Contacts of the helix formed by residues 291 - 304 (chain K) in PDB entry 1F1H
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 SER 291 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281K LEU 2.6 28.9 + - - -
282K PHE* 2.9 9.9 + - - -
283K SER 3.4 17.7 - - - -
284K GLY* 3.5 8.7 - - - +
285K ASP 4.9 0.2 - - - +
286K LYS* 4.0 3.1 - - - -
290K LEU* 1.3 76.6 - - - +
292K GLU* 1.3 62.4 + - - +
293K GLN* 3.2 6.6 + - - +
294K ALA* 3.1 22.4 + - - +
295K LEU* 3.5 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 292 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286K LYS* 3.8 36.1 + - + +
291K SER* 1.3 73.7 - - - +
293K GLN* 1.3 67.0 + - + +
295K LEU* 3.2 12.6 + - + +
296K TYR* 3.1 56.5 + - + +
385K LYS* 5.0 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 293 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120K ILE* 3.7 20.2 + - - +
274K LEU* 5.1 2.1 - - - +
281K LEU* 3.0 46.3 - - - +
282K PHE* 4.8 5.4 - - + -
291K SER* 3.1 11.6 - - - +
292K GLU* 1.3 85.4 - - + +
294K ALA* 1.3 59.7 + - - +
296K TYR* 3.4 5.8 + - - -
297K TYR* 3.1 19.4 + - - +
382K ILE* 3.5 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282K PHE* 3.7 37.9 - - + +
290K LEU* 3.7 22.0 - - + -
291K SER* 3.1 18.2 + - - +
292K GLU 3.2 0.2 - - - -
293K GLN* 1.3 77.9 - - - +
295K LEU* 1.3 58.5 + - - +
297K TYR* 3.1 10.2 - - - +
298K ILE* 2.9 32.5 + - - +
356K ILE* 5.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286K LYS* 4.0 29.8 - - + -
287K TYR* 4.9 7.2 - - + +
290K LEU* 3.8 27.6 - - + -
291K SER 3.6 9.0 - - - +
292K GLU* 3.2 11.8 + - + +
294K ALA* 1.3 77.5 - - - +
296K TYR* 1.3 60.2 + - + +
298K ILE* 3.2 6.5 + - + +
299K GLY 2.8 23.7 + - - -
334K TYR* 4.0 28.5 - - + +
387K HIS* 4.6 15.9 - - + +
388K PRO* 3.2 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 296 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292K GLU* 3.1 44.9 + - + +
293K GLN* 3.8 8.5 - - - +
294K ALA 3.3 0.2 - - - -
295K LEU* 1.3 76.8 - - + +
297K TYR* 1.3 66.4 + - - +
299K GLY* 3.3 0.5 + - - -
300K GLY 3.0 18.7 + - - -
381K GLY* 3.1 28.7 - - - +
382K ILE* 3.7 11.9 - - + -
385K LYS* 3.5 59.9 + - + +
386K ILE 3.4 19.6 - - - +
387K HIS* 4.2 22.5 - + + -
388K PRO* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 297 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124K VAL* 4.7 5.1 - - + +
126K PHE* 4.8 0.2 - - - -
272K MET* 3.6 31.3 - - + +
273K SER 6.1 0.2 - - - -
274K LEU* 3.8 26.5 - - + -
282K PHE* 3.6 22.7 - + + -
293K GLN 3.1 12.9 + - - +
294K ALA 3.1 11.6 + - - +
296K TYR* 1.3 77.3 - - - +
298K ILE* 1.3 61.8 + - - +
300K GLY 3.1 10.2 + - - -
301K VAL* 3.1 22.6 + - + +
356K ILE* 3.8 20.6 - - + -
374K LEU 4.2 1.8 - - - -
375K LEU* 3.3 35.3 - - + +
378K GLY* 3.5 42.2 - - - -
379K LEU* 4.8 0.2 - - + -
382K ILE* 4.0 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 298 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290K LEU* 4.4 8.7 - - + -
294K ALA 2.9 18.8 + - - +
295K LEU* 3.2 12.8 + - + +
297K TYR* 1.3 74.0 - - - +
299K GLY* 1.3 67.3 + - - +
301K VAL* 3.0 9.8 + - - +
302K ILE* 2.9 38.3 + - + +
334K TYR* 4.1 24.5 - - + -
343K ILE* 4.0 15.9 - - + -
345K ILE* 4.0 26.9 - - + -
356K ILE* 4.0 22.2 - - + -
388K PRO* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 299 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295K LEU 2.8 12.1 + - - -
296K TYR 3.3 0.4 + - - -
298K ILE* 1.3 75.8 - - - +
300K GLY* 1.3 56.7 + - - +
302K ILE* 3.3 5.4 + - - +
303K LYS* 2.9 29.8 + - - +
386K ILE* 3.6 31.0 - - - +
388K PRO* 3.8 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 300 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296K TYR 3.0 9.9 + - - -
297K TYR 3.1 2.2 + - - -
299K GLY* 1.3 76.1 - - - +
301K VAL* 1.3 56.2 + - - +
303K LYS* 3.2 1.4 + - - +
304K HIS* 3.0 36.5 + - - +
377K ALA 3.2 24.5 - - - -
381K GLY* 3.7 13.1 - - - -
386K ILE* 4.4 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 301 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297K TYR* 3.1 35.2 + - + +
298K ILE* 3.0 9.7 + - - +
300K GLY* 1.3 74.6 - - - +
302K ILE* 1.3 57.7 + - - +
304K HIS 3.6 0.5 - - - -
305K ALA* 2.8 29.9 + - + +
308K ILE* 4.1 17.5 - - + -
343K ILE* 4.3 17.3 - - + -
356K ILE* 5.2 1.1 - - + -
358K VAL* 4.4 18.4 - - + -
360K PHE* 4.5 8.3 - - + -
374K LEU* 4.2 28.3 - - + +
377K ALA* 4.1 1.1 + - + -
378K GLY 4.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 302 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298K ILE* 2.9 39.1 + - + +
299K GLY* 3.7 5.4 - - - +
301K VAL* 1.3 76.5 - - - +
303K LYS* 1.3 63.7 + - - +
304K HIS 3.5 0.3 + - - -
305K ALA* 3.6 14.9 + - - +
332K LEU* 3.6 54.5 - - + +
333K ALA* 4.1 11.7 - - - +
334K TYR* 4.7 1.3 - - + -
343K ILE* 4.2 10.3 - - + -
388K PRO* 4.6 15.9 - - + +
408K PRO* 4.9 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 303 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299K GLY 2.9 16.3 + - - +
300K GLY* 3.2 6.7 + - - +
302K ILE* 1.3 79.9 - - - +
304K HIS* 1.3 79.6 + - + +
305K ALA 3.7 0.7 + - - -
306K LYS 5.2 0.9 + - - -
380K ASP* 4.4 6.1 + - - -
384K ASN* 5.6 3.8 + - - +
386K ILE* 3.6 34.3 - - + +
424K ASP* 4.1 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 304 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300K GLY* 3.0 24.0 + - - +
301K VAL 3.6 2.0 - - - -
303K LYS* 1.3 102.0 + - + +
305K ALA* 1.3 64.8 + - - +
306K LYS 3.4 1.6 - - - -
307K ALA* 3.1 5.7 + - - +
308K ILE* 2.9 22.6 + - - +
377K ALA* 4.0 14.6 - - + -
380K ASP* 2.9 29.2 + - - -
386K ILE* 5.1 0.2 - - - +
424K ASP* 2.7 39.4 + - - +
427K PHE* 3.6 42.4 - + + +
----------------------------------------------------------
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