Contacts of the helix formed by residues 304 - 313 (chain F) in PDB entry 1FPY
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 HIS 304 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300F GLY* 2.8 22.4 + - - +
301F VAL 3.6 0.7 - - - -
303F LYS* 1.3 98.1 - - + +
305F ALA* 1.3 65.9 + - - +
306F LYS 3.4 2.0 - - - -
307F ALA* 2.9 7.0 + - - +
308F ILE* 2.8 21.2 + - + -
377F ALA* 3.4 33.0 - - + -
380F ASP* 3.0 30.9 + - - -
424F ASP* 2.8 37.8 + - - +
427F PHE* 3.5 31.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301F VAL 2.8 17.4 + - - +
302F ILE 3.6 5.6 - - - +
303F LYS 3.3 2.2 - - - -
304F HIS* 1.3 73.1 - - - +
306F LYS* 1.3 54.2 + - + +
308F ILE* 2.8 11.5 + - - +
309F ASN* 2.7 38.3 + - - -
332F LEU* 3.4 42.8 - - + -
360F PHE* 4.8 7.4 - - + -
410F VAL* 4.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 306 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F LYS 5.1 1.0 + - - -
304F HIS 3.2 0.8 + - - -
305F ALA* 1.3 78.6 - - + +
307F ALA* 1.3 61.1 + - - +
309F ASN* 3.2 24.2 + - - +
332F LEU* 5.7 0.2 - - + -
409F GLN* 2.9 31.4 + - - +
410F VAL 3.8 7.5 + - - -
411F ALA* 3.8 15.3 - - + +
416F GLU* 3.3 31.8 + - + +
417F ALA* 3.2 16.0 - - - +
420F ALA* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304F HIS 2.9 9.8 + - - +
306F LYS* 1.3 75.2 - - - +
308F ILE* 1.3 68.7 + - - +
310F ALA* 3.1 21.1 + - - +
311F LEU* 3.9 3.1 + - - +
420F ALA* 3.9 5.5 - - + +
421F LEU* 3.7 39.7 - - + +
424F ASP* 4.0 18.1 + - + +
427F PHE* 4.2 16.6 - - + -
428F LEU* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 308 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301F VAL* 3.7 27.1 - - + +
304F HIS* 2.8 21.6 + - + +
305F ALA* 2.8 7.9 + - - +
307F ALA* 1.3 77.2 - - - +
309F ASN* 1.3 62.1 + - - +
311F LEU* 2.8 13.9 + - - +
312F ALA* 2.9 18.2 + - + +
360F PHE* 4.5 10.5 - - + -
370F CYS 4.7 1.1 - - - +
373F ALA* 3.9 28.3 - - + +
374F LEU* 3.3 35.2 - - + -
377F ALA* 3.6 25.6 - - + -
427F PHE* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 309 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F ALA 2.7 15.5 + - - -
306F LYS* 3.2 15.9 + - - +
307F ALA 3.1 0.2 - - - -
308F ILE* 1.3 71.3 - - - +
310F ALA* 1.3 59.4 + - - +
311F LEU 2.8 0.3 + - - -
312F ALA 3.0 0.2 + - - -
313F ASN* 2.6 58.1 + - - +
319F TYR* 3.8 9.9 - - - +
322F LEU* 5.1 1.0 - - - +
360F PHE* 3.2 24.0 - - - -
410F VAL* 3.4 14.7 - - - +
411F ALA* 2.6 34.9 + - - +
417F ALA* 3.6 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F LYS 3.6 1.4 + - - -
307F ALA 3.1 10.8 + - - +
309F ASN* 1.3 78.2 - - - +
311F LEU* 1.3 59.6 + - + +
313F ASN 4.4 3.4 - - - -
314F PRO* 3.8 9.8 - - - +
414F LEU* 5.1 1.6 - - - -
417F ALA* 3.3 33.5 - - - +
418F LEU* 4.0 13.5 - - + +
421F LEU* 3.9 22.4 - - + -
442F TYR* 2.8 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F ALA 4.6 4.9 - - - +
308F ILE 2.8 15.1 + - - +
310F ALA* 1.3 84.8 - - + +
312F ALA* 1.3 56.4 + - - +
313F ASN 3.4 0.9 - - - -
314F PRO* 3.3 10.3 - - - +
365F ALA* 3.3 17.7 - - - +
366F ASN* 3.7 6.1 + - - +
369F LEU* 3.0 38.8 - - + +
370F CYS* 3.8 15.6 + - - +
373F ALA* 3.6 16.8 - - + -
421F LEU* 4.5 12.3 - - + -
428F LEU* 5.6 3.6 - - + -
434F PHE* 4.1 16.8 - - + -
442F TYR* 3.6 33.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F ILE* 2.9 16.0 + - + +
311F LEU* 1.3 75.6 - - - +
313F ASN* 1.3 78.2 + - - +
314F PRO* 3.7 4.0 - - - -
360F PHE* 4.5 3.4 - - + -
361F PRO* 3.5 18.6 - - + -
362F ASP* 2.9 22.9 + - - +
365F ALA* 3.5 10.7 - - - +
370F CYS* 3.1 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 313 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F ASN* 2.6 43.2 + - - +
312F ALA* 1.3 100.6 + - - +
314F PRO* 1.4 59.9 - - - +
315F THR 3.2 9.2 + - - -
318F SER* 3.5 16.2 - - - -
319F TYR* 2.9 34.2 + - + +
321F ARG* 4.1 0.3 + - - -
322F LEU* 3.8 13.7 - - - +
360F PHE* 2.9 27.3 - - - +
362F ASP* 3.3 12.5 - - - +
414F LEU* 3.6 2.4 - - - +
----------------------------------------------------------
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