Contacts of the helix formed by residues 302 - 328 (chain F) in PDB entry 6M04
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 302 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300F ASP* 3.9 12.9 - - + +
301F SER* 1.3 79.7 - - - +
303F LEU* 1.3 75.9 + - + +
306F LYS* 2.8 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186F TYR* 5.7 1.3 - - - +
188F LYS* 5.2 15.7 - - + +
189F THR* 4.0 32.5 - - + +
192F LYS* 4.4 15.9 - - + +
300F ASP* 6.0 0.2 - - - +
302F ASP* 1.3 90.8 - - + +
304F ILE* 1.3 60.8 + - - +
306F LYS* 4.7 0.9 - - - -
307F LEU* 2.9 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F TRP* 4.0 22.1 + - + +
189F THR* 5.8 2.5 - - - -
192F LYS* 6.3 3.1 - - + -
193F VAL* 6.1 4.7 - - + -
300F ASP 5.2 7.2 - - - +
301F SER* 5.3 3.4 - - - -
303F LEU* 1.3 78.6 - - - +
305F TYR* 1.3 61.9 + - + +
307F LEU* 3.4 6.3 + - - +
308F TYR* 3.0 28.4 + - + +
417F ALA* 5.1 8.3 - - + -
418F PHE* 4.9 18.6 - - + +
419F LEU* 3.7 46.2 - - + +
422F MET* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 305 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301F SER* 3.2 33.1 + - - +
302F ASP 3.9 0.6 + - - -
303F LEU 3.4 0.2 - - - -
304F ILE* 1.3 83.3 - - + +
306F LYS* 1.3 66.3 + - + +
308F TYR* 3.3 16.3 + + - +
309F VAL* 3.0 50.8 + - + +
387F LEU 6.1 0.2 - - - -
388F PHE* 3.2 37.0 + + - -
392F LEU* 5.2 5.8 - - - -
393F LYS* 4.4 18.6 - - + -
418F PHE* 4.4 35.0 - + + -
----------------------------------------------------------
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
----------------------------------------------------------
302F ASP* 2.8 24.9 + - - +
303F LEU* 4.0 2.0 - - - +
305F TYR* 1.3 86.4 - - + +
307F LEU* 1.3 62.4 + - + +
309F VAL* 3.3 18.3 + - + +
310F VAL* 2.9 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F PHE* 5.3 4.3 - - + +
183F TRP* 3.3 40.4 - - + +
186F TYR* 3.3 37.0 - - + +
189F THR* 4.5 14.1 - - + +
303F LEU* 2.9 34.7 + - + +
304F ILE* 3.8 3.6 - - - +
306F LYS* 1.3 80.1 - - + +
308F TYR* 1.3 60.1 + - - +
310F VAL* 3.3 14.3 - - + +
311F GLN* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 308 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TRP* 4.6 14.3 - + - -
183F TRP* 3.3 21.0 - + + +
304F ILE* 3.0 15.1 + - + +
305F TYR* 3.4 19.1 - + + +
307F LEU* 1.3 77.3 - - - +
309F VAL* 1.3 71.0 + - + +
311F GLN* 3.3 8.3 + - + +
312F THR* 3.1 27.8 + - - -
384F LEU* 3.4 35.7 + - + +
387F LEU* 3.3 45.1 - - + +
388F PHE* 4.4 13.5 - + + -
418F PHE* 4.5 22.4 - + + -
422F MET* 6.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F TYR* 3.0 48.1 + - + +
306F LYS* 3.3 21.1 + - + +
307F LEU 3.3 0.2 - - - -
308F TYR* 1.3 80.0 - - + +
310F VAL* 1.3 60.2 + - - +
312F THR* 3.2 8.0 + - - +
313F VAL* 2.9 38.8 + - + +
388F PHE* 4.3 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 310 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F PHE* 3.7 30.1 - - + -
306F LYS* 2.9 20.3 + - + +
307F LEU* 3.3 24.0 - - + +
309F VAL* 1.3 74.7 - - - +
311F GLN* 1.3 60.2 + - - +
