Contacts of the helix formed by residues 366 - 384 (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 ASN 366 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K THR* 4.1 0.4 - - - +
23K ASP 3.3 15.2 + - - -
24K THR 2.8 26.4 + - - +
25K LYS 4.0 5.5 + - - +
26K GLY* 3.4 19.3 - - - -
104K PRO* 3.8 7.7 - - - +
311K LEU 4.0 4.7 + - - +
314K PRO* 4.8 2.0 - - - +
364K ALA 3.6 2.4 + - - -
365K ALA* 1.3 70.0 - - - +
367K PRO* 1.3 70.0 - - - +
368K TYR* 3.0 27.7 + - - +
369K LEU* 3.6 26.2 - - + +
370K CYS* 2.8 24.7 + - - +
442K TYR* 5.6 2.7 - - + +
446K ARG* 5.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 367 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K GLY 4.7 2.0 - - - +
232K ALA* 3.7 34.5 - - + +
235K ILE* 3.8 23.6 - - + -
236K GLN* 3.7 25.8 - - - +
239K LYS* 4.5 3.1 - - - +
268K MET* 5.2 3.1 - - + -
365K ALA 3.0 12.0 - - - +
366K ASN* 1.3 85.6 - - - +
368K TYR* 1.3 61.1 + - + +
370K CYS* 4.5 1.6 - - + -
371K PHE* 2.9 50.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 368 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K THR* 3.4 29.0 + - + -
88K ARG* 3.8 13.9 + - - -
104K PRO* 3.3 32.3 - - + +
105K ARG* 3.9 23.9 + - + -
107K ILE* 6.0 0.2 - - - -
108K ALA* 4.0 21.9 - - + +
229K THR* 4.0 5.4 - - + -
232K ALA* 3.3 24.8 + - + -
233K ASP* 2.6 36.5 + - - -
236K GLN* 4.1 10.6 - - + +
366K ASN* 3.0 14.0 + - - +
367K PRO* 1.3 78.9 - - + +
369K LEU* 1.3 59.5 + - - +
371K PHE* 3.9 2.1 - - - +
372K ALA* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K THR* 3.8 25.6 - - + +
104K PRO* 3.8 27.6 - - + -
107K ILE* 3.8 24.2 - - + -
311K LEU* 3.5 19.4 - - + +
366K ASN* 3.3 20.2 + - + +
368K TYR* 1.3 80.1 - - - +
370K CYS* 1.3 58.4 + - - +
372K ALA* 3.9 3.8 - - - +
373K ALA* 3.0 30.8 + - - +
434K PHE* 4.2 13.8 - - + -
442K TYR* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 370 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268K MET* 4.9 2.0 - - + -
270K CYS* 5.0 0.2 - - - -
308K ILE* 4.9 1.6 - - - +
311K LEU* 3.7 23.2 - - - +
312K ALA* 3.5 31.0 - - - -
361K PRO* 4.3 8.5 - - - -
365K ALA* 3.9 10.3 - - + -
366K ASN 2.8 22.2 + - - +
367K PRO* 4.0 2.5 - - + +
369K LEU* 1.3 74.5 - - - +
371K PHE* 1.3 72.4 + - + +
373K ALA* 3.3 3.5 + - - +
374K LEU* 3.0 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 371 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126K PHE* 3.3 36.2 - + + -
128K PRO* 3.4 31.9 - - + -
228K MET* 3.6 36.2 - - + +
231K LYS* 4.1 7.0 - - + -
232K ALA* 3.8 28.5 - - + -
235K ILE* 4.2 3.4 - - + -
268K MET* 4.3 13.7 - - + -
270K CYS* 4.0 21.8 - - - -
367K PRO* 2.9 32.4 + - + +
368K TYR* 3.9 2.7 - - - +
370K CYS* 1.3 82.2 - - - +
372K ALA* 1.3 63.0 + - - +
374K LEU* 3.2 2.3 + - - -
375K LEU 3.1 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 372 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K ILE* 4.5 3.6 - - + -
108K ALA* 4.4 8.1 - - - -
111K ALA* 4.2 17.0 - - + -
228K MET* 3.7 15.6 - - + -
368K TYR 2.9 19.9 + - - +
369K LEU 3.9 2.9 - - - +
371K PHE* 1.3 75.9 - - - +
373K ALA* 1.3 58.5 + - - +
375K LEU* 3.1 4.1 + - - +
376K MET* 2.9 34.4 + - - +
434K PHE* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308K ILE* 4.1 15.2 - - + +
311K LEU* 3.7 26.7 - - + -
369K LEU 3.0 19.9 + - - +
370K CYS 3.6 4.3 - - - +
372K ALA* 1.3 76.0 - - - +
374K LEU* 1.3 63.1 + - - +
377K ALA* 3.2 24.8 + - - +
427K PHE* 3.7 4.6 - - + -
428K LEU* 3.9 19.7 - - + -
434K PHE* 4.6 2.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126K PHE* 4.1 11.7 - - + -
270K CYS* 4.5 9.9 - - + -
272K MET* 3.9 25.6 - - + -
297K TYR* 3.8 6.0 + - - -
301K VAL* 4.2 20.9 - - + +
308K ILE* 3.5 32.8 - - + -
358K VAL* 4.4 12.1 - - + -
360K PHE* 4.7 1.3 - - + -
361K PRO* 4.5 12.1 - - + -
370K CYS* 3.0 38.3 + - - +
371K PHE 3.4 7.9 - - - +
373K ALA* 1.3 78.4 - - - +
375K LEU* 1.3 62.6 + - - +
377K ALA* 3.3 3.3 + - - +
