Contacts of the helix formed by residues 191 - 209 (chain B) in PDB entry 1PZY
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
----------------------------------------------------------
188B PHE* 3.4 21.7 - - + -
189B ARG 3.7 0.7 - - - +
190B ASN* 1.3 83.8 - - - +
192B GLN* 1.3 64.8 + - - +
193B GLU 3.3 2.9 - - - -
194B HIS* 3.0 41.7 + - + +
195B LEU 3.0 18.0 + - - -
253B VAL* 3.3 28.0 - - + +
254B ASP* 3.4 11.9 + - - -
347B HIS* 3.1 25.2 + - - +
350B ASP* 2.8 37.3 + - - -
407B UDP 3.2 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 4.6 9.7 - - - +
188B PHE* 3.8 17.2 - - + -
190B ASN* 3.7 2.5 + - - -
191B ARG* 1.3 77.0 - - - +
193B GLU* 1.3 66.0 + - + +
195B LEU* 3.2 17.3 + - - +
196B LYS* 3.0 41.1 + - + +
199B LEU* 5.8 0.2 - - - +
391B TYR* 3.7 20.8 + - - -
393B LYS* 4.8 8.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
152B PRO* 6.0 1.2 - - - +
153B VAL* 5.1 2.4 + - - +
191B ARG 3.3 1.0 - - - -
192B GLN* 1.3 80.2 - - + +
194B HIS* 1.3 70.3 + - + +
196B LYS* 3.1 45.9 + - - +
197B TYR* 3.3 29.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ARG* 3.0 48.6 + - - +
193B GLU* 1.3 79.9 - - + +
195B LEU* 1.3 67.1 + - - +
197B TYR* 3.0 7.1 + + - +
198B TRP* 2.9 21.5 + - - +
253B VAL* 3.8 23.5 - - + +
254B ASP* 3.8 4.8 - - + +
345B ILE* 3.4 41.1 - - + +
346B ARG 4.5 1.0 + - - -
347B HIS* 3.6 35.4 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 4.7 2.2 - - + -
188B PHE* 4.3 11.0 - - + -
191B ARG 3.0 13.8 + - - +
192B GLN* 3.2 24.9 + - - +
194B HIS* 1.3 75.7 - - - +
196B LYS* 1.3 58.0 + - - +
198B TRP* 3.1 12.0 + - + -
199B LEU* 2.8 54.1 + - + +
217B VAL* 3.8 25.6 - - + -
253B VAL* 3.6 17.4 - - + +
391B TYR* 3.7 36.3 - - + +
393B LYS* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PRO* 6.0 1.8 - - - +
153B VAL* 3.1 55.6 + - + +
154B ASP* 5.4 0.2 - - - +
155B LEU* 4.1 29.7 - - + +
192B GLN* 3.0 35.6 + - + +
193B GLU* 3.1 39.6 + - - +
195B LEU* 1.3 77.4 - - - +
197B TYR* 1.3 56.0 + - - +
199B LEU* 3.4 2.6 + - - +
200B TYR* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLU 4.2 4.9 - - - -
149B PHE* 3.1 59.7 + + + -
150B ASN 3.7 3.7 + - - -
151B ILE 3.1 30.0 + - - -
152B PRO* 4.3 4.4 - - + +
153B VAL* 3.9 17.0 - - + -
193B GLU* 3.3 31.3 + - + -
194B HIS* 3.0 7.4 + + - +
196B LYS* 1.3 75.6 - - - +
198B TRP* 1.3 67.1 + - - +
200B TYR* 3.2 5.5 + + - +
201B TYR* 3.0 34.1 + + - -
256B ILE* 4.3 1.8 - - - -
345B ILE* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ILE* 3.7 26.9 - - + -
186B ILE* 3.8 26.4 - - + +
194B HIS 2.9 12.7 + - - +
195B LEU* 3.4 13.5 - - + +
197B TYR* 1.3 76.6 - - - +
199B LEU* 1.3 70.7 + - + +
202B LEU* 2.7 70.0 + - + +
203B HIS* 5.6 1.1 - + - -
206B LEU* 5.0 0.2 - - + -
215B ILE* 3.5 40.2 - - + -
251B SER* 3.7 19.9 + - - -
252B ASP 4.0 1.0 + - - -
253B VAL* 3.5 26.7 - - + +
255B LEU 3.6 19.8 + - - -
256B ILE* 3.4 15.2 - - + +
264B TYR* 4.9 3.9 - + - -
345B ILE* 5.2 0.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
155B LEU* 3.9 25.6 - - + -
158B VAL* 4.1 3.7 - - - +
195B LEU* 2.8 40.4 + - + +
196B LYS* 3.7 3.4 - - + +
198B TRP* 1.3 91.4 - - + +
200B TYR* 1.3 67.1 + - - +
203B HIS* 3.3 42.6 + - + +
215B ILE* 4.4 0.9 - - + -
390B LEU* 3.7 28.7 - - + +
391B TYR* 3.5 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 4.0 25.8 - - + -
158B VAL* 4.0 27.8 - - + +
