Contacts of the helix formed by residues 195 - 209 (chain B) in PDB entry 3ZXR
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 TYR 195 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ILE* 3.8 53.1 + - + -
140B ASP* 5.0 1.0 + - - -
157B ALA* 4.0 4.7 - - - +
158B ILE* 3.9 11.4 + - + +
159B SER* 2.7 45.8 + - - -
193B ASP* 3.1 2.6 + - - -
194B GLN* 1.3 90.0 - - + +
196B VAL* 1.3 60.1 + - - +
197B ASP 3.4 2.0 - - - -
198B LEU* 3.3 15.7 + - + +
199B ARG* 2.9 45.6 + - + +
218B HIS* 3.9 17.3 - + - -
223B GLY 4.0 1.7 - - - -
224B GLY* 3.3 22.9 + - - -
258B LYS* 4.4 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A HIS* 4.0 13.2 - - + -
84A ARG* 3.4 50.4 + - + +
190B ALA* 4.3 12.8 - - + -
193B ASP* 3.4 38.3 + - + +
194B GLN 3.7 2.0 - - - -
195B TYR* 1.3 77.3 - - - +
197B ASP* 1.3 60.0 + - - +
199B ARG* 3.9 10.3 - - - +
200B ASP* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE 4.7 4.9 - - - +
84A ARG* 3.8 15.3 - - - +
85A ALA* 3.7 31.7 + - - +
86A ALA 5.2 0.3 + - - -
255A GLN* 5.1 5.4 + - - -
195B TYR 3.4 0.4 - - - -
196B VAL* 1.3 79.6 - - - +
198B LEU* 1.3 62.1 + - - +
200B ASP* 3.2 11.0 + - - +
201B LYS* 3.1 33.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
138B ILE* 3.7 22.9 - - + -
195B TYR* 3.3 19.2 + - + +
197B ASP* 1.3 77.9 - - - +
199B ARG* 1.3 62.7 + - - +
201B LYS* 3.0 13.3 + - + +
202B MET* 3.0 34.1 + - + +
252B THR* 4.1 13.9 - - + +
253B ALA* 4.4 1.3 - - - -
256B ASN* 3.8 36.3 - - + +
258B LYS* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A HIS* 4.2 11.7 - - - -
36A THR* 5.4 3.4 + - - -
138B ILE* 4.3 17.3 - - + -
193B ASP* 2.7 42.0 + - - -
195B TYR* 2.9 27.5 + - - +
196B VAL* 3.9 11.0 - - - +
198B LEU* 1.3 74.6 - - - +
200B ASP* 1.3 59.6 + - - +
202B MET* 3.2 15.6 + - - +
203B LEU* 2.8 36.9 + - + +
216B GLY* 4.4 4.1 + - - -
217B HIS* 3.5 32.1 - - - +
218B HIS* 3.4 25.3 - - - +
226B ALA* 3.8 16.4 - - + +
227B GLU 4.9 2.5 - - - +
228B ILE* 4.2 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.4 14.9 + - + -
84A ARG* 2.7 50.4 + - - +
86A ALA* 3.9 22.6 + - + +
88A THR* 4.3 0.3 + - - -
196B VAL 3.0 16.5 + - - +
197B ASP* 3.4 15.8 - - - +
198B LEU 3.2 0.2 - - - -
199B ARG* 1.3 78.0 - - - +
201B LYS* 1.3 56.7 + - + +
203B LEU* 3.3 15.9 + - - +
204B THR* 2.9 33.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
85A ALA* 6.4 2.9 - - - -
197B ASP* 3.1 23.4 + - - +
198B LEU* 3.0 13.5 + - - +
200B ASP* 1.3 72.7 - - + +
202B MET* 1.3 60.6 + - - +
204B THR* 3.4 6.5 + - - -
205B ASN* 3.0 36.6 + - - +
252B THR* 4.0 12.8 - - + -
256B ASN* 3.2 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 3.9 24.9 - - + -
138B ILE* 3.9 22.7 - - + -
198B LEU* 3.0 28.5 + - + +
