Contacts of the helix formed by residues 413 - 424 (chain L) 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 413 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415F GLU* 6.0 2.0 - - - -
454F ARG* 6.5 0.4 - - - -
319L TYR* 3.6 20.4 - - - -
411L ALA* 3.3 3.6 + - - +
412L GLY* 1.3 80.5 - - - +
414L LEU* 1.3 65.4 + - - +
415L GLU* 3.8 8.7 + - - +
416L GLU* 3.3 23.6 + - - +
417L ALA 3.2 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 414 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465F TYR* 4.5 4.3 - - - +
310L ALA* 5.0 2.2 - - - +
313L ASN 4.0 11.0 - - - +
314L PRO* 3.8 35.2 - - + +
315L THR* 4.4 0.4 - - - -
316L THR* 4.0 28.0 - - + +
319L TYR* 3.3 18.7 - - + +
413L SER* 1.3 72.2 - - - +
415L GLU* 1.3 56.4 + - - +
417L ALA* 2.9 5.9 + - + +
418L LEU* 2.7 58.9 + - + +
446L ARG* 4.0 23.1 - - + +
450L ASP* 4.0 14.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 415 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412F GLY 5.8 0.5 - - - +
413F SER* 6.0 2.3 - - - -
413L SER* 3.8 9.2 + - - +
414L LEU* 1.3 77.8 - - - +
416L GLU* 1.3 57.5 + - - +
418L LEU* 3.6 7.4 + - - -
419L ASN* 3.0 31.0 + - - +
447L ARG* 3.5 17.4 + - - +
450L ASP* 3.8 20.0 + - - +
454L ARG* 3.9 22.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 416 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306L LYS* 3.1 32.8 + - + +
411L ALA* 3.8 7.0 - - + -
412L GLY* 2.8 31.0 + - - -
413L SER* 3.3 17.8 + - - +
414L LEU 3.1 0.4 - - - -
415L GLU* 1.3 79.8 - - - +
417L ALA* 1.3 58.9 + - - +
419L ASN* 3.3 7.7 - - + +
420L ALA* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 417 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306L LYS 3.5 13.0 - - - +
309L ASN* 3.8 4.0 - - + -
310L ALA* 3.5 31.9 - - - +
319L TYR* 3.3 26.0 - - - +
411L ALA* 3.8 4.7 - - + +
413L SER 3.2 6.8 + - - +
414L LEU* 2.9 9.5 + - + +
416L GLU* 1.3 73.8 - - - +
418L LEU* 1.3 67.2 + - - +
420L ALA* 3.3 3.0 + - - +
421L LEU 2.9 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310L ALA* 4.1 17.7 - - + -
414L LEU* 2.7 38.0 + - + +
415L GLU* 3.8 7.6 - - - +
417L ALA* 1.3 76.4 - - - +
419L ASN* 1.3 62.8 + - - +
421L LEU* 3.2 4.3 + - - +
422L ASP* 2.9 22.4 + - - +
442L TYR* 4.6 3.6 - - + -
443L ILE* 3.9 25.6 - - + +
446L ARG* 4.0 24.0 - - + +
447L ARG* 3.8 54.3 - - + +
450L ASP* 5.2 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 419 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415L GLU* 3.0 21.3 + - - +
416L GLU* 3.3 13.2 - - + +
418L LEU* 1.3 76.1 - - - +
420L ALA* 1.3 64.2 + - - +
422L ASP* 2.9 25.7 + - - +
423L LEU* 3.1 33.0 + - + +
447L ARG* 3.9 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 420 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306L LYS* 3.5 41.1 - - + -
307L ALA* 3.6 4.3 - - + +
416L GLU 3.0 11.2 + - - +
417L ALA 3.5 4.9 - - - +
419L ASN* 1.3 79.1 - - - +
421L LEU* 1.3 55.7 + - - +
423L LEU* 5.0 4.7 - - - -
424L ASP* 2.7 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307L ALA* 3.8 19.2 - - + +
310L ALA* 3.8 21.3 - - + -
311L LEU* 4.3 11.2 - - + -
417L ALA 2.9 15.5 + - - +
418L LEU 3.5 6.7 - - - +
420L ALA* 1.3 76.0 - - - +
422L ASP* 1.3 66.7 + - - +
425L ARG* 3.3 21.1 + - - +
428L LEU* 3.5 31.6 - - + -
434L PHE* 6.5 0.4 - - + -
439L ILE* 4.1 20.8 - - + +
442L TYR* 4.1 16.4 - - + -
443L ILE* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 422 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418L LEU 2.9 13.1 + - - +
419L ASN* 2.9 17.9 + - - +
421L LEU* 1.3 76.3 - - - +
423L LEU* 1.3 74.0 + - + +
425L ARG* 2.7 59.2 + - - +
443L ILE* 3.9 11.4 - - + -
447L ARG* 5.0 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419L ASN* 3.1 30.2 + - - +
420L ALA* 4.0 3.6 - - - +
422L ASP* 1.3 89.5 - - - +
424L ASP* 1.3 58.2 + - + +
425L ARG* 2.9 14.4 + - - +
426L GLU* 4.7 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 424 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303L LYS 4.1 3.7 - - - +
304L HIS* 2.7 53.0 + - - +
307L ALA* 3.8 10.9 + - + +
420L ALA* 2.7 23.4 + - + +
421L LEU 3.9 3.8 - - - -
423L LEU* 1.3 70.7 - - + +
425L ARG* 1.3 56.4 + - - +
426L GLU* 3.5 2.6 + - - +
427L PHE* 3.0 22.4 + - - -
----------------------------------------------------------
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