161B GLN* 4.2 17.5 - - - -
162B ASN* 5.4 0.2 + - - -
196B LYS 2.9 16.0 + - - +
197B TYR* 3.3 9.2 - + - +
199B LEU* 1.3 79.7 - - - +
201B TYR* 1.3 101.0 + + - +
204B PRO* 3.3 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B MET* 6.3 0.7 - - - -
146B LEU 3.8 9.8 + - - -
147B ILE* 3.5 32.0 - - + -
148B GLU* 2.7 44.7 + - - +
149B PHE* 4.1 12.3 - + - -
197B TYR* 3.0 27.9 + + - +
200B TYR* 1.3 106.7 - + - +
202B LEU* 1.3 65.6 + - - +
204B PRO* 3.5 9.2 - - - +
205B ILE* 3.2 25.2 - - + +
256B ILE* 3.5 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B TRP* 2.7 59.7 + - + +
201B TYR* 1.3 74.1 - - - +
203B HIS* 1.3 54.9 + - - +
205B ILE* 3.0 11.0 + - + +
206B LEU* 2.7 51.9 + - + +
256B ILE* 3.5 30.5 - - + -
257B PRO* 3.6 25.6 - - + -
264B TYR* 3.8 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 4.8 0.4 - - + -
162B ASN* 4.2 13.2 - - - +
165B VAL* 3.8 24.4 - - + +
169B GLY* 4.4 1.1 - - - -
198B TRP* 5.8 0.9 - + - -
199B LEU* 3.3 35.7 + - + +
202B LEU* 1.3 78.4 - - - +
204B PRO* 1.3 73.6 - - + +
206B LEU* 3.3 2.4 + - + +
207B GLN* 3.2 27.0 + - - +
213B TYR* 3.1 28.4 + + - -
215B ILE* 3.9 18.2 - - + -
390B LEU* 2.8 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ASN* 3.9 20.8 - - - +
199B LEU 4.2 0.2 - - - +
200B TYR 3.3 23.6 - - - +
201B TYR* 3.5 10.1 - - - +
203B HIS* 1.3 96.1 - - + +
205B ILE* 1.3 59.4 + - - +
207B GLN* 3.4 6.2 + - + +
208B ARG* 3.1 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B MET* 3.3 40.6 - - + -
147B ILE* 5.4 1.6 - - + -
201B TYR* 3.2 28.3 - - + +
202B LEU* 3.0 17.6 + - + +
204B PRO* 1.3 75.3 - - - +
206B LEU* 1.3 66.1 + - - +
208B ARG* 3.0 17.6 + - - +
209B GLN* 2.9 46.8 + - + +
256B ILE* 5.2 0.2 - - + -
257B PRO* 4.2 22.7 - - + +
260B ASP* 4.1 14.1 - - + -
264B TYR* 5.8 1.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
184B ILE* 3.4 36.6 - - + -
198B TRP* 4.5 0.7 - - + -
202B LEU* 2.7 41.6 + - + +
203B HIS* 4.6 1.8 - - - +
205B ILE* 1.3 73.4 - - + +
207B GLN* 1.3 61.2 + - - +
209B GLN* 3.3 15.4 + - - +
211B LEU* 3.5 29.6 + - + +
213B TYR* 3.3 38.5 - - + +
215B ILE* 3.8 8.5 - - + -
264B TYR* 3.8 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 4.5 4.8 - - - +
162B ASN* 3.0 27.4 + - - +
164B LYS* 3.5 21.0 - - - +
165B VAL* 3.6 15.4 - - - +
171B TYR* 3.3 52.3 + - + +
203B HIS 3.2 11.5 + - - +
204B PRO* 3.7 8.1 - - + +
205B ILE 3.1 0.8 - - - -
206B LEU* 1.3 71.8 - - - +
208B ARG* 1.3 60.1 + - - +
209B GLN 3.0 1.8 - - - -
210B GLN* 2.8 24.3 + - - +
213B TYR* 3.5 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B SER* 2.5 31.5 + - - -
140B LEU* 3.7 38.6 - - + +
141B LEU* 3.2 10.2 - - + +
142B VAL* 3.4 17.4 - - - +
145B MET* 3.4 25.1 - - - +
204B PRO* 3.1 30.6 + - - +
205B ILE* 3.0 29.6 + - - +
207B GLN* 1.3 75.6 - - - +
209B GLN* 1.3 53.6 + - + +
210B GLN* 3.3 1.7 + - - +
260B ASP* 2.8 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B SER* 4.3 10.0 - - - -
141B LEU* 4.3 4.0 - - + -
180B HIS* 5.1 2.1 - - - -
205B ILE* 2.9 28.6 + - + +
206B LEU* 3.6 12.1 - - - +
207B GLN 3.0 0.6 - - - -
208B ARG* 1.3 75.3 - - + +
210B GLN* 1.3 72.1 + - - +
211B LEU* 3.3 22.7 - - + +
260B ASP* 2.9 30.7 + - + +
262B ASN 3.2 8.5 + - - -
263B THR* 3.1 31.2 - - + +
264B TYR* 2.8 33.8 + - - +
----------------------------------------------------------
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