1 - - + -
194B ILE* 3.6 29.2 - - + -
230B TRP* 3.7 21.8 - - + -
235B ALA 2.9 3.6 + - - +
237B PRO* 1.3 78.5 - - + +
239B ALA* 1.3 65.3 + - - +
241B THR* 3.2 4.7 + - - -
242B VAL* 3.2 23.4 + - + +
260B ALA* 3.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 4.9 0.4 - - + +
24B HIS* 3.5 39.7 - - + +
25B ILE* 3.6 16.1 - - + +
28B VAL* 3.9 10.1 - - + -
235B ALA* 3.0 15.1 + - + +
236B THR* 3.7 3.6 - - - +
238B VAL* 1.3 75.7 - - + +
240B LYS* 1.3 64.8 + - - +
241B THR 3.0 1.5 + - - -
242B VAL* 3.3 4.0 + - - +
243B CYS* 3.1 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 5.6 0.9 - - - +
28B VAL* 4.4 20.2 - - + +
236B THR* 2.8 36.2 + - - +
237B PRO* 3.6 6.9 + - + +
239B ALA* 1.3 72.6 - - - +
241B THR* 1.3 61.8 + - - +
243B CYS* 3.3 7.7 + - - +
244B ALA* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 4.3 10.5 - - + -
237B PRO 2.9 16.2 + - - -
238B VAL 3.2 10.1 + - - -
239B ALA 3.0 0.8 - - - -
240B LYS* 1.3 76.8 - - - +
242B VAL* 1.3 65.9 + - - +
244B ALA* 3.0 22.4 - - + +
245B LEU* 3.1 10.9 + - + +
258B ILE* 3.9 24.5 - - + -
260B ALA* 3.4 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.7 24.5 - - + -
92B VAL* 4.5 4.0 - - + -
145B VAL* 3.9 23.1 - - + -
147B MET* 3.8 28.7 - - - -
189B VAL* 4.0 12.6 - - + -
238B VAL 3.2 13.4 + - - +
239B ALA 3.6 7.6 - - - +
241B THR* 1.3 78.6 - - - +
243B CYS* 1.3 63.3 + - - +
245B LEU* 2.9 15.3 + - - +
246B LEU* 3.0 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.2 9.6 - - + -
5B LEU* 3.5 28.0 - - + +
25B ILE* 4.1 12.1 - - - -
28B VAL* 4.1 14.8 - - + -
29B ALA* 3.7 30.1 - - - -
32B GLN* 6.0 1.3 - - + -
239B ALA 3.1 21.0 + - - +
240B LYS* 3.3 7.4 + - - +
242B VAL* 1.3 73.9 - - - +
244B ALA* 1.3 51.4 + - - +
246B LEU* 3.1 11.4 + - - +
247B SER* 2.7 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.6 5.9 - - - +
240B LYS 3.1 13.5 + - - +
241B THR* 3.0 19.3 - - + +
243B CYS* 1.3 73.5 - - - +
245B LEU* 1.3 60.3 + - + +
247B SER* 2.9 29.2 + - - +
249B TRP* 6.1 0.4 - - + -
250B LEU* 3.2 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B SER* 3.5 7.4 + - - +
145B VAL* 3.6 21.8 - - + -
185B ARG* 2.6 34.0 + - - +
187B ASN* 3.5 37.0 - - + +
188B LEU 4.1 9.9 - - - +
189B VAL* 3.5 31.9 - - + -
241B THR* 3.1 8.5 + - + +
242B VAL 2.9 5.0 + - - +
244B ALA* 1.3 77.8 - - - +
246B LEU* 1.3 56.8 + - - +
247B SER 3.1 1.4 - - - +
250B LEU* 4.4 19.5 - - + +
253B THR* 4.4 6.5 - - - +
258B ILE* 4.2 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.4 8.7 - - + -
8B LYS* 3.9 17.7 - - - +
10B ILE* 4.0 31.1 - - + +
25B ILE* 4.4 8.1 - - + -
29B ALA* 5.5 0.7 - - + -
89B ASP 4.9 4.6 - - - +
90B GLY* 4.0 15.3 - - - -
91B VAL 4.1 3.6 - - - +
92B VAL* 4.0 16.8 - - + -
141B GLY 5.5 1.2 - - - +
142B GLY* 5.8 0.7 - - - -
143B SER* 3.9 31.1 - - - +
145B VAL* 4.4 7.4 - - + -
185B ARG* 4.4 2.3 + - - -
242B VAL* 3.0 37.0 + - + +
243B CYS* 3.3 14.6 - - - +
245B LEU* 1.3 69.8 - - - +
247B SER* 1.3 67.4 + - - +
248B ASP* 4.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.6 29.8 - - - -
5B LEU* 4.4 6.7 - - - -
8B LYS* 4.9 1.8 - - - +
185B ARG* 3.0 19.4 + - - -
243B CYS 2.7 15.9 + - - -
244B ALA* 2.9 18.7 + - - +
245B LEU 3.1 0.7 - - - +
246B LEU* 1.3 82.8 - - - +
248B ASP* 1.3 62.4 + - - +
249B TRP* 2.4 45.3 + - - +
----------------------------------------------------------
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