Contacts of the helix formed by residues 200 - 219 (chain D) in PDB entry 1OY1
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 ASN 200 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C SER* 3.9 10.3 - - - +
195D TYR* 3.6 10.6 + - - -
198D ALA* 3.6 2.3 - - - +
199D GLN* 1.3 80.4 - - - +
201D ILE* 1.3 64.1 + - - +
202D ALA* 2.8 15.6 + - - +
203D GLU* 2.7 54.8 + - - +
204D ALA* 3.3 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C VAL* 3.7 39.7 - - + +
29C LEU* 3.6 18.6 - - + +
30C LEU* 3.8 13.2 - - + +
33C SER* 3.4 22.2 - - - -
23D HIS* 3.7 29.2 - - + +
27D LEU* 3.6 17.7 - - + -
195D TYR* 3.1 15.4 + - - +
200D ASN* 1.3 74.8 - - - +
202D ALA* 1.3 60.7 + - - +
204D ALA* 3.3 0.5 + - - +
205D ALA* 2.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 4.2 11.0 - - - -
33C SER* 2.9 34.9 + - - +
34C ARG* 4.2 11.3 - - + +
200D ASN* 2.8 6.4 + - - +
201D ILE* 1.3 81.6 - - - +
203D GLU* 1.3 63.4 + - - +
205D ALA* 3.3 4.0 + - - +
206D SER* 3.0 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D VAL* 3.8 28.9 - - + +
179D ASP* 6.5 0.9 - - + -
197D LEU 3.9 2.3 - - - +
198D ALA* 3.6 4.5 - - - -
199D GLN* 2.9 43.1 + - - +
200D ASN* 2.7 37.4 + - - +
202D ALA* 1.3 74.2 - - - +
204D ALA* 1.3 64.4 + - - +
206D SER* 2.9 25.3 - - - -
207D GLY 3.4 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 4.2 8.7 - - + -
178D VAL* 4.6 2.9 - - - -
194D ALA* 5.0 7.8 - - + +
195D TYR* 3.7 32.3 - - + +
198D ALA* 3.9 15.8 - - + +
200D ASN 3.3 3.8 + - - +
201D ILE 3.6 7.2 - - - +
202D ALA 3.3 0.2 - - - -
203D GLU* 1.3 81.3 - - - +
205D ALA* 1.3 63.4 + - - +
206D SER 3.2 0.3 + - - -
207D GLY* 3.3 1.2 + - - -
208D ILE* 3.0 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.6 23.8 - - + -
34C ARG* 5.7 3.6 - - - +
27D LEU* 3.8 20.5 - - + +
34D ARG* 6.0 0.7 - - - +
201D ILE 2.8 16.9 + - - +
202D ALA 3.5 5.8 - - - +
203D GLU 3.2 0.2 - - - -
204D ALA* 1.3 75.1 - - - +
206D SER* 1.3 64.8 + - - +
208D ILE* 3.2 3.7 + - - -
209D ASP* 2.8 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D ASP* 3.1 30.4 + - - +
202D ALA 3.0 12.8 + - - -
203D GLU* 2.9 19.3 - - - -
205D ALA* 1.3 77.1 - - - +
207D GLY* 1.3 58.7 + - - +
209D ASP* 3.7 7.0 + - - +
210D LYS* 3.5 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D VAL 3.5 19.4 + - - -
179D ASP 4.3 9.0 - - - -
180D ASP 4.9 0.4 - - - -
181D ILE* 3.8 2.8 - - - +
192D THR* 3.8 15.3 - - - -
193D PRO 5.4 0.2 - - - -
203D GLU 3.4 3.0 + - - -
204D ALA 3.3 4.7 + - - -
205D ALA 3.3 0.4 - - - -
206D SER* 1.3 75.2 + - - +
208D ILE* 1.3 66.8 + - - +
209D ASP 3.1 1.8 - - - -
210D LYS* 3.0 6.5 + - - +
211D LEU* 2.9 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLU* 3.7 43.7 - - + +
27D LEU* 4.0 19.1 - - + +
28D THR* 3.7 33.0 - - - +
137D MSE 3.8 19.3 - - + -
192D THR* 4.5 4.0 - - + +
194D ALA* 4.8 7.4 - - + -
204D ALA* 3.0 20.4 + - + +
205D ALA* 3.8 4.7 - - - +
207D GLY* 1.3 74.1 - - - +
209D ASP* 1.3 64.6 + - - +
211D LEU* 3.2 7.4 + - - +
212D VAL* 2.9 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ARG* 5.3 1.7 + - - -
27D LEU* 4.6 6.6 - - - +
31D ALA* 3.8 19.3 - - + +
34D ARG* 3.4 28.0 + - - -
205D ALA* 2.8 32.6 + - - +
206D SER* 3.8 6.6 + - - +
208D ILE* 1.3 78.0 - - - +
