Contacts of the helix formed by residues 205 - 217 (chain B) in PDB entry 2VKZ
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 PRO 205 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B MET 4.4 1.6 - - - +
169B SER 3.6 13.0 - - - +
170B LYS 3.4 16.2 - - - +
171B THR* 4.3 7.4 - - - -
203B GLU 3.2 10.5 - - - +
204B THR* 1.4 87.6 - - + +
206B LEU* 1.3 61.0 + - - +
207B GLU* 3.5 1.8 - - + +
208B GLU* 3.0 43.6 + - + +
209B LEU 2.9 24.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
151B LEU* 3.6 28.9 - - + +
152B HIS* 5.7 2.2 - - - +
155B VAL* 4.4 14.8 - - + -
166B ILE* 4.0 15.7 - - + -
167B PRO 4.1 1.8 - - - +
168B MET* 3.1 52.4 + - + +
170B LYS 3.3 6.5 + - - +
172B ILE* 4.3 24.9 - - + +
175B LEU* 3.4 32.1 - - + -
205B PRO* 1.3 69.3 - - - +
207B GLU* 1.3 58.4 + - - +
209B LEU* 4.3 6.3 - - + +
210B ALA 3.0 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B MET* 3.0 43.1 + - + +
169B SER* 3.8 22.6 + - - -
205B PRO* 3.5 1.2 - - + +
206B LEU* 1.3 75.5 - - - +
208B GLU* 1.3 63.0 + - + +
210B ALA* 3.6 4.3 + - - +
211B GLU* 3.3 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B THR* 3.9 17.1 - - + +
205B PRO* 3.0 41.2 + - + +
207B GLU* 1.3 83.6 - - + +
209B LEU* 1.3 57.8 + - - +
211B GLU* 3.8 23.2 - - - +
212B THR* 3.3 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.9 14.6 - - + -
172B ILE* 4.6 12.3 - - + -
190B LEU* 5.1 4.9 - - + -
198B PRO* 3.1 37.0 - - + -
201B PRO* 3.6 24.2 - - + +
204B THR* 3.5 29.8 - - + +
205B PRO 2.9 9.1 + - - +
206B LEU* 3.4 7.4 + - + +
208B GLU* 1.3 76.1 - - - +
210B ALA* 1.3 58.5 - - - +
211B GLU 3.1 1.6 - - - -
212B THR* 3.2 8.1 + - - +
213B PHE* 3.0 53.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 3.5 11.2 - - - +
148B SER* 4.0 25.1 - - - +
151B LEU* 3.7 6.4 - - + +
168B MET* 4.0 14.8 - - + -
206B LEU 3.0 17.3 + - - +
207B GLU* 3.9 7.0 - - - +
209B LEU* 1.3 73.7 - - - +
211B GLU* 1.3 63.0 + - - +
213B PHE* 4.6 2.0 - - - -
214B GLN* 3.2 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLU 3.3 13.7 + - - +
208B GLU* 3.8 24.2 - - - +
209B LEU 3.1 0.2 - - - -
210B ALA* 1.3 79.1 - - - +
212B THR* 1.3 61.3 + - - +
214B GLN* 3.3 10.9 + - - +
215B ASP* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B THR* 5.6 9.7 - - + +
198B PRO* 4.5 22.2 - - + +
204B THR* 5.4 2.3 - - - +
208B GLU 3.3 15.2 + - - -
209B LEU* 3.2 16.2 + - - +
211B GLU* 1.3 77.9 - - - +
213B PHE* 1.3 62.5 + - + +
214B GLN 3.6 0.3 + - - -
215B ASP* 3.8 21.3 - - - +
216B THR* 4.0 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 4.4 3.8 - - + -
151B LEU* 4.4 16.8 - - + -
190B LEU* 4.6 19.3 - - + -
194B PHE* 3.4 62.1 - + + +
196B THR* 2.9 34.3 - - - -
197B THR* 5.3 0.4 - - - -
198B PRO* 3.7 17.5 - - + -
209B LEU* 3.0 38.0 + - + +
210B ALA 4.3 3.6 - - - +
211B GLU 3.3 0.2 - - - -
212B THR* 1.3 77.2 - - + +
214B GLN* 1.3 64.3 + - - +
215B ASP 3.3 0.8 + - - -
216B THR* 3.5 7.2 + - - -
217B PHE* 3.3 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL 4.9 0.9 + - - +
146B LYS* 4.4 9.0 - - - +
147B ALA* 3.3 30.3 - - + +
210B ALA 3.2 19.6 + - - +
211B GLU* 3.3 8.0 + - - +
213B PHE* 1.3 75.2 - - - +
215B ASP* 1.3 70.4 + - - +
217B PHE* 3.2 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLU 3.0 18.7 - - - +
212B THR* 3.8 15.6 - - - +
214B GLN* 1.3 81.4 - - - +
216B THR* 1.3 65.9 + - + +
217B PHE 3.9 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B PHE* 5.2 5.9 + - - +
196B THR* 4.1 26.6 + - + +
212B THR 4.0 8.4 + - - +
213B PHE* 3.6 11.3 + - - -
214B GLN 3.2 0.2 - - - -
215B ASP* 1.3 84.6 - - + +
217B PHE* 1.3 60.3 + - - +
218B SER 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 3.1 30.5 - - + -
146B LYS 4.0 1.6 - - - -
147B ALA* 3.4 35.0 - - + -
150B LEU* 4.1 11.0 - - + -
194B PHE* 4.0 25.1 - + + +
213B PHE 3.3 22.1 + - - +
214B GLN* 3.2 32.6 + - - +
215B ASP 4.8 0.7 - - - +
216B THR* 1.3 79.4 - - - +
218B SER* 1.3 75.7 + - - +
219B GLY 3.7 14.8 - - - -
220B ALA* 3.4 37.5 - - + -
----------------------------------------------------------
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