Contacts of the helix formed by residues 190 - 203 (chain B) in PDB entry 3HCE
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 ASP 190 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B SER* 3.3 1.8 - - - -
189B PRO* 1.3 87.3 - - - +
191B LEU* 1.3 65.0 + - - +
192B ALA* 2.9 10.8 + - - +
193B SER* 2.8 39.3 + - - -
194B PHE* 3.0 20.2 + - - +
196B ARG* 4.7 3.3 + - - -
232B VAL* 4.0 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ASP* 1.3 74.9 - - - +
192B ALA* 1.3 58.1 + - - +
194B PHE* 3.4 21.7 - - + +
195B GLN* 3.1 25.1 + - + +
232B VAL* 4.3 9.1 - - + +
234B VAL* 5.1 5.6 - - + -
238B GLU* 4.4 47.8 - - + +
241B GLU* 5.9 2.2 - - - +
242B ALA* 5.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ASP* 3.0 10.7 + - - +
191B LEU* 1.3 76.6 - - - +
193B SER* 1.3 56.9 + - - +
195B GLN* 3.2 9.2 + - - +
196B ARG* 2.8 51.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLN* 5.0 5.0 + - - +
160B HIS* 3.7 18.0 + - - -
188B SER* 3.8 1.8 - - - -
189B PRO* 3.2 30.7 - - - +
190B ASP* 2.8 18.3 + - - -
192B ALA* 1.3 74.2 - - - +
194B PHE* 1.3 54.7 - - - +
196B ARG* 3.2 24.5 + - - +
197B ALA* 2.7 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.7 42.0 - - + +
185B ASP* 3.9 19.1 - - + -
188B SER* 3.1 17.2 + - - +
190B ASP 3.0 12.1 + - - +
191B LEU* 3.4 25.1 - - + +
193B SER* 1.3 76.4 - - - +
195B GLN* 1.3 64.5 + - - +
197B ALA* 3.2 2.6 + - - +
198B LEU* 2.8 34.3 + - + +
213B LEU* 5.2 5.4 - - + -
232B VAL* 5.2 2.7 - - + -
234B VAL* 4.5 14.8 - - + -
238B GLU 5.0 1.1 - - - -
239B VAL* 4.6 26.2 - - + -
242B ALA* 3.9 27.4 - - + -
273B PHE* 5.0 7.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 3.1 14.5 + - + +
192B ALA* 3.2 12.8 + - - +
194B PHE* 1.3 85.1 - - + +
196B ARG* 1.3 66.2 + - + +
198B LEU* 3.3 4.6 + - - +
199B ASP* 3.1 34.5 + - - +
242B ALA* 3.4 31.8 - - - +
245B ARG* 3.5 37.3 - - + +
246B SER* 3.3 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER* 3.8 30.0 - - - +
20B GLN* 4.9 4.6 - - - +
190B ASP* 4.7 3.2 + - - -
192B ALA* 2.8 36.8 + - - +
193B SER* 3.2 29.4 + - - +
195B GLN* 1.3 75.1 - - + +
197B ALA* 1.3 64.9 + - - +
199B ASP* 2.9 22.8 + - - +
200B HIS* 3.0 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 3.4 28.5 - - + +
160B HIS* 4.3 6.9 - - + -
184B LEU* 4.0 22.9 - - + -
188B SER* 4.4 5.2 - - - +
193B SER 2.7 21.5 + - - +
194B PHE 3.5 4.0 - - - +
196B ARG* 1.3 74.1 - - - +
198B LEU* 1.3 62.9 + - - +
200B HIS* 3.1 13.0 + - - +
201B ILE* 3.3 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.9 16.5 - - + +
194B PHE* 2.8 22.5 + - + +
195B GLN* 3.5 9.6 - - - +
197B ALA* 1.3 76.5 - - - +
199B ASP* 1.3 54.5 + - - +
201B ILE* 3.6 11.8 + - + +
202B THR* 2.6 40.9 + - - +
211B LEU* 4.1 23.8 - - + -
213B LEU* 5.1 6.1 - - + -
239B VAL* 6.4 0.2 - - + -
242B ALA* 3.6 42.0 - - + +
243B LEU* 3.8 15.0 - - + +
246B SER* 3.4 10.8 - - - +
248B TYR* 4.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLN* 3.1 27.3 + - - +
196B ARG* 2.9 13.4 + - - +
198B LEU* 1.3 76.7 - - - +
200B HIS* 1.3 64.8 + - + +
202B THR* 3.3 15.6 + - - -
203B THR* 3.3 15.9 - - - +
245B ARG 4.4 2.2 - - - +
246B SER* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLN* 6.1 0.4 - - - -
159B VAL 2.8 22.6 + - - +
160B HIS* 3.2 23.5 + + - -
161B GLN 3.5 15.9 - - - +
162B PRO* 3.6 25.7 - - + +
164B PRO* 3.3 14.4 - - + +
196B ARG* 3.0 41.1 + - + +
197B ALA* 3.1 6.1 + - - +
199B ASP* 1.3 80.7 - - + +
201B ILE* 1.3 58.3 - - - +
203B THR* 2.9 31.5 + - + -
204B LEU* 4.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 4.1 33.9 - - + -
159B VAL* 3.8 29.4 - - + -
164B PRO* 4.1 6.5 - - + -
178B LEU* 3.5 18.5 - - + +
180B SER* 5.1 3.6 - - - -
184B LEU* 4.0 23.1 - - + -
197B ALA 3.3 12.7 + - - +
198B LEU* 3.6 17.5 - - + +
200B HIS* 1.3 71.9 - - - +
202B THR* 1.3 63.1 + - - +
203B THR 3.0 5.4 - - - -
204B LEU* 2.9 35.4 + - - +
211B LEU* 4.9 12.1 - - + -
213B LEU* 5.4 1.3 - - + -
248B TYR* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 4.8 0.2 - - - -
198B LEU* 2.6 20.1 + - - +
199B ASP* 3.4 13.6 - - - -
200B HIS 3.2 0.6 - - - -
201B ILE* 1.3 77.6 - - - +
203B THR* 1.3 58.0 + - - +
204B LEU 3.1 2.8 + - - -
205B LEU* 3.4 9.7 + - - +
246B SER* 4.1 16.8 - - - +
248B TYR* 2.6 46.5 + - + +
279B LYS* 3.0 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PRO 4.3 14.6 + - - +
163B GLN* 5.2 1.6 - - - +
164B PRO* 4.3 1.9 - - - +
173B LEU* 5.8 0.7 - - - +
174B PRO* 5.3 3.5 - - - +
199B ASP 3.3 13.0 - - - +
200B HIS* 2.9 26.1 + - + +
201B ILE 3.0 0.4 - - - -
202B THR* 1.3 76.0 - - - +
204B LEU* 1.3 70.3 + - - +
205B LEU 3.4 3.0 + - - +
279B LYS* 4.5 5.5 + - - +
----------------------------------------------------------
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