Contacts of the helix formed by residues 191 - 206 (chain B) in PDB entry 3URZ
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 ARG 191 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TYR* 3.9 18.2 + - - -
151B TYR* 3.5 30.0 - - + +
154B THR* 3.0 39.6 + - - +
155B ALA* 3.6 24.0 - - + +
158B GLU* 3.8 22.8 + - - +
187B LEU* 3.0 20.3 + - + +
190B THR* 1.3 95.4 - - + +
192B TYR* 1.3 64.8 + - - +
193B GLU 3.3 1.6 - - - -
194B LYS 3.4 1.3 + - - -
195B ALA* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 3.8 24.0 - + - -
155B ALA* 3.4 26.4 + - + -
156B GLU* 2.7 25.8 + - - -
159B LYS* 3.5 13.7 - - + +
184B LEU 5.5 0.7 - - - -
187B LEU* 3.4 35.5 + - + -
188B PHE* 3.1 44.2 + + + +
191B ARG* 1.3 76.6 - - - +
193B GLU* 1.3 57.6 + - - +
195B ALA* 3.3 5.9 + - - +
196B ARG* 2.9 27.5 + - - +
218B ILE* 3.9 20.2 - - + +
221B ILE* 3.4 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PHE* 2.8 29.4 + - + +
189B THR* 3.7 21.5 - - + +
191B ARG 3.3 0.2 - - - -
192B TYR* 1.3 70.2 - - - +
194B LYS* 1.3 59.6 + - + +
196B ARG* 3.2 13.2 + - - +
197B ASN* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B TYR* 4.0 42.7 + - + +
189B THR 5.0 4.0 - - - +
190B THR* 3.2 31.6 + - - +
191B ARG 3.4 7.9 + - - +
193B GLU* 1.3 76.6 - - + +
195B ALA* 1.3 61.2 - - - +
197B ASN* 3.5 8.6 + - - +
198B SER* 3.3 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLY* 3.2 27.2 - - - +
151B TYR* 3.7 5.6 - - + +
152B TYR* 3.6 20.2 - - + +
191B ARG 3.0 14.3 + - - +
192B TYR* 3.5 10.5 - - - +
194B LYS* 1.3 77.6 - - - +
196B ARG* 1.3 61.6 + - - +
198B SER 3.6 0.2 + - - -
199B LEU* 3.1 30.1 + - + +
218B ILE* 4.1 10.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
188B PHE* 3.4 27.7 - - - -
192B TYR 2.9 13.9 + - - +
193B GLU* 3.2 13.8 + - - +
195B ALA* 1.3 74.2 - - - +
197B ASN* 1.3 55.5 + - - +
199B LEU* 3.2 0.9 + - - +
200B GLN* 2.8 64.5 + - - +
215B LEU* 3.6 26.8 + - + +
218B ILE* 4.0 21.9 - - + +
219B LEU* 4.8 11.1 - - - +
222B GLU* 3.2 37.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLU 3.0 15.6 + - - +
194B LYS* 3.7 10.1 + - - +
196B ARG* 1.3 76.6 - - - +
198B SER* 1.3 64.1 + - - +
200B GLN* 3.9 10.4 - - - +
201B LYS* 3.4 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 5.0 3.5 - - - +
144B ASN* 3.1 44.6 + - - +
147B LEU* 4.0 10.9 - - - +
148B GLY* 3.6 18.9 + - - -
151B TYR* 5.6 0.5 - - - -
194B LYS 3.3 11.4 + - - -
196B ARG 3.3 0.2 - - - -
197B ASN* 1.3 80.9 + - - +
199B LEU* 1.3 63.1 + - - +
201B LYS* 3.3 12.0 + - - +
202B VAL* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ASN 4.7 5.2 - - - +
145B ILE* 4.8 4.0 - - + +
148B GLY* 3.9 20.4 - - - +
149B ASN* 4.1 19.3 - - - +
195B ALA 3.1 22.0 + - - +
196B ARG 3.2 0.2 + - - -
198B SER* 1.3 76.3 - - - +
200B GLN* 1.3 60.7 + - - +
202B VAL* 3.5 8.6 + - + +
203B ILE* 3.2 28.1 + - - +
211B ALA* 4.3 23.7 - - + +
214B THR* 3.4 37.2 - - + -
215B LEU* 3.7 20.4 - - + -
218B ILE* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ARG* 2.8 48.3 + - - +
197B ASN* 3.9 10.6 - - - +
198B SER 3.3 0.4 - - - -
199B LEU* 1.3 73.2 - - - +
201B LYS* 1.3 60.8 + - + +
203B ILE* 3.5 4.2 + - - +
204B LEU* 3.1 29.8 + - - +
215B LEU* 4.2 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 6.1 1.2 - - - +
138B ALA* 3.2 35.2 + - - +
139B ASP* 4.6 14.8 - - + +
141B LEU* 5.0 1.6 - - - +
144B ASN* 3.9 26.2 + - - +
197B ASN* 3.4 35.3 + - - +
198B SER 3.3 7.9 + - - +
200B GLN* 1.3 77.4 - - + +
202B VAL* 1.3 62.8 + - - +
204B LEU* 3.7 21.9 - - + +
205B ARG* 3.8 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.9 16.9 - - + +
144B ASN* 3.9 8.5 - - + +
145B ILE* 3.8 45.5 - - + +
198B SER 3.2 16.4 - - - +
199B LEU* 3.5 14.1 - - + +
200B GLN 3.2 0.4 - - - -
201B LYS* 1.3 76.9 - - - +
203B ILE* 1.3 53.6 + - - +
205B ARG 3.3 3.1 + - - -
206B PHE* 2.7 54.0 + - + +
208B SER* 4.6 2.5 - - - -
211B ALA* 4.4 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU 3.2 16.7 + - - +
200B GLN* 3.5 4.5 + - - +
202B VAL* 1.3 76.5 - - - +
204B LEU* 1.3 63.9 + - - +
205B ARG 3.4 0.5 + - - -
206B PHE 3.5 11.6 + - - +
207B PRO* 4.4 5.5 - - + +
208B SER 3.3 38.4 - - - +
211B ALA* 3.4 18.4 - - + -
212B GLN* 3.8 30.7 - - + +
215B LEU* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B GLN 3.1 19.0 + - - +
201B LYS* 3.7 15.3 - - + +
202B VAL 3.3 0.4 - - - -
203B ILE* 1.3 77.4 - - - +
205B ARG* 1.3 64.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASP* 3.2 44.6 + - - +
141B LEU* 5.2 9.2 - - + -
201B LYS 3.8 10.1 + - - +
202B VAL 3.3 4.8 + - - +
203B ILE 4.4 0.4 - - - -
204B LEU* 1.3 90.2 - - + +
206B PHE* 1.3 60.9 + - + +
207B PRO* 4.3 4.5 - - - +
301B EDO 5.5 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.8 33.2 - - + -
145B ILE* 4.6 12.3 - - + -
202B VAL* 2.7 40.0 + - + +
203B ILE* 3.5 10.8 + - - -
205B ARG* 1.3 77.2 - - - +
207B PRO* 1.4 78.3 - - + +
208B SER* 3.1 20.1 + - - -
----------------------------------------------------------
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