313F VAL* 3.7 13.7 - - + -
314F ILE* 2.9 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F ASP* 5.7 0.9 - - - +
179F SER 2.7 30.3 + - - +
180F SER* 4.2 7.8 + - - +
182F PHE* 3.2 19.3 - - + +
183F TRP* 3.3 45.7 - - + +
307F LEU 2.9 17.6 + - - +
308F TYR* 3.3 12.1 + - + +
310F VAL* 1.3 76.6 - - - +
312F THR* 1.3 56.4 + - - +
314F ILE* 3.3 6.4 - - - +
315F LYS* 3.0 28.1 + - - +
384F LEU* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 312 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F TYR* 3.1 18.9 + - - -
309F VAL* 3.6 10.0 - - - -
311F GLN* 1.3 76.8 - - - +
313F VAL* 1.3 62.3 + - + +
315F LYS* 3.2 13.6 - - - +
316F THR* 2.9 35.4 + - - +
380F CYS* 5.8 0.2 - - - -
381F LEU* 6.2 0.2 - - - -
384F LEU* 3.3 49.6 + - + +
385F PHE* 5.0 4.7 - - + +
388F PHE* 6.0 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F VAL* 2.9 33.5 + - + +
310F VAL* 3.5 20.2 - - + +
312F THR* 1.3 83.3 - - + +
314F ILE* 1.3 62.3 + - - +
316F THR* 3.9 7.8 - - - +
317F ALA* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 314 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175F ILE* 6.1 4.7 - - + -
176F LEU* 5.4 0.7 - - - +
179F SER* 3.7 35.3 + - - +
182F PHE* 3.8 27.6 - - + -
310F VAL* 2.9 25.4 + - + +
311F GLN* 3.3 14.1 - - - +
313F VAL* 1.3 75.5 - - + +
315F LYS* 1.3 67.9 + - - +
317F ALA* 4.5 4.4 - - + +
318F LYS* 3.7 18.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 315 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176F LEU* 5.6 5.3 - - - +
179F SER* 5.9 0.4 - - - -
311F GLN 3.0 14.8 + - - +
312F THR* 3.2 16.3 - - - +
314F ILE* 1.3 78.6 - - - +
316F THR* 1.3 84.7 + - - +
318F LYS* 3.3 5.1 + - - +
319F PHE* 2.9 40.4 + - + +
376F TYR* 4.4 22.9 - - + +
377F GLY* 4.2 7.9 + - - -
380F CYS* 3.5 44.4 - - + -
381F LEU* 3.4 36.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 316 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F THR* 2.9 21.4 + - - +
313F VAL* 3.1 9.4 + - - +
315F LYS* 1.3 102.0 + - - +
317F ALA* 1.3 57.7 + - - +
319F PHE* 3.6 4.0 - - + +
320F ILE* 2.9 43.3 + - + +
381F LEU* 5.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 317 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F VAL 2.9 16.6 + - - +
314F ILE* 5.0 4.0 - - + -
316F THR* 1.3 77.5 - - - +
318F LYS* 1.3 57.6 + - - +
320F ILE* 4.1 2.0 - - - +
321F PHE* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 318 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F HIS* 4.2 19.7 - - + +
175F ILE* 5.2 13.2 - - + -
176F LEU* 5.3 6.7 - - + -
314F ILE* 3.7 18.0 + - + +
315F LYS* 3.3 3.4 + - - +
317F ALA* 1.3 78.4 - - - +
319F PHE* 1.3 58.7 + - - +
321F PHE* 4.2 6.3 - - - -
322F ILE* 3.0 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 319 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F HIS* 5.6 0.9 - - - -
315F LYS* 2.9 29.2 + - + +
316F THR* 3.6 9.6 - - + +
318F LYS* 1.3 77.6 - - - +
320F ILE* 1.3 83.0 + - + +
322F ILE* 3.7 6.0 - - - +
323F LEU* 2.9 58.9 + - + +
