Contacts of the helix formed by residues 191 - 209 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D PHE* 3.3 20.2 - - + -
189D ARG 3.3 6.7 - - - +
190D ASN* 1.3 83.0 - - - +
192D GLN* 1.3 64.3 + - - +
193D GLU* 3.3 3.5 + - - +
194D HIS* 3.1 42.2 + - - +
195D LEU* 3.1 17.2 + - - +
253D VAL* 3.5 29.3 - - + +
254D ASP* 3.7 4.9 + - - -
347D HIS* 3.4 21.8 + - - +
350D ASP* 2.9 38.4 + - - -
409D UDP 3.2 51.7 + - - +
410D MN 3.8 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 4.5 10.7 - - - +
188D PHE* 3.6 20.7 - - + -
190D ASN* 3.6 2.1 - - - -
191D ARG* 1.3 74.9 - - - +
193D GLU* 1.3 70.3 + - + +
195D LEU* 3.3 17.6 + - - +
196D LYS* 3.1 37.9 + - + +
391D TYR* 3.8 19.9 + - - -
393D LYS* 4.2 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D PRO* 5.5 7.6 - - - +
153D VAL 5.7 0.2 + - - -
191D ARG 3.3 0.6 - - - -
192D GLN* 1.3 79.9 - - + +
194D HIS* 1.3 73.9 + - + +
196D LYS* 2.6 50.0 + - - +
197D TYR* 3.2 26.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D ARG* 3.1 50.9 + - - +
192D GLN 3.4 0.2 - - - -
193D GLU* 1.3 84.4 - - + +
195D LEU* 1.3 51.4 + - - +
197D TYR* 3.0 6.6 + + - +
198D TRP* 2.7 34.5 + - - +
253D VAL* 3.7 19.3 - - + +
254D ASP* 3.7 8.7 - - + +
345D ILE* 3.5 42.4 - - + +
346D ARG 4.1 5.1 + - - -
347D HIS* 3.9 27.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D ILE* 4.5 13.9 - - + -
188D PHE* 4.2 16.4 - - + -
191D ARG 3.1 12.9 + - - +
192D GLN* 3.4 33.7 - - - +
193D GLU 3.1 0.4 - - - -
194D HIS* 1.3 77.1 - - - +
196D LYS* 1.3 56.4 + - - +
198D TRP* 3.2 7.5 + - + -
199D LEU* 2.8 49.3 + - + +
217D VAL* 3.9 33.2 - - + -
253D VAL* 4.7 7.4 - - + +
391D TYR* 4.0 18.8 - - + +
393D LYS* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D PRO* 6.3 0.6 - - - +
153D VAL* 3.2 38.5 + - + +
155D LEU* 3.3 40.5 - - + +
192D GLN* 3.1 30.3 + - + +
193D GLU* 2.6 48.2 + - - +
195D LEU* 1.3 76.2 - - - +
197D TYR* 1.3 58.2 + - + +
199D LEU* 3.8 1.4 - - - +
200D TYR* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D GLU 4.3 4.9 - - - -
149D PHE* 2.8 56.2 + + + -
150D ASN 4.1 0.9 - - - -
151D ILE 3.5 32.3 + - - -
152D PRO* 3.7 10.5 - - + +
153D VAL* 3.5 18.6 - - + -
193D GLU* 3.2 28.4 + - + -
194D HIS* 3.0 7.9 + + - +
196D LYS* 1.3 79.3 - - + +
198D TRP* 1.3 62.1 + - - +
200D TYR* 3.3 2.1 + + - +
201D TYR* 3.1 36.9 + + + -
256D ILE* 4.5 0.4 - - - -
345D ILE* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ILE* 3.9 25.1 - - + -
186D ILE* 3.8 22.2 - - + +
194D HIS 2.7 19.2 + - - +
195D LEU* 3.5 9.9 - - + +
197D TYR* 1.3 73.3 - - - +
199D LEU* 1.3 72.8 + - + +
202D LEU* 2.8 74.6 + - + +
203D HIS* 5.4 1.3 - + - -
206D LEU* 4.9 0.2 - - + -
215D ILE* 3.4 44.9 - - + -
251D SER* 3.4 21.3 + - - -
252D ASP 3.9 5.3 + - - -
253D VAL* 3.4 23.8 - - - +
255D LEU 3.7 17.2 + - - -
256D ILE* 3.6 10.0 - - + +
264D TYR* 5.0 3.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 4.0 24.0 - - + -
158D VAL* 4.3 2.4 - - - +
195D LEU* 2.8 38.6 + - + +
196D LYS 3.8 3.1 - - - +
198D TRP* 1.3 93.7 - - + +
200D TYR* 1.3 67.3 + - - +
203D HIS* 3.2 44.5 + - + +
215D ILE* 4.4 1.6 - - + -
390D LEU* 3.5 31.4 - - + +
391D TYR* 3.5 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D VAL* 4.2 20.6 - - + -
158D VAL* 3.7 32.5 - - + +
161D GLN* 3.6 28.6 + - - -
162D ASN* 5.1 0.5 - - - +
196D LYS 2.9 18.3 + - - +
