Contacts of the helix formed by residues 209 - 223 (chain D) in PDB entry 2R2N
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 THR 209 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D SER* 4.1 23.3 + - - +
208D LEU* 1.3 75.5 - - - +
210D SER* 1.3 57.5 + - - +
211D GLU* 3.6 25.3 + - - +
212D ARG* 3.3 27.4 + - - +
213D LYS* 3.0 31.7 + - - +
243D VAL* 4.0 3.1 - - - -
430D GOL 3.5 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D THR* 1.3 69.1 - - - +
211D GLU* 1.3 75.9 + - - +
213D LYS* 3.3 7.7 + - - +
214D LYS* 3.1 43.3 + - - +
243D VAL* 3.6 15.3 - - - +
244D PRO* 4.0 29.4 - - - +
249D MET* 4.8 1.5 - - - +
430D GOL 4.9 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D THR* 3.6 27.3 + - - +
210D SER* 1.3 87.7 + - - +
212D ARG* 1.3 62.6 + - + +
214D LYS* 3.3 21.2 + - + +
215D GLU* 3.3 24.4 + - + +
430D GOL 5.2 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ASP* 2.6 43.8 + - - -
164D SER* 3.3 27.6 + - - -
165D GLY 3.1 17.4 + - - -
166D ILE 3.2 15.9 + - - -
167D VAL* 3.9 12.9 - - - +
168D PRO* 3.5 24.9 - - + +
208D LEU* 3.7 13.0 - - + -
209D THR* 3.3 17.7 + - - +
211D GLU* 1.3 75.3 - - + +
213D LYS* 1.3 60.3 + - - +
215D GLU* 3.2 8.2 + - - +
216D ILE* 2.8 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D PRO* 3.6 31.0 - - - +
199D ASN* 4.5 8.5 + - - +
208D LEU* 4.1 13.2 + - + -
209D THR 3.0 12.7 + - - +
210D SER* 3.3 8.3 + - - +
212D ARG* 1.3 76.3 - - - +
214D LYS* 1.3 57.2 + - - +
216D ILE* 3.3 0.6 + - - +
217D TYR* 2.9 27.7 + - - +
229D GLU* 4.3 2.5 + - - -
243D VAL* 3.5 29.2 + - + +
244D PRO 2.8 29.6 + - - +
245D THR* 3.8 8.9 - - - +
246D PHE* 3.3 45.2 - - + +
249D MET* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D SER* 3.1 32.9 + - - +
211D GLU* 3.3 10.9 + - - +
213D LYS* 1.3 73.9 - - - +
215D GLU* 1.3 57.0 + - + +
217D TYR* 3.5 3.3 + - - +
218D GLU* 3.1 34.4 + - - +
244D PRO* 6.3 0.4 - - - -
249D MET* 4.0 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D PRO* 3.7 28.3 - - + +
169D ASP* 4.8 1.9 - - - +
172D ARG* 3.7 24.9 + - - +
211D GLU* 3.3 20.1 + - + +
212D ARG* 3.2 13.4 + - - +
214D LYS* 1.3 73.9 - - + +
216D ILE* 1.3 65.1 + - - +
218D GLU* 3.6 13.1 + - - +
219D LEU* 3.2 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ILE* 3.7 29.2 - - + +
168D PRO* 4.4 9.2 - - + -
171D LEU* 3.8 14.4 - - + +
194D LEU* 3.2 33.7 - - + -
208D LEU* 3.6 39.5 - - + -
212D ARG* 2.8 23.4 + - + +
213D LYS 3.8 3.6 - - - +
215D GLU* 1.3 74.1 - - - +
217D TYR* 1.3 58.8 - - - +
219D LEU* 3.2 4.7 + - - +
220D ALA* 3.0 26.2 + - - +
227D ILE* 4.4 4.7 - - + -
246D PHE* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D LYS 2.9 17.8 + - - +
214D LYS* 3.6 5.6 - - - +
216D ILE* 1.3 78.2 - - - +
218D GLU* 1.3 59.1 + - + +
220D ALA* 3.2 3.1 + - - +
221D ARG* 2.9 54.7 + - - +
227D ILE* 3.8 20.6 - - + -
246D PHE* 4.2 3.1 - + + -
249D MET* 3.6 35.7 - - + -
250D ASP* 2.8 37.8 + - - -
251D VAL 3.3 0.9 + - - -
252D ASP* 2.9 32.3 + - - +
254D ARG* 3.7 16.3 - - + +
255D VAL* 3.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D ARG* 5.2 5.5 + - - -
214D LYS* 3.1 21.3 + - - +
215D GLU* 3.6 11.8 - - - +
216D ILE 3.4 0.2 - - - -
217D TYR* 1.3 77.3 - - + +
219D LEU* 1.3 58.3 + - + +
221D ARG* 3.2 10.4 + - - +
222D LYS* 2.8 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D PRO 3.9 9.4 - - - +
171D LEU* 3.7 23.3 - - + -
172D ARG* 3.6 59.0 - - + +
175D LEU* 4.2 13.7 - - + -
215D GLU 3.2 14.0 + - - +
216D ILE* 3.2 8.9 + - - +
218D GLU* 1.3 81.5 - - + +
220D ALA* 1.3 60.3 + - - +
222D LYS* 4.3 14.1 - - + -
223D TYR* 2.9 40.6 + - + +
225D PHE* 3.7 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D ILE 3.0 12.0 + - - +
217D TYR 3.5 8.1 - - - +
219D LEU* 1.3 74.8 - - - +
221D ARG* 1.3 57.3 + - - +
224D ASP* 2.8 23.7 + - - -
225D PHE* 3.0 53.9 + - + +
227D ILE* 3.7 20.0 - - + -
254D ARG* 3.4 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D TYR* 2.9 30.2 + - + +
218D GLU* 3.5 11.6 - - - +
219D LEU 3.2 0.2 - - - -
220D ALA* 1.3 75.1 - - - +
222D LYS* 1.3 68.3 + - - +
224D ASP* 3.2 13.5 + - - +
251D VAL* 2.9 33.7 - - - +
252D ASP* 2.9 33.5 + - - +
254D ARG* 3.6 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D ARG* 6.3 0.4 - - - +
179D LYS* 6.1 1.5 - - - +
180D PRO* 3.4 50.7 - - + +
218D GLU 2.8 20.2 + - - +
219D LEU* 3.8 14.8 - - + +
221D ARG* 1.3 79.0 - - - +
223D TYR* 1.3 84.0 + - + +
224D ASP* 3.7 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D ARG* 5.1 4.3 + - + +
175D LEU* 3.4 57.2 + - + -
176D SER* 4.2 7.6 + - - -
178D TRP* 3.7 19.6 + - + -
179D LYS* 4.3 4.8 - - - -
180D PRO* 3.8 29.4 - - + +
183D ALA* 3.6 14.5 - - - +
190D THR* 4.8 10.1 + - + -
191D PRO* 4.8 3.8 - - + +
219D LEU* 2.9 30.3 + - + +
220D ALA 3.7 0.2 - - - -
222D LYS* 1.3 108.3 + - + +
224D ASP* 1.3 69.0 + - - +
225D PHE* 3.3 20.0 + - + +
----------------------------------------------------------
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