373F ILE* 3.3 35.7 - - + -
374F CYS* 4.3 6.1 - - - -
376F TYR* 4.8 7.4 - + + -
377F GLY* 3.5 33.4 - - - -
378F PHE 4.5 1.1 - - - -
381F LEU* 5.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 320 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F THR* 2.9 28.2 + - + +
317F ALA* 4.3 2.2 - - - +
319F PHE* 1.3 100.5 - - + +
321F PHE* 1.3 62.7 + - - +
323F LEU* 3.9 8.9 - - + +
324F CYS* 3.0 28.4 + - + +
381F LEU* 6.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 321 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317F ALA 2.9 22.7 + - - +
318F LYS* 3.7 6.1 - - - +
320F ILE* 1.3 78.2 - - - +
322F ILE* 1.3 74.0 + - + +
324F CYS* 4.0 2.6 - - - +
325F TYR* 3.0 51.3 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 322 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F LEU* 5.8 6.5 - - + -
172F HIS* 3.3 52.9 - - + +
318F LYS* 3.0 22.4 + - + +
319F PHE* 3.7 5.2 - - - +
321F PHE* 1.3 90.8 - - + +
323F LEU* 1.3 55.0 + - - +
325F TYR* 4.0 9.0 - - + -
326F THR* 2.4 45.9 + - + +
369F TYR* 4.0 16.2 - - + +
370F ILE* 6.2 0.7 - - + -
373F ILE* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F PHE* 2.9 53.1 + - + +
320F ILE* 3.9 10.3 - - + +
321F PHE 3.2 0.2 - - - -
322F ILE* 1.3 78.4 - - + +
324F CYS* 1.3 59.8 + - - +
326F THR* 3.5 4.9 + - - -
327F ALA* 2.7 38.1 + - + +
370F ILE* 5.6 14.4 - - + +
373F ILE* 5.5 4.3 - - + -
374F CYS* 4.8 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 324 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F ILE* 3.0 21.1 + - + +
321F PHE* 4.1 2.2 - - - +
323F LEU* 1.3 79.8 - - + +
325F TYR* 1.3 57.2 + - - +
327F ALA* 3.5 5.9 - - - +
328F ASN* 2.9 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 325 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F TRP* 5.0 6.8 + - - -
165F PHE* 5.7 2.0 - + - -
168F LEU* 3.7 41.0 - - + +
321F PHE* 3.0 39.7 + + + +
322F ILE* 3.8 9.4 - - + +
324F CYS* 1.3 76.7 - - - +
326F THR* 1.3 68.1 + - + +
328F ASN* 2.8 21.7 - - - +
329F PHE* 3.0 46.0 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F PHE* 3.8 32.1 - - + -
168F LEU* 5.2 4.5 - - + -
322F ILE* 2.4 39.5 + - + +
323F LEU* 3.5 2.8 + - - -
325F TYR* 1.3 81.7 - - + +
327F ALA* 1.3 57.1 + - - +
329F PHE* 3.1 10.2 + - - +
330F VAL* 2.9 30.8 + - - +
366F LEU* 4.9 5.2 - - - +
369F TYR* 4.4 13.2 - - + +
370F ILE* 3.2 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323F LEU* 2.7 32.4 + - + +
324F CYS* 3.5 7.6 - - - +
325F TYR 3.2 0.4 - - - -
326F THR* 1.3 76.8 + - - +
328F ASN* 1.3 58.6 + - - +
330F VAL* 3.1 30.1 + - - +
331F ASN 4.6 1.0 + - - -
370F ILE* 6.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 328 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324F CYS* 2.9 25.0 + - - +
325F TYR* 2.8 30.5 - - - +
327F ALA* 1.3 76.1 - - - +
329F PHE* 1.3 70.5 + - - +
330F VAL 3.5 0.7 - - - -
331F ASN 5.3 0.9 - - - -
332F ALA* 4.6 8.3 + - - +
----------------------------------------------------------
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