Contacts of the helix formed by residues 430 - 443 (chain F) in PDB entry 1I43
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 ASP 430 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F GLN* 4.6 5.6 + - - +
429F GLU* 1.3 74.2 - - - +
431F PHE* 1.3 68.8 + - - +
432F ASP* 4.5 14.6 + - + +
433F ASP* 3.1 10.5 + - + +
434F LEU* 3.0 20.5 + - - +
56G SER* 2.8 41.8 + - - +
58G GLY* 4.7 5.9 + - - -
59G SER* 3.1 10.7 + - - +
311G HIS* 4.8 6.3 + - - +
315G GLN* 5.4 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 431 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F GLN* 4.7 5.5 - - - +
320F THR* 3.9 28.0 - - + +
323F ARG* 3.0 61.2 - - + +
324F MET* 3.4 30.5 - - + -
327F ILE* 4.0 12.6 - - + -
429F GLU 3.5 3.8 + - - -
430F ASP* 1.3 72.9 - - - +
432F ASP* 1.3 68.7 + - - +
434F LEU* 2.9 8.5 + - - +
435F LYS* 2.6 62.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 432 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430F ASP* 3.4 14.2 + - + +
431F PHE* 1.3 91.9 - - - +
433F ASP* 1.3 59.7 + - - +
435F LYS* 3.9 15.1 + - - +
436F ALA* 2.9 33.1 + - - +
56G SER* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 433 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F ILE* 3.3 18.8 - - + +
429F GLU* 5.4 0.2 - - + -
430F ASP* 3.1 9.9 + - - +
432F ASP* 1.3 80.6 - - - +
434F LEU* 1.3 63.3 + - + +
436F ALA* 3.8 4.5 - - - +
437F ASP* 3.2 16.3 + - - +
53G PHE 3.2 12.3 - - - +
54G LEU* 3.9 1.3 - - - -
55G ASN* 2.8 40.2 + - - +
56G SER* 2.9 27.3 + - - -
59G SER* 2.6 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F THR* 3.8 27.4 - - + +
324F MET* 5.6 0.7 - - + -
382F ILE* 3.9 21.1 - - + -
383F PRO* 5.3 0.7 - - + -
394F SER* 3.3 28.7 - - - +
424F PHE* 4.6 14.1 - - + -
426F PHE* 4.5 10.1 - - + -
427F GLY 4.9 4.7 - - - +
429F GLU* 3.6 39.7 - - + +
430F ASP 3.0 8.7 + - - +
431F PHE* 2.9 6.4 + - + +
433F ASP* 1.3 75.1 - - - +
435F LYS* 1.3 66.6 + - - +
437F ASP* 2.9 14.7 + - + +
438F ILE* 2.9 19.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 435 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324F MET* 3.7 26.3 - - - +
327F ILE* 3.7 26.1 - - + +
431F PHE* 2.6 38.3 + - + +
432F ASP* 3.9 12.5 + - - +
434F LEU* 1.3 71.3 - - - +
436F ALA* 1.3 66.4 + - - +
437F ASP 3.1 0.3 + - - -
438F ILE* 3.1 3.8 + - - +
439F LEU* 2.9 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432F ASP 2.9 20.2 + - - +
433F ASP* 3.8 5.8 - - - +
435F LYS* 1.3 80.7 - - - +
437F ASP* 1.3 57.3 + - - +
439F LEU* 3.5 7.1 + - - +
440F GLN* 2.9 32.2 + - - +
53G PHE 6.1 0.4 - - - +
55G ASN* 6.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 437 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380F LEU* 3.8 7.3 - - - +
381F LYS* 3.1 38.1 + - - +
382F ILE* 3.1 25.6 + - + +
383F PRO* 3.3 13.0 - - - +
424F PHE* 5.8 0.3 - - - -
433F ASP 3.2 11.2 + - - +
434F LEU* 2.9 11.0 + - + +
436F ALA* 1.3 75.9 - - - +
438F ILE* 1.3 67.6 + - + +
440F GLN* 2.9 35.7 - - - +
441F ALA* 2.9 12.1 + - - +
53G PHE* 5.4 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 438 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324F MET* 3.4 29.6 - - + -
328F LEU* 4.0 27.8 - - + -
364F PHE* 5.4 1.1 - - + -
376F PHE* 3.7 17.8 - - + -
380F LEU* 3.9 9.6 - - + -
424F PHE* 3.9 25.4 - - + -
426F PHE* 3.4 29.8 - - + -
434F LEU* 2.9 17.6 + - + +
435F LYS 3.7 5.6 - - - +
437F ASP* 1.3 76.6 - - + +
439F LEU* 1.3 66.2 + - + +
441F ALA* 3.4 2.8 + - - +
442F LEU* 3.1 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324F MET* 5.8 1.3 - - + -
327F ILE* 4.3 20.0 - - + -
328F LEU* 6.2 1.3 - - + -
331F HIS* 4.1 26.2 + - + +
435F LYS* 2.9 45.3 + - + +
436F ALA* 3.8 6.7 - - - +
438F ILE* 1.3 78.6 - - + +
440F GLN* 1.3 66.6 + - - +
441F ALA 3.0 1.3 - - - -
442F LEU* 3.0 16.7 + - + +
443F ASP* 3.2 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 440 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379F ALA* 3.7 20.4 + - - +
381F LYS* 3.9 24.5 - - - +
436F ALA 2.9 17.7 + - - +
437F ASP* 2.9 33.2 - - - +
439F LEU* 1.3 75.6 - - - +
441F ALA* 1.3 66.1 + - - +
443F ASP* 3.5 22.6 + - - +
444F SER* 3.7 8.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 441 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376F PHE* 3.5 23.1 - - + -
379F ALA* 3.8 23.2 - - + +
380F LEU* 3.5 26.5 - - + +
437F ASP 2.9 17.8 + - - +
438F ILE 3.5 0.4 - - - +
439F LEU 3.0 0.2 + - - -
440F GLN* 1.3 80.9 + - - +
442F LEU* 1.3 61.6 + - - +
443F ASP 3.1 2.0 - - - -
444F SER* 3.2 18.1 + - - -
445F ILE* 4.6 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 442 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328F LEU* 4.3 13.2 - - + -
331F HIS* 3.7 43.1 - - + +
333F LYS* 3.2 35.8 + - + +
334F VAL* 3.8 15.9 - - + -
364F PHE* 5.9 0.2 - - + -
366F VAL* 4.5 12.3 - - + -
376F PHE* 3.8 22.0 - - + -
438F ILE* 3.1 11.1 + - + +
439F LEU* 3.0 11.0 + - + +
441F ALA* 1.3 76.0 - - - +
443F ASP* 1.3 60.2 + - - +
444F SER 3.2 0.4 - - - -
445F ILE* 3.4 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 443 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F HIS* 4.8 7.1 + - - -
333F LYS* 3.8 14.9 + - - +
439F LEU* 3.2 17.0 - - - +
440F GLN* 3.6 15.9 - - - +
441F ALA 3.1 0.6 - - - -
442F LEU* 1.3 78.4 - - - +
444F SER* 1.3 56.7 + - - +
445F ILE 3.1 9.5 + - - -
----------------------------------------------------------
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