Contacts of the helix formed by residues 189 - 202 (chain B) in PDB entry 3R9X
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 189 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B VAL* 3.8 6.3 + - - +
188B LYS* 1.3 90.1 - - + +
190B LEU* 1.3 63.3 + - - +
191B LYS* 3.5 22.8 - - - +
192B ASN* 2.9 40.0 + - + +
193B TYR 3.6 7.4 + - - -
240B TYR* 4.1 1.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL 3.8 22.9 - - - +
116B TYR* 3.9 32.3 - - + +
118B LYS* 4.0 18.8 - - + -
119B ASP* 4.9 2.9 - - - +
148B PHE* 3.9 9.7 - - + -
152B PHE* 3.4 33.0 - - + -
187B VAL* 3.6 28.5 - - + +
188B LYS* 6.2 1.8 - - - +
189B ASP* 1.3 70.8 - - - +
191B LYS* 1.3 67.4 + - + +
193B TYR* 3.0 8.1 + - - +
194B LYS* 2.8 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR* 4.0 30.0 - - + +
189B ASP* 3.5 23.1 - - - +
190B LEU* 1.3 82.0 - - - +
192B ASN* 1.3 55.2 + - - +
194B LYS* 3.4 7.9 + - + +
195B LYS* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ASP* 2.9 27.6 + - - +
191B LYS* 1.3 74.1 - - - +
193B TYR* 1.3 66.8 + - - +
195B LYS* 2.9 23.7 + - - +
196B PHE* 2.8 22.9 + - - +
240B TYR* 3.6 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL* 4.2 6.9 - - - +
148B PHE* 3.7 23.6 - + - -
151B THR* 2.7 42.6 + - + -
152B PHE* 4.0 10.3 - + - -
185B PHE* 4.1 9.0 - + - -
187B VAL* 3.8 20.2 - - + -
189B ASP 3.6 1.2 + - - -
190B LEU 3.0 8.7 + - - +
192B ASN* 1.3 78.2 - - - +
194B LYS* 1.3 51.4 + - - +
196B PHE* 3.1 15.7 + + - +
197B LEU* 2.7 54.3 + - + +
236B PHE* 4.4 3.1 - - - +
237B PHE* 3.5 19.2 - - - -
240B TYR* 3.5 47.3 + + + -
----------------------------------------------------------
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
----------------------------------------------------------
112B GLU* 3.3 21.5 - - - -
116B TYR* 3.2 22.2 - - - +
144B TRP* 3.5 35.0 - - + -
148B PHE* 4.0 18.5 - - + -
190B LEU 2.8 12.8 + - - +
191B LYS* 3.5 10.5 - - + +
193B TYR* 1.3 73.0 - - - +
195B LYS* 1.3 59.5 + - - +
197B LEU* 3.6 3.5 - - - +
198B THR* 2.7 58.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
191B LYS 2.9 14.2 + - - +
192B ASN* 3.1 23.8 - - - +
194B LYS* 1.3 77.7 - - - +
196B PHE* 1.3 57.9 + - - +
198B THR* 3.0 12.5 - - + +
199B LYS* 3.0 70.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASN* 2.8 12.8 + - - +
193B TYR* 3.3 13.7 - + - +
195B LYS* 1.3 74.2 - - - +
197B LEU* 1.3 85.8 + - + +
199B LYS* 3.3 4.5 + - - +
200B ILE* 3.0 37.9 + - + +
212B ILE* 4.2 16.6 - - + -
236B PHE* 3.8 9.2 - + - -
239B LEU* 3.7 25.4 - - + -
240B TYR* 3.6 42.8 - + + -
243B ILE* 4.0 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TRP* 3.8 14.6 - - + +
147B VAL* 3.6 22.7 - - + -
148B PHE* 3.4 55.9 - - + +
193B TYR* 2.7 37.8 + - + +
194B LYS* 3.7 4.5 - - - +
196B PHE* 1.3 85.7 - - + +
198B THR* 1.3 63.7 + - - +
200B ILE* 3.2 6.4 - - + +
201B PHE* 3.2 27.5 + - + -
236B PHE* 4.0 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TRP* 3.8 22.7 + - - -
194B LYS* 2.7 42.0 + - - +
195B LYS* 3.0 26.0 - - + +
197B LEU* 1.3 74.0 - - - +
199B LYS* 1.3 69.4 + - + +
201B PHE* 3.5 1.9 + - - +
202B GLN* 3.3 27.2 + - - +
1511C G 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LYS* 3.0 64.3 + - + +
196B PHE* 4.0 3.6 - - - +
197B LEU 3.2 0.2 - - - -
198B THR* 1.3 84.8 - - + +
200B ILE* 1.3 62.5 + - - +
201B PHE 3.5 0.2 + - - -
202B GLN* 3.4 33.8 + - - +
211B LYS* 4.1 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 3.0 37.0 + - + +
197B LEU* 3.2 19.7 - - + +
199B LYS* 1.3 77.6 - - - +
201B PHE* 1.3 69.2 + - + +
208B LEU* 3.8 27.1 - - + -
211B LYS* 2.8 35.8 + - + -
212B ILE* 4.3 18.4 - - + -
228B VAL* 2.8 13.2 - - + +
231B LEU* 4.2 10.1 - - + -
236B PHE* 4.1 26.9 - - + -
239B LEU* 4.9 4.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
142B THR* 4.6 9.4 - - - -
143B GLY* 3.7 25.8 - - - -
144B TRP* 3.3 36.3 - - + +
147B VAL* 3.6 30.3 - - + -
197B LEU* 3.2 21.1 + - + +
198B THR 4.0 3.1 - - - +
199B LYS 3.2 0.2 - - - -
200B ILE* 1.3 82.5 - - + +
202B GLN* 1.3 68.2 + - - +
203B ASN 3.2 2.4 + - - -
204B ARG* 3.4 38.4 + - - +
228B VAL* 3.5 21.3 - - + -
229B GLU* 5.5 1.6 - - + -
236B PHE* 3.8 21.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B THR* 3.3 16.8 + - - +
199B LYS* 3.4 37.0 + - - +
201B PHE* 1.3 74.3 - - - +
203B ASN* 1.3 79.7 + - - +
211B LYS* 2.9 21.4 + - + +
----------------------------------------------------------
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