197D TYR* 3.3 4.0 + + - +
199D LEU* 1.3 76.1 - - - +
201D TYR* 1.3 98.2 + + - +
204D PRO* 3.2 23.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D LEU 4.0 7.8 + - - -
147D ILE* 3.8 31.2 - - + -
148D GLU* 2.5 48.2 + - - +
149D PHE* 4.1 9.0 - + - -
197D TYR* 3.1 29.3 + + - +
198D TRP 4.2 0.9 - - - +
200D TYR* 1.3 108.5 - + - +
202D LEU* 1.3 61.1 + - - +
204D PRO* 3.1 21.7 - - - +
205D ILE* 3.4 19.1 - - + +
256D ILE* 3.6 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D TRP* 2.8 82.2 + - + +
201D TYR* 1.3 73.3 - - - +
203D HIS* 1.3 59.9 + - - +
205D ILE* 3.1 8.8 + - + -
206D LEU* 2.8 47.6 + - + +
256D ILE* 3.8 17.7 - - + -
257D PRO* 3.9 34.8 - - + -
264D TYR* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D VAL* 5.1 0.7 - - + -
162D ASN* 3.8 16.2 - - - +
165D VAL* 3.2 33.8 - - + +
169D GLY* 4.5 1.1 - - - -
198D TRP* 5.4 1.1 - + - -
199D LEU* 3.2 40.8 + - + +
202D LEU* 1.3 75.7 - - - +
204D PRO* 1.3 71.2 - - + +
206D LEU* 4.5 2.4 - - + +
207D GLN* 2.9 29.0 + - - +
213D TYR* 3.0 38.1 + + - -
215D ILE* 3.9 9.9 - - + +
390D LEU* 2.8 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D GLN* 6.3 0.9 - - - +
162D ASN* 3.7 19.7 - - - +
200D TYR 3.2 22.7 - - - +
201D TYR* 3.1 15.9 - - - +
203D HIS* 1.3 94.3 - - + +
205D ILE* 1.3 60.3 + - - +
207D GLN* 3.3 5.6 + - + +
208D ARG* 3.0 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D MET* 3.5 39.0 - - + -
147D ILE* 5.6 1.6 - - + -
201D TYR* 3.4 26.7 - - + +
202D LEU* 3.1 16.9 + - + +
204D PRO* 1.3 78.5 - - - +
206D LEU* 1.3 60.5 + - + +
208D ARG* 3.0 20.2 + - - +
209D GLN* 2.9 51.0 + - - +
256D ILE* 5.1 0.7 - - + -
257D PRO* 4.0 24.0 - - + +
260D ASP* 4.0 11.6 - - + +
264D TYR* 5.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ILE* 3.3 36.3 - - + -
198D TRP* 4.3 0.9 - - + -
202D LEU* 2.8 42.0 + - + +
203D HIS* 4.0 0.9 - - - +
205D ILE* 1.3 74.4 - - + +
207D GLN* 1.3 60.4 + - - +
209D GLN* 3.5 11.6 + - - +
210D GLN 3.5 0.2 + - - -
211D LEU* 3.5 43.4 + - + +
213D TYR* 3.5 27.6 - - + -
215D ILE* 3.8 17.3 - - + -
264D TYR* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D LEU* 4.3 5.4 - - - +
162D ASN* 2.8 36.2 + - - +
164D LYS* 4.0 18.0 - - - +
165D VAL* 3.7 8.4 - - - +
171D TYR* 3.5 57.2 + - + +
203D HIS 2.9 17.5 + - - +
204D PRO* 3.7 5.4 - - + +
205D ILE 3.1 0.8 - - - -
206D LEU* 1.3 74.7 - - - +
208D ARG* 1.3 65.9 + - + +
209D GLN 3.0 1.6 - - - -
210D GLN* 2.9 18.5 + - - +
213D TYR* 3.6 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D SER* 2.5 30.8 + - - -
140D LEU* 3.7 35.7 - - + +
141D LEU* 3.5 9.5 - - + +
142D VAL* 3.5 17.9 - - - +
145D MET* 3.4 26.9 - - - -
204D PRO* 3.0 41.4 + - - +
205D ILE* 3.0 18.5 + - - +
207D GLN* 1.3 77.3 - - + +
209D GLN* 1.3 55.9 + - - +
210D GLN* 3.1 5.4 + - - +
260D ASP* 3.3 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D SER* 4.4 5.1 - - - -
141D LEU* 4.3 8.7 - - + -
180D HIS* 5.4 1.9 - - - -
205D ILE* 2.9 36.3 + - + +
206D LEU* 3.7 7.7 - - - +
207D GLN 3.0 0.4 - - - -
208D ARG* 1.3 75.6 - - - +
210D GLN* 1.3 69.6 + - - +
211D LEU* 3.2 25.5 + - + +
257D PRO* 6.2 0.4 - - - +
260D ASP* 3.1 30.2 + - + +
262D ASN 3.3 20.6 + - - -
263D THR* 3.4 18.8 - - + +
264D TYR* 2.8 26.8 + - - +
----------------------------------------------------------
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