378K GLY* 3.0 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K ALA* 3.7 32.3 - - + +
115K LEU* 4.4 5.6 - - + -
124K VAL* 3.7 41.1 - - + -
126K PHE* 4.6 1.1 - - + -
228K MET* 4.2 11.0 - - - -
274K LEU* 4.4 3.4 - - + -
297K TYR* 3.3 20.2 + - + +
371K PHE 3.1 8.7 + - - +
372K ALA 3.3 9.0 - - - +
374K LEU* 1.3 77.7 - - - +
376K MET* 1.3 56.5 + - - +
378K GLY* 2.8 4.7 + - - -
379K LEU* 2.8 59.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 376 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K ALA* 4.1 16.2 - - + +
114K TYR* 4.1 21.8 - - + -
372K ALA 2.9 26.0 + - - +
373K ALA 4.1 0.2 - - - +
375K LEU* 1.3 73.2 - - - +
377K ALA* 1.3 56.8 + - - +
379K LEU* 3.6 9.3 + - - +
380K ASP* 3.1 26.9 + - - +
427K PHE* 3.5 29.5 - - - +
428K LEU* 3.7 25.6 - - + +
430K ALA* 3.2 34.5 - - + +
433K VAL* 3.5 25.6 - - + -
434K PHE* 4.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 377 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300K GLY* 3.2 27.5 - - - +
301K VAL* 4.2 1.1 - - - -
304K HIS* 4.0 4.9 - - + -
308K ILE* 3.6 20.0 - - + -
373K ALA 3.2 18.7 + - - +
374K LEU 3.5 4.7 - - - +
375K LEU 3.1 0.6 - - - -
376K MET* 1.3 73.4 - - - +
378K GLY* 1.3 65.5 + - - +
380K ASP* 3.3 3.6 + - - +
381K GLY 3.1 16.1 + - - -
427K PHE* 3.5 21.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 378 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297K TYR* 3.5 52.7 - - - -
301K VAL* 4.5 0.8 - - - +
374K LEU 3.0 8.4 + - - -
375K LEU 2.8 6.3 + - - -
377K ALA* 1.3 78.1 - - - +
379K LEU* 1.3 55.6 + - - +
381K GLY* 3.0 15.4 + - - -
382K ILE* 3.0 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 379 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K TYR* 3.7 38.8 - - + +
115K LEU* 3.4 38.8 - - + -
118K THR* 5.0 2.5 - - - +
120K ILE* 4.2 17.7 - - + +
274K LEU* 4.3 14.1 - - + -
375K LEU* 2.8 37.8 + - + +
376K MET* 3.9 8.7 - - - +
378K GLY* 1.3 72.0 - - - +
380K ASP* 1.3 62.1 + - - +
381K GLY 3.0 2.2 - - - -
382K ILE* 3.2 5.3 + - + +
383K LYS* 2.8 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 380 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303K LYS* 4.4 5.2 + - - -
304K HIS* 2.9 29.1 + - - +
376K MET 3.1 19.4 + - - +
377K ALA 3.6 5.4 - - - +
378K GLY 3.3 0.2 - - - -
379K LEU* 1.3 76.7 - - - +
381K GLY* 1.3 60.2 + - - +
383K LYS* 4.0 21.0 + - - +
384K ASN* 3.4 32.5 + - - +
386K ILE* 3.6 10.0 - - - +
427K PHE* 4.0 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 381 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296K TYR* 3.1 26.7 - - - +
300K GLY* 3.7 6.0 - - - -
377K ALA 3.1 5.3 + - - -
378K GLY 3.0 5.7 + - - -
380K ASP* 1.3 79.6 - - - +
382K ILE* 1.3 56.5 + - - +
385K LYS 3.0 6.1 + - - -
386K ILE* 2.8 43.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 382 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120K ILE* 3.5 38.6 - - + -
274K LEU* 4.1 7.9 - - + -
282K PHE* 5.3 0.2 - - + -
293K GLN* 3.5 48.7 - - + +
296K TYR* 3.7 12.5 - - + -
297K TYR* 4.0 17.0 - - + +
378K GLY 3.0 15.6 + - - +
379K LEU* 3.2 9.8 + - + +
381K GLY* 1.3 73.3 - - - +
383K LYS* 1.3 68.7 + - - +
384K ASN 3.0 2.6 + - - -
385K LYS* 3.0 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 383 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K TYR* 3.3 28.3 + - + +
118K THR* 5.0 8.1 - - + -
120K ILE* 4.2 16.4 - - + -
379K LEU* 2.8 21.9 + - + +
380K ASP* 4.0 27.0 + - - +
382K ILE* 1.3 75.3 - - - +
384K ASN* 1.3 73.3 + - - +
385K LYS* 3.9 7.7 + - - +
430K ALA* 4.8 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 384 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303K LYS* 5.6 3.7 + - - +
380K ASP* 3.4 29.3 + - - +
381K GLY 3.5 0.4 - - - -
382K ILE 3.0 0.8 - - - -
383K LYS* 1.3 104.8 + - - +
385K LYS* 1.3 70.8 + - - +
386K ILE* 2.9 15.9 + - + +
----------------------------------------------------------
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