Contacts of the helix formed by residues 320 - 338 (chain F) in PDB entry 4R8A
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 320 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F PRO* 3.3 4.5 + - - +
319F GLU* 1.3 87.4 + - - +
321F ASP* 1.3 65.8 + - - +
322F ALA* 3.4 12.8 + - - +
323F GLU* 3.1 21.4 + - - +
324F ARG* 3.1 25.1 + - - +
497F ASP* 5.6 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 321 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F SER* 1.3 73.5 - - - +
322F ALA* 1.3 62.2 + - - +
324F ARG* 3.4 24.9 + - + +
325F GLN* 3.4 25.5 + - - +
493F ARG* 4.8 11.2 + - - +
536F ARG* 4.0 17.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
292F LEU* 4.7 3.3 - - - +
320F SER* 3.4 11.6 - - - +
321F ASP* 1.3 80.0 - - - +
323F GLU* 1.3 60.2 + - - +
325F GLN* 3.2 19.3 + - - +
326F GLY* 3.3 7.6 + - - -
536F ARG* 3.6 33.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 323 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F ARG* 2.6 48.8 + - - -
292F LEU* 3.9 30.6 + - + +
314F ALA* 4.4 0.6 - - - +
318F PRO* 3.3 4.1 - - + +
319F GLU* 2.8 42.5 + - + +
320F SER* 3.1 21.4 + - - +
322F ALA* 1.3 74.1 - - - +
324F ARG* 1.3 60.5 + - - +
326F GLY* 3.2 0.9 + - - +
327F LEU* 2.8 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 324 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F SER 4.9 7.7 + - - -
316F CYS 5.7 0.4 + - - -
318F PRO* 3.3 37.8 - - + +
320F SER 3.1 15.2 + - - +
321F ASP* 3.5 29.4 + - + +
322F ALA 3.2 0.4 - - - -
323F GLU* 1.3 79.0 - - - +
325F GLN* 1.3 57.0 + - - +
327F LEU* 3.6 9.0 + - + +
328F ALA* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 325 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321F ASP 3.4 8.6 - - - +
322F ALA* 3.2 16.3 + - - +
324F ARG* 1.3 76.9 - - + +
326F GLY* 1.3 62.0 + - - +
328F ALA* 3.6 13.4 - - + +
329F ARG* 3.4 28.6 + - - +
532F ASP* 3.2 41.4 + - - +
535F LEU* 5.2 1.8 - - - +
536F ARG* 2.9 46.6 - - - +
539F GLN* 4.7 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 326 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F LEU* 4.0 24.0 - - - -
296F ARG* 4.0 4.7 + - - -
322F ALA 3.3 8.5 + - - -
323F GLU 3.2 6.1 + - - -
325F GLN* 1.3 76.4 - - - +
327F LEU* 1.3 62.7 + - - +
329F ARG* 3.3 20.3 + - - +
330F LEU* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F LEU* 4.0 8.7 - - + +
295F ILE* 3.9 18.2 - - + -
311F ALA* 3.6 28.5 - - + +
314F ALA* 3.8 15.0 - - + +
315F SER* 3.7 34.1 - - - +
318F PRO* 4.6 3.4 - - + -
323F GLU* 2.8 36.9 + - + +
324F ARG* 3.7 9.2 - - + +
326F GLY* 1.3 72.4 - - - +
328F ALA* 1.3 60.9 + - - +
330F LEU* 4.1 6.5 - - + -
331F LEU* 2.8 39.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
324F ARG 3.1 18.4 + - - +
325F GLN* 3.6 14.8 - - + +
326F GLY 3.2 0.8 - - - -
327F LEU* 1.3 76.2 - - - +
329F ARG* 1.3 59.3 + - - +
331F LEU* 5.4 0.4 - - - -
332F PRO* 3.2 13.0 - - - +
345F ARG* 3.2 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 329 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F ARG* 3.8 16.2 - - - +
325F GLN* 3.4 26.8 + - - +
326F GLY* 3.3 16.9 + - - +
327F LEU 3.1 0.2 - - - -
328F ALA* 1.3 81.5 - - + +
330F LEU* 1.3 64.5 + - - +
