Contacts of the helix formed by residues 316 - 328 (chain F) in PDB entry 4E2I
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 TYR 316 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F TYR* 3.7 31.6 - + + -
279F GLU* 3.5 50.4 + - + +
280F THR* 4.6 6.2 - - + +
295F PHE* 4.6 3.7 - - + -
311F PRO 3.3 23.1 - - - -
312F SER* 3.9 17.3 - - - +
313F HIS 3.1 4.6 + - - +
315F LYS* 1.3 102.6 + - + +
317F HIS* 1.3 64.8 + - - +
318F GLU 3.5 1.6 - - - -
319F LYS* 3.3 25.0 + - + -
320F HIS* 3.0 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 317 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F GLU 3.7 17.3 - - - -
295F PHE* 3.3 40.3 - + + -
298F SER 3.6 9.0 - - - -
299F PHE* 3.4 29.9 + - + +
302F CYS* 3.9 4.7 - - - -
305F CYS* 5.4 0.9 - - - -
313F HIS* 2.9 15.7 + - - +
314F TYR* 4.5 3.5 - - - -
315F LYS 3.9 0.2 - - - -
316F TYR* 1.3 77.8 - - - +
318F GLU* 1.3 57.4 + - + +
319F LYS 3.0 0.6 + - - -
320F HIS 3.1 1.0 + - - -
321F TYR* 2.6 62.1 + - + +
700F ZN 2.7 28.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F PHE* 3.6 51.2 - - + -
305F CYS* 5.1 6.2 - - - -
314F TYR 4.8 10.5 + - - +
315F LYS 5.6 0.4 - - - -
316F TYR 3.5 0.2 - - - -
317F HIS* 1.3 76.7 - - + +
319F LYS* 1.3 60.0 + - - +
321F TYR* 4.1 6.0 + - - +
322F ALA 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 319 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F LEU* 4.9 9.2 - - + +
275F GLU* 3.2 37.3 + - - -
279F GLU* 5.5 5.4 - - - -
315F LYS 4.8 4.2 + - - +
316F TYR* 3.3 32.0 + - + +
317F HIS 3.0 0.8 - - - -
318F GLU* 1.3 80.9 - - - +
320F HIS* 1.3 78.4 + - + +
321F TYR 3.6 0.4 - - - -
322F ALA* 5.3 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 320 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F LEU* 3.2 34.8 + - + +
275F GLU* 3.9 17.9 - - - -
276F TYR* 3.2 40.9 - + + +
279F GLU* 5.6 0.2 - - - +
292F TYR* 3.4 28.0 + + + +
295F PHE* 4.6 6.5 - + + -
316F TYR* 3.0 26.4 + - + +
317F HIS 3.4 1.6 - - - -
319F LYS* 1.3 100.6 + - + +
321F TYR* 1.3 58.9 + - - +
322F ALA* 3.3 3.1 - - - +
323F ASN* 3.6 4.9 + - - +
324F ALA* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 321 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F PHE 3.2 21.1 - - - -
296F GLN* 4.6 1.8 - - - -
297F TYR 2.9 36.2 + - - -
298F SER* 3.8 11.7 - - - -
299F PHE* 3.5 28.0 - + + -
300F GLU* 4.3 7.9 + - - -
317F HIS* 2.6 33.5 + - + +
318F GLU* 4.1 5.8 + - - +
319F LYS 3.6 1.6 - - - -
320F HIS* 1.3 74.4 - - - +
322F ALA* 1.3 64.9 + - - +
325F ALA* 3.2 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F LEU* 5.8 3.4 - - + -
318F GLU 5.3 0.6 + - - -
319F LYS 5.8 2.2 - - - +
320F HIS* 3.3 1.0 - - - -
321F TYR* 1.3 85.4 - - - +
323F ASN* 1.3 62.1 + - - +
325F ALA* 3.5 14.0 - - - +
326F ILE* 3.9 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 323 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267F GLN 4.8 0.3 - - - +
268F VAL* 3.5 9.2 - - - +
269F SER* 2.6 51.0 + - - -
272F LEU* 3.5 22.3 - - + +
273F VAL* 3.2 12.7 - - - +
292F TYR* 2.8 28.3 + - - +
320F HIS* 3.6 4.2 + - - +
321F TYR 3.4 0.2 - - - -
322F ALA* 1.3 75.1 - - - +
324F ALA* 1.3 54.9 + - - +
325F ALA 3.0 1.8 - - - -
326F ILE* 3.0 8.6 + - - +
327F PHE* 2.8 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F TYR* 3.9 20.1 + - + +
295F PHE* 3.1 36.8 - - + +
296F GLN* 3.2 19.8 - - + +
320F HIS 3.0 20.0 + - - +
323F ASN* 1.3 78.2 - - - +
325F ALA* 1.3 60.1 + - - +
327F PHE* 3.2 19.5 + - - +
328F ALA 3.3 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 325 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F PHE 4.2 0.6 + - - -
296F GLN* 4.3 12.7 - - - +
321F TYR* 3.2 29.6 + - + +
322F ALA* 3.5 10.3 - - - +
323F ASN 3.0 0.6 - - - -
324F ALA* 1.3 77.8 - - - +
326F ILE* 1.3 62.1 + - + +
328F ALA* 4.1 5.9 - - - +
329F ASP* 4.0 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F LYS* 4.3 17.5 - - + -
267F GLN* 3.7 28.3 - - - +
268F VAL* 3.5 23.3 - - + +
322F ALA 3.9 15.0 - - - +
323F ASN* 3.0 9.0 + - - +
325F ALA* 1.3 76.1 - - + +
327F PHE* 1.3 67.5 + - - +
328F ALA 3.1 2.7 - - - -
329F ASP* 3.0 22.5 + - + +
330F SER 3.5 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 327 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F VAL* 3.9 9.2 - - + +
273F VAL* 4.8 2.2 - - + -
289F LEU* 3.7 10.8 - - + -
292F TYR* 3.7 30.7 - + + -
293F LEU* 3.5 33.0 - - + -
323F ASN* 2.8 16.0 + - - +
324F ALA* 3.2 16.6 + - - +
326F ILE* 1.3 77.8 - - - +
328F ALA* 1.3 61.7 + - - +
330F SER* 3.1 17.2 - - - -
333F GLN* 3.3 41.6 - - + +
336F ILE* 3.5 44.2 - - + -
337F CYS* 3.5 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 328 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E TRP* 5.9 1.7 - - - +
271E LYS* 4.6 23.2 + - + +
339E GLN* 5.6 0.2 - - - +
293F LEU* 4.9 0.2 - - - -
296F GLN* 3.2 47.5 + - + +
324F ALA 3.3 2.0 + - - -
325F ALA 4.1 6.1 - - - +
327F PHE* 1.3 80.2 - - - +
329F ASP* 1.3 67.6 + - - +
330F SER 3.1 3.5 + - - +
333F GLN* 3.0 19.7 - - - +
----------------------------------------------------------
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