Contacts of the helix formed by residues 207 - 221 (chain K) in PDB entry 1F9E
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 207 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206K CYS* 1.3 77.3 - - - +
208K VAL* 1.3 64.9 + - - +
209K GLU* 3.3 11.6 + - - +
210K GLN* 2.8 47.8 + - - +
211K ILE* 2.8 22.1 + - - +
245K GLY* 4.3 1.3 - - - -
246K THR* 3.3 20.0 - - + +
247K ASP* 3.0 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207K THR* 1.3 73.0 - - - +
209K GLU* 1.3 65.5 + - - +
211K ILE* 3.0 10.1 + - + +
212K TYR* 2.9 54.0 + - + -
245K GLY* 3.7 11.9 - - - +
247K ASP* 3.1 4.0 + - - +
254K GLN* 3.0 53.6 - - + +
255K GLU 3.7 15.5 - - - +
256K ALA* 4.2 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207K THR* 3.3 10.7 + - - +
208K VAL* 1.3 82.4 - - - +
210K GLN* 1.3 66.2 + - + +
212K TYR* 3.4 11.7 + - - +
213K GLU* 3.1 41.7 + - - +
247K ASP* 5.5 0.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 210 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204K HIS 5.1 1.6 - - - +
205K ASP 4.2 5.9 + - - +
206K CYS* 3.9 16.1 - - + +
207K THR* 2.8 50.3 + - - +
209K GLU* 1.3 80.0 - - + +
211K ILE* 1.3 56.6 + - - +
213K GLU* 3.2 15.8 - - - +
214K ILE* 2.9 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168K ILE* 3.8 31.2 - - + -
170K ASN* 4.5 8.1 - - - +
206K CYS* 3.8 19.1 - - + +
207K THR 2.8 26.0 + - - +
208K VAL* 3.0 12.5 + - + +
210K GLN* 1.3 68.4 - - - +
212K TYR* 1.3 69.6 + - + +
214K ILE* 3.0 11.0 + - - +
215K LEU* 2.9 40.7 + - + +
234K ILE* 5.2 5.6 - - + -
243K ILE* 4.5 20.9 - - + -
245K GLY* 4.7 2.5 - - - -
256K ALA* 5.5 2.9 - - + -
261K LEU* 4.4 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 212 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208K VAL* 2.9 43.9 + - + -
209K GLU* 3.7 12.8 - - - +
211K ILE* 1.3 77.6 - - + +
213K GLU* 1.3 52.5 + - - +
215K LEU* 3.2 7.4 + - + +
216K LYS* 2.8 35.1 + - - +
255K GLU 4.5 1.0 + - - -
256K ALA* 3.9 5.9 - - + -
257K PRO* 3.6 18.4 - - - +
260K GLU* 3.5 34.3 + - + +
261K LEU* 3.6 27.1 - - + -
264K GLN* 4.8 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 213 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209K GLU* 3.1 37.5 + - + +
210K GLN* 3.2 17.7 - - - +
211K ILE 3.1 0.2 - - - -
212K TYR* 1.3 76.0 - - - +
214K ILE* 1.3 63.5 + - + +
216K LYS* 3.1 17.3 + - - +
217K ILE* 3.1 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K LEU* 4.0 12.6 - - + -
168K ILE* 4.1 10.3 - - + -
203K HIS* 3.2 60.3 - - + +
206K CYS* 3.8 16.6 - - + -
210K GLN* 2.9 22.2 + - + +
211K ILE* 3.0 6.5 + - - +
213K GLU* 1.3 73.5 - - + +
215K LEU* 1.3 62.4 + - + +
217K ILE* 3.3 17.9 + - + +
218K TYR* 3.1 36.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K LEU* 3.6 26.0 - - + -
168K ILE* 5.7 4.0 - - + -
211K ILE* 2.9 26.7 + - + +
212K TYR* 3.7 8.5 - - + +
214K ILE* 1.3 74.8 - - + +
216K LYS* 1.3 54.4 + - - +
218K TYR* 3.2 2.2 + - - +
219K GLN* 2.6 38.8 + - - +
232K CYS* 4.1 16.8 - - + -
234K ILE* 5.6 1.1 - - + -
261K LEU* 3.7 48.5 - - + +
264K GLN* 4.5 11.2 - - + +
265K PHE* 3.8 26.2 - - + -
280K PHE* 5.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212K TYR 2.8 14.2 + - - +
213K GLU* 3.2 13.7 - - - +
215K LEU* 1.3 77.4 - - - +
217K ILE* 1.3 64.4 + - + +
219K GLN* 3.1 36.0 + - - +
220K LEU* 3.0 51.8 + - + +
264K GLN* 4.5 8.6 - - - +
269K LYS* 4.8 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 217 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203K HIS* 6.3 1.8 - - + -
213K GLU* 3.1 14.5 + - + +
214K ILE* 3.4 16.6 - - + +
216K LYS* 1.3 78.1 - - + +
218K TYR* 1.3 82.7 + - + +
220K LEU* 2.9 8.5 + - - +
221K MET* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 218 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164K TYR* 3.7 35.4 - + + -
166K LEU* 3.4 36.8 - - + -
201K LYS* 3.3 30.0 + - - +
203K HIS* 4.4 7.3 + + - -
214K ILE* 3.1 33.7 - - + +
215K LEU 3.2 5.6 + - - +
217K ILE* 1.3 89.3 - - + +
219K GLN* 1.3 66.4 + - - +
220K LEU 3.3 0.3 + - - -
221K MET* 3.3 25.2 + - - -
224K HIS* 2.9 27.0 + + - +
230K PHE* 4.2 18.8 - + + -
265K PHE* 3.9 7.8 - - + -
270K CYS* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 219 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215K LEU 2.6 23.1 + - - +
216K LYS* 3.1 38.1 + - - +
218K TYR* 1.3 75.6 - - - +
220K LEU* 1.3 81.6 + - - +
221K MET 4.1 0.9 - - - +
264K GLN* 3.2 40.0 + - + +
265K PHE* 3.8 13.6 - - + -
269K LYS* 3.2 36.4 + - - +
270K CYS* 3.5 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216K LYS* 3.0 41.4 + - + +
217K ILE* 2.9 7.6 + - - +
219K GLN* 1.3 100.9 - - - +
221K MET* 1.3 66.3 + - - +
269K LYS 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 221 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164K TYR* 3.2 44.6 - - + +
217K ILE* 2.9 26.8 + - + +
218K TYR* 3.3 30.9 + - - +
219K GLN 4.1 3.6 - - - +
220K LEU* 1.3 84.5 - - - +
222K ASP* 1.3 73.5 + - - +
224K HIS* 3.7 12.1 - - - +
272K SER* 3.3 13.2 + - - -
----------------------------------------------------------
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