Contacts of the helix formed by residues 206 - 215 (chain K) in PDB entry 1FQV
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 GLU 206 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182K MET 2.6 8.5 + - - -
183K ASP* 3.6 27.4 - - + +
184K GLN* 4.8 3.1 - - - +
204K VAL* 5.8 0.2 - - - +
205K ILE* 1.3 70.7 - - - +
207K VAL* 1.3 76.1 + - - +
208K SER* 2.8 41.2 + - - +
209K THR* 2.9 19.3 + - - +
210K LEU 2.8 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 207 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205K ILE 3.1 5.5 + - - +
206K GLU* 1.3 83.2 + - - +
208K SER* 1.3 60.8 + - - +
210K LEU* 4.2 3.1 - - - -
211K HIS* 3.0 23.4 + - + +
229K ARG* 3.1 39.3 - - + +
230K LEU* 3.6 22.0 - - - +
231K SER* 4.3 16.4 - - - +
234K ILE* 3.2 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 208 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184K GLN 5.3 1.2 + - - -
185K PRO* 5.5 4.5 - - - +
187K ALA* 2.9 30.8 - - - +
206K GLU* 2.8 35.3 + - - +
207K VAL* 1.3 75.1 - - - +
209K THR* 1.3 60.4 + - - +
211K HIS* 3.5 7.7 + - - +
212K GLY 3.0 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 209 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161K PRO* 3.3 30.3 - - + -
182K MET* 4.0 12.6 - - + -
184K GLN 2.6 25.6 + - - -
185K PRO* 5.0 0.2 - - - +
187K ALA* 4.2 9.5 - - - +
205K ILE* 3.9 15.5 - - + -
206K GLU* 2.9 22.0 + - - +
208K SER* 1.3 76.2 + - - +
210K LEU* 1.3 67.4 + - - +
212K GLY* 3.4 0.9 + - - -
213K ILE* 3.1 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200K LEU* 3.8 28.3 - - + -
205K ILE* 3.7 28.0 - - + +
206K GLU 2.8 12.4 + - - +
207K VAL* 3.5 10.1 - - - +
209K THR* 1.3 79.4 - - - +
211K HIS* 1.3 61.4 + - - +
213K ILE* 3.4 4.9 + - + +
214K LEU* 3.1 39.2 + - + +
225K LEU* 4.5 1.6 - - + -
228K LEU* 4.1 18.2 - - + -
229K ARG 3.9 8.1 - - - +
230K LEU* 3.3 34.1 - - + -
234K ILE* 3.5 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 211 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187K ALA* 5.5 2.9 - - + -
207K VAL* 3.0 13.8 + - + +
208K SER* 3.6 9.0 - - - +
209K THR 3.2 0.2 - - - -
210K LEU* 1.3 75.8 - - - +
212K GLY* 1.3 61.7 + - - +
213K ILE 3.1 0.2 + - - -
214K LEU* 3.2 3.4 + - - +
215K SER* 2.8 41.4 + - - -
231K SER* 5.3 0.2 - - - +
233K PRO* 3.2 34.9 + - + +
234K ILE* 3.6 20.6 + - + +
237K THR* 2.8 29.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 212 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187K ALA* 3.4 21.1 - - - -
188K GLU* 2.4 37.2 - - - +
208K SER 3.0 12.1 + - - -
209K THR 3.4 0.8 + - - -
211K HIS* 1.3 79.0 - - - +
213K ILE* 1.3 58.6 + - - +
215K SER* 2.9 14.9 + - - -
216K GLN* 3.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161K PRO* 5.2 0.9 - - + +
164K THR* 3.3 27.4 - - - +
165K GLY 5.6 0.2 - - - +
168K LEU* 3.7 27.4 - - + -
175K PHE* 6.1 1.8 - - + -
182K MET* 3.9 20.6 - - + -
188K GLU* 3.7 20.0 - - + -
193K PHE* 3.9 3.5 - - + -
198K MET* 4.6 14.1 - - + -
200K LEU* 5.6 9.4 - - + -
205K ILE* 5.6 1.1 - - + -
209K THR* 3.1 26.4 + - + +
210K LEU* 3.9 5.6 - - + +
212K GLY* 1.3 72.9 - - - +
214K LEU* 1.3 69.3 + - + +
215K SER 3.1 2.0 - - - -
216K GLN* 3.2 15.2 + - - +
217K CYS* 3.2 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198K MET* 4.5 13.5 - - - -
200K LEU* 5.2 1.6 - - + -
210K LEU* 3.1 24.2 + - + +
211K HIS* 4.0 4.0 - - - +
213K ILE* 1.3 74.2 - - + +
215K SER* 1.3 56.1 + - - +
216K GLN 3.0 5.2 - - - -
217K CYS* 3.1 32.9 + - - +
220K LEU* 4.1 26.7 - - + -
223K LEU* 4.2 10.3 - - + -
225K LEU* 3.6 32.8 - - + -
234K ILE* 3.8 20.4 - - + +
237K THR* 3.5 17.1 - - - +
238K LEU* 4.3 14.5 - - + -
241K ASN* 4.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 215 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188K GLU 3.7 1.4 + - - -
211K HIS* 2.8 25.2 + - - -
212K GLY* 2.9 21.7 + - - -
213K ILE 3.1 0.2 - - - -
214K LEU* 1.3 73.7 - - - +
216K GLN* 1.3 72.7 + - - +
237K THR* 3.0 23.8 - - - +
240K LYS* 2.4 22.5 + - - -
----------------------------------------------------------
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