210D LYS* 1.3 64.3 + - + +
212D VAL* 3.3 2.1 + - - +
213D SER* 2.9 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D ASP* 2.7 34.7 + - - +
180D ASP* 3.8 23.7 + - - +
181D ILE* 3.6 17.7 - - + +
206D SER* 3.5 12.9 + - - +
207D GLY 3.0 8.3 + - - +
209D ASP* 1.3 79.6 - - + +
211D LEU* 1.3 63.3 + - - +
213D SER* 3.4 5.8 + - - -
214D ARG* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ILE* 3.8 36.1 - - + -
135D GLY* 4.2 3.1 - - - -
136D PHE 3.7 17.9 - - - +
137D MSE 4.4 12.6 - - + -
181D ILE* 3.6 6.4 - - - +
190D VAL* 3.9 15.9 - - + +
191D THR* 3.9 6.7 - - - -
192D THR* 3.5 36.3 - - - +
207D GLY 2.9 12.1 + - - +
208D ILE* 3.4 9.6 - - - +
210D LYS* 1.3 76.7 - - - +
212D VAL* 1.3 64.5 + - + +
214D ARG* 3.2 3.6 + - - +
215D VAL* 2.9 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D THR* 4.2 20.2 - - + +
31D ALA* 3.7 33.2 - - + +
32D ILE* 3.9 20.2 - - + +
35D SER* 4.6 1.8 - - - +
93D ILE* 5.0 4.0 - - + -
208D ILE* 2.9 29.6 + - + +
209D ASP 3.8 1.3 - - - +
211D LEU* 1.3 85.0 - - + +
213D SER* 1.3 58.8 + - - +
215D VAL* 3.2 5.0 + - + +
216D LEU* 2.9 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D SER* 4.5 9.5 + - - -
209D ASP* 2.9 18.4 + - - +
210D LYS* 3.7 7.0 - - - -
212D VAL* 1.3 78.5 - - - +
214D ARG* 1.3 58.7 + - - +
216D LEU* 3.4 8.3 + - - +
217D VAL* 2.9 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D ILE* 4.5 14.4 - - + +
183D VAL* 3.9 21.1 - - + +
185D GLU* 3.3 26.9 + - - -
190D VAL* 3.7 26.2 - - + -
210D LYS 3.0 17.7 + - - +
211D LEU 3.7 3.1 - - - +
213D SER* 1.3 74.6 - - - +
215D VAL* 1.3 66.9 + - - +
217D VAL* 4.3 11.8 - - - +
218D LEU* 2.9 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ILE* 5.1 2.2 - - + -
91D ALA* 3.6 28.3 - - + -
93D ILE* 3.6 32.1 - - + -
133D PRO* 3.6 19.1 - - + +
134D LEU 4.3 2.9 - - - +
135D GLY* 4.1 7.4 - - - -
190D VAL* 4.1 18.6 - - + -
211D LEU* 2.9 27.8 + - + +
212D VAL* 3.7 4.0 - - + +
214D ARG* 1.3 75.8 - - - +
216D LEU* 1.3 61.2 + - + +
218D LEU* 3.4 0.8 + - - -
219D ALA* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LYS* 5.2 9.1 + - + +
7D ILE* 3.4 38.8 - - + -
32D ILE* 4.9 1.3 - - + +
35D SER* 3.2 39.5 - - - +
37D ALA* 3.9 16.2 - - + -
212D VAL* 2.9 33.8 + - + +
213D SER* 3.6 5.4 - - - +
215D VAL* 1.3 75.9 - - + +
217D VAL* 1.3 66.3 + - + +
219D ALA* 3.1 21.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D SER* 2.9 25.5 + - - +
214D ARG* 3.7 16.8 - - - +
216D LEU* 1.3 76.0 - - + +
218D LEU* 1.3 69.3 + - + +
219D ALA 3.1 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D GLY 5.2 0.7 - - - +
133D PRO* 3.4 21.6 - - + +
183D VAL* 4.4 8.3 - - + -
185D GLU* 4.9 11.9 - - - +
188D LYS* 3.9 56.0 + - + +
190D VAL* 4.0 22.2 - - + -
214D ARG* 2.9 36.3 + - + +
215D VAL 3.7 0.2 - - - +
217D VAL* 1.3 81.7 - - + +
219D ALA* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LYS* 3.2 34.4 + - + -
7D ILE* 5.2 0.2 - - + -
90D ASP* 3.8 29.8 - - + +
91D ALA* 4.2 7.4 - - + -
133D PRO* 3.6 11.0 - - + -
215D VAL 2.8 19.1 + - - +
216D LEU* 3.5 20.9 - - + +
217D VAL 3.1 5.0 - - - -
218D LEU* 1.3 81.3 - - - +
----------------------------------------------------------
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