199B ARG* 3.3 16.4 - - - +
201B LYS* 1.3 74.4 - - - +
203B LEU* 1.3 63.7 + - - +
205B ASN* 3.5 2.3 + - - +
206B LEU* 3.1 31.7 + - - +
228B ILE* 3.7 11.2 - - + -
248B ILE* 4.3 1.3 - - - +
249B ILE* 3.8 37.2 - - + +
252B THR* 3.7 20.9 - - + -
253B ALA* 4.0 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.3 35.4 - - + +
36A THR* 4.2 15.5 - - + +
38A PRO* 5.8 2.7 - - + -
199B ARG* 2.8 25.0 + - + +
200B ASP* 3.3 18.8 + - - +
202B MET* 1.3 71.2 - - - +
204B THR* 1.3 57.7 + - - +
206B LEU* 3.4 6.9 + - - +
207B ILE* 2.9 33.9 + - + +
213B LEU* 3.8 18.2 - - + +
215B LYS* 4.3 9.0 - - - +
216B GLY* 4.4 9.6 - - - +
228B ILE* 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 4.2 13.8 + - - +
20A TYR* 2.7 24.7 + - - -
86A ALA* 5.1 2.6 - - - +
200B ASP 2.9 14.1 + - - -
201B LYS* 3.8 7.5 - - - -
202B MET 3.3 0.2 - - - -
203B LEU* 1.3 75.9 - - - +
205B ASN* 1.3 60.5 + - - +
207B ILE* 3.2 8.6 + - + +
208B ASN* 2.8 49.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO* 4.4 22.4 - - + +
83B PHE* 3.8 10.7 - - - -
201B LYS* 3.0 22.2 + - - +
202B MET 3.9 1.3 - - - +
203B LEU 3.4 0.2 - - - -
204B THR* 1.3 79.4 - - - +
206B LEU* 1.3 59.6 + - - +
208B ASN* 3.5 9.5 + - - +
209B SER* 3.0 28.2 + - - -
248B ILE* 3.8 19.4 - - + +
252B THR* 2.7 29.7 + - - +
255B GLN* 5.8 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B MET 3.1 24.4 + - - +
203B LEU* 3.6 4.3 - - - +
204B THR 3.2 0.2 - - - -
205B ASN* 1.3 74.7 - - - +
207B ILE* 1.3 65.7 + - - +
209B SER 3.0 10.4 + - - -
211B PHE* 3.1 52.5 + - + -
213B LEU* 3.9 16.4 - - + -
228B ILE* 3.7 29.8 - - + -
230B TYR* 5.7 0.7 - - + -
245B TYR* 3.8 28.0 - - + +
248B ILE* 3.8 24.2 - - + -
249B ILE* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU 5.5 1.1 - - - +
20A TYR* 3.7 30.5 - - + +
38A PRO* 4.4 14.4 - - + -
40A SER* 5.7 1.1 - - - +
203B LEU 2.9 18.9 + - - +
204B THR* 3.5 8.3 - - + +
206B LEU* 1.3 73.4 - - - +
208B ASN* 1.3 66.9 + - - +
210B GLY* 2.9 21.5 + - - -
211B PHE 3.9 12.1 + - - +
213B LEU* 3.5 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 5.4 4.2 - - - +
82B PRO* 6.0 4.3 - - + -
204B THR* 2.8 42.5 + - - +
205B ASN* 4.0 9.4 + - - +
206B LEU 3.2 0.2 - - - -
207B ILE* 1.3 79.4 - - - +
209B SER* 1.3 57.2 + - - +
210B GLY 3.4 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 3.2 31.9 + - - +
80B ILE 4.3 9.1 + - - +
82B PRO* 3.9 15.6 - - - +
205B ASN 3.0 13.1 + - - -
206B LEU 3.0 8.8 + - - -
208B ASN* 1.3 76.2 - - - +
210B GLY* 1.3 59.5 + - - +
211B PHE* 3.3 12.4 + - - -
244B LEU* 4.6 8.0 - - - +
248B ILE* 3.4 23.7 - - - +
----------------------------------------------------------
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