331F LEU 3.4 0.7 - - - -
332F PRO* 3.3 10.0 - - - +
333F ARG* 3.6 30.1 + - - +
345F ARG* 5.1 10.5 - - - +
532F ASP* 2.2 41.9 + - - -
535F LEU* 6.3 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F LEU* 3.7 34.1 - - + +
295F ILE* 3.8 32.1 - - + -
296F ARG* 3.9 24.9 - - + +
299F GLU* 3.7 17.0 - - - +
311F ALA* 5.6 0.2 - - + -
326F GLY 3.1 13.9 + - - +
327F LEU* 3.2 9.2 + - + +
329F ARG* 1.3 76.9 - - - +
331F LEU* 1.3 58.0 + - - +
333F ARG* 3.3 30.8 + - - +
334F LEU* 2.9 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F HIS* 4.1 19.1 - - + +
311F ALA* 4.1 25.6 - - + +
312F ARG* 4.8 9.9 - - + +
315F SER* 3.8 29.8 - - - +
327F LEU* 2.8 24.8 + - + +
328F ALA* 5.4 0.2 - - - -
330F LEU* 1.3 73.6 - - - +
332F PRO* 1.3 61.3 - - + +
334F LEU* 3.1 4.8 + - + +
335F GLN* 2.8 55.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 332 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328F ALA* 3.2 27.4 - - - +
329F ARG* 3.3 9.6 - - - +
331F LEU* 1.3 93.0 - - + +
333F ARG* 1.3 59.8 + - - +
335F GLN* 3.3 15.1 + - - +
336F GLY 3.0 17.8 + - - -
342F ARG* 3.1 40.8 + - + +
343F GLN 5.8 4.0 - - - +
345F ARG* 4.2 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F ARG* 4.2 13.5 - - - +
299F GLU* 2.6 30.2 + - - +
329F ARG* 3.6 33.7 + - - +
330F LEU* 3.3 34.8 - - - +
331F LEU 3.2 0.4 - - - -
332F PRO* 1.3 80.3 - - - +
334F LEU* 1.3 62.5 + - - +
336F GLY* 3.3 2.4 + - - -
337F LYS* 3.2 26.2 + - + +
342F ARG* 3.8 18.2 + - - +
11G T 6.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F ILE* 3.8 18.8 - - + -
299F GLU* 4.5 11.9 - - + +
304F PHE* 3.7 31.0 - - + +
307F ALA* 3.5 45.1 - - + +
308F HIS* 4.1 12.1 - - + +
311F ALA* 3.9 12.8 - - + -
330F LEU* 2.9 28.0 + - + +
331F LEU* 3.5 4.7 - - - +
333F ARG* 1.3 74.6 - - - +
335F GLN* 1.3 64.7 + - - +
336F GLY 3.1 1.8 - - - -
337F LYS* 3.2 5.0 + - - +
338F LEU* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 335 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F HIS* 4.1 22.1 + - + +
331F LEU* 2.8 39.0 + - - +
332F PRO* 3.3 21.3 + - - +
334F LEU* 1.3 75.9 - - - +
336F GLY* 1.3 58.5 + - - +
338F LEU* 3.0 16.4 - - - +
340F LEU* 2.8 43.3 + - + +
341F PRO 4.4 7.6 - - - +
342F ARG* 4.0 13.6 - - + -
343F GLN* 3.5 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332F PRO 3.0 13.1 + - - -
333F ARG 3.3 4.7 + - - -
334F LEU 3.1 0.4 - - - -
335F GLN* 1.3 77.3 - - - +
337F LYS* 1.3 57.3 + - - +
338F LEU 2.7 15.0 - - - +
340F LEU 4.3 4.7 - - - +
342F ARG* 4.5 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 337 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F GLU* 6.0 1.3 - - - +
304F PHE* 3.5 57.1 - - + -
333F ARG* 3.2 18.1 + - + +
334F LEU* 3.2 6.5 + - - +
336F GLY* 1.3 75.7 - - - +
338F LEU* 1.3 64.5 + - - +
12G C 3.1 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304F PHE* 3.8 25.1 - - + -
305F ALA* 4.0 20.9 - - + +
308F HIS* 3.8 37.0 - - + +
334F LEU 3.1 12.8 + - - +
335F GLN 3.0 6.9 - - - +
336F GLY 2.7 18.0 - - - +
337F LYS* 1.3 80.5 - - - +
339F GLY* 1.3 62.9 + - - +
340F LEU* 3.2 24.1 - - + +
----------------------------------------------------------
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