Contacts of the helix formed by residues 193 - 201 (chain B) in PDB entry 4PAR
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 THR 193 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 3.3 3.8 - - - +
192B LYS* 1.3 82.4 - - + +
194B THR* 1.3 77.8 + - - +
195B LYS* 3.5 30.5 + - + +
196B ASP* 3.1 41.8 + - - +
197B VAL* 3.4 10.4 - - - +
207B ASN* 5.9 1.2 - - - +
208B TYR 5.4 1.4 + - - -
285B TYR* 4.0 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B THR* 1.3 82.1 + - - +
195B LYS* 1.3 63.6 + - - -
197B VAL* 3.1 11.2 - - - +
198B CYS* 3.0 26.7 + - - +
208B TYR* 3.0 33.1 + - - +
209B GLN 6.0 0.2 - - - +
210B ARG 4.8 4.5 - - - +
225B PHE* 3.6 33.0 - - + -
285B TYR* 3.6 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B THR* 3.5 17.4 + - + +
194B THR* 1.3 81.2 + - - +
196B ASP* 1.3 89.6 + - - +
198B CYS* 3.5 4.2 - - - +
199B ASN* 2.9 39.5 + - - +
205B TYR* 3.8 17.0 + - + +
206B LYS 3.1 29.2 - - - +
207B ASN* 3.7 23.1 - - + -
208B TYR* 3.9 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B TYR 4.5 5.0 - - - +
174B PRO* 3.7 27.8 - - + +
191B LEU* 4.3 12.3 - - + -
192B LYS* 4.1 11.8 + - - +
193B THR* 3.1 33.5 + - - +
195B LYS* 1.3 100.9 + - - +
197B VAL* 1.3 67.2 + - - +
199B ASN* 3.0 18.1 + - - +
200B CYS* 3.0 18.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 3.8 21.0 - - + +
193B THR 3.4 12.6 - - - +
194B THR* 3.1 25.4 - - - +
196B ASP* 1.3 74.6 - - - +
198B CYS* 1.3 61.4 + - - +
200B CYS* 3.1 11.4 + - - +
201B PHE* 3.1 17.8 - - + -
223B ILE* 4.0 7.4 - - + -
225B PHE* 3.6 22.7 - - + -
272B PHE* 3.5 44.4 - - + -
285B TYR* 5.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B THR 3.0 20.7 + - - +
195B LYS 3.5 5.8 - - - +
197B VAL* 1.3 78.0 - - - +
199B ASN* 1.3 56.4 + - - +
201B PHE* 3.0 19.1 + - - +
202B GLY 3.6 0.5 + - - -
203B TYR* 3.3 27.0 + - + +
205B TYR* 3.9 22.2 - - + -
208B TYR* 4.0 18.2 - - - -
213B ALA* 3.9 27.4 - - - -
223B ILE* 4.7 7.2 - - - -
225B PHE* 4.0 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PRO* 4.7 9.4 - - + +
178B ILE* 3.6 16.1 - - - +
195B LYS* 2.9 32.6 + - - +
196B ASP* 3.0 12.9 + - - +
198B CYS* 1.3 71.9 - - - +
200B CYS* 1.3 61.3 + - - +
201B PHE 3.4 0.4 - - - -
202B GLY 4.1 3.6 + - - -
203B TYR* 3.0 28.7 - - - +
204B SER* 4.3 1.8 - - - +
205B TYR* 3.3 36.3 + - - +
314B TYR 4.4 0.3 - - - +
316B PRO* 4.5 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PRO* 3.7 26.5 - - - -
177B TYR* 5.0 4.0 - - + -
178B ILE* 4.1 5.3 - - - +
183B ILE* 4.0 20.6 - - + -
191B LEU* 3.8 22.9 - - - -
196B ASP 3.0 18.3 + - - -
197B VAL 3.1 9.8 + - - +
199B ASN* 1.3 78.0 - - - +
201B PHE* 1.3 60.2 + - + +
202B GLY 3.4 0.4 - - - -
313B THR* 2.4 32.9 + - - +
314B TYR 2.8 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ILE* 4.4 8.5 - - + -
197B VAL* 3.1 26.2 - - + -
198B CYS 3.0 5.4 + - - +
200B CYS* 1.3 85.5 - - + +
202B GLY* 1.3 55.6 + - - +
203B TYR 3.7 1.6 - - - -
215B HIS* 3.8 30.9 - + + +
216B PRO* 3.6 20.2 - - + +
217B TYR* 4.8 1.4 - - - -
223B ILE* 3.5 28.3 - - + -
270B ILE* 3.7 26.2 - - + -
272B PHE* 4.0 20.0 - + - -
311B VAL* 3.6 22.4 - - + -
312B GLN 3.2 28.3 - - - -
313B THR* 4.5 3.8 - - - -
314B TYR* 4.0 13.9 - + - +
----------------------------------------------------------
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