Contacts of the helix formed by residues 384 - 398 (chain C) in PDB entry 4AY6
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 PHE 384 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C ALA* 4.5 11.4 - - + -
352C ALA* 4.5 11.7 - - + -
355C SER* 3.5 36.8 - - - -
377C ALA* 4.5 9.9 - - + +
378C ILE* 4.1 2.6 - - + +
381C SER* 3.0 33.1 + - - +
382C PRO 3.3 1.2 - - - -
383C THR* 1.3 71.0 + - - +
385C ALA* 1.3 65.0 + - - +
386C ASP* 3.2 31.6 - - + -
387C ALA* 3.3 23.1 + - + +
388C TYR* 3.4 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C THR 2.6 13.4 + - - +
384C PHE* 1.3 74.0 - - - +
386C ASP* 1.3 62.4 - - - +
388C TYR* 3.3 21.2 + - - +
389C SER 3.3 9.9 + - - -
411C ALA* 3.9 11.5 - - - +
414C ILE* 4.6 4.9 - - + -
415C ASN* 3.9 26.5 - - + +
418C PHE* 3.5 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C SER* 5.0 2.9 + - - -
384C PHE* 3.2 23.5 - - + -
385C ALA* 1.3 78.5 - - - +
387C ALA* 1.3 59.6 + - - +
389C SER* 3.6 3.3 - - - -
390C ASN* 2.8 48.4 + - - -
418C PHE* 3.2 30.3 - - + -
420C ASP* 4.4 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C SER* 4.3 11.0 - - - +
374C TYR* 4.1 11.3 - - + +
377C ALA* 4.5 9.4 - - + -
378C ILE* 3.4 23.7 - - + +
384C PHE* 3.3 26.9 + - + +
385C ALA 3.2 0.8 - - - -
386C ASP* 1.3 76.9 - - - +
388C TYR* 1.3 66.8 + - - +
390C ASN* 3.4 5.6 + - - +
391C MET* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C ILE* 3.3 40.2 - - + +
382C PRO* 3.8 16.3 + - - +
384C PHE 3.4 22.3 + - - -
385C ALA* 3.3 9.5 + - - +
387C ALA* 1.3 79.0 - - - +
389C SER* 1.3 62.7 + - - +
391C MET* 3.3 16.0 + - + +
392C GLY 3.0 18.5 + - - -
407C CYS* 3.3 21.4 - - - +
410C ARG* 3.8 38.1 - - + +
411C ALA* 3.5 16.6 - - + -
414C ILE* 3.7 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C ALA 3.3 1.8 + - - -
386C ASP 3.6 9.4 - - - -
388C TYR* 1.3 78.8 - - - +
390C ASN* 1.3 65.6 + - - +
392C GLY 3.2 0.5 + - - -
393C ASN* 3.2 3.8 + - - -
408C TYR* 3.2 31.8 - - - -
411C ALA* 4.2 4.2 - - - +
418C PHE* 3.6 24.9 - - - -
420C ASP* 4.0 12.8 - - - +
421C ALA* 4.1 7.4 + - - -
424C ASN* 2.7 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C SER* 5.1 2.6 + - - -
359C SER* 5.7 3.0 - - - -
362C GLN* 3.9 3.7 - - - +
374C TYR* 3.3 32.8 + - + +
386C ASP* 2.8 41.1 + - - +
387C ALA* 4.0 2.4 - - - +
388C TYR 3.4 0.2 - - - -
389C SER* 1.3 75.1 + - - +
391C MET* 1.3 59.5 + - - +
393C ASN* 2.8 38.1 + - - +
394C THR* 3.0 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C LEU* 3.9 19.3 - - + -
374C TYR* 4.0 28.1 - - + +
375C LYS* 4.0 32.5 - - + -
378C ILE* 4.7 11.2 - - + -
387C ALA 3.0 18.4 + - - +
388C TYR* 3.6 20.2 - - + +
390C ASN* 1.3 71.7 - - - +
392C GLY* 1.3 65.4 + - - +
394C THR* 3.3 3.0 + - - -
395C LEU* 2.9 30.3 + - + +
407C CYS* 3.4 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C TYR 3.0 11.5 + - - -
390C ASN 3.1 0.2 - - - -
391C MET* 1.3 74.8 - - - +
393C ASN* 1.3 55.6 + - - +
395C LEU 2.9 3.3 + - - -
396C LYS 2.8 25.8 + - - -
404C ALA* 3.2 12.8 - - - +
407C CYS* 3.8 15.1 - - - +
408C TYR* 3.2 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C GLN* 3.7 17.4 + - - +
389C SER* 3.2 8.4 + - - -
390C ASN* 2.8 27.8 + - - +
392C GLY* 1.3 72.0 - - - +
394C THR* 1.3 57.4 + - - +
396C LYS* 3.5 8.6 + - - +
397C GLU* 3.0 28.4 + - - +
408C TYR* 2.9 19.4 + - - -
424C ASN* 3.5 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C GLN* 3.0 29.5 + - + +
367C LEU* 4.0 38.1 - - + +
370C ALA* 4.8 2.7 - - + -
371C LEU* 4.5 20.0 - - + +
374C TYR* 3.4 11.6 - - - -
390C ASN 3.0 8.2 + - - -
391C MET* 3.5 9.2 - - - -
393C ASN* 1.3 75.2 - - - +
395C LEU* 1.3 63.4 + - - +
397C GLU* 3.1 7.9 + - - +
398C MET* 3.1 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C LEU* 4.2 27.6 - - + -
391C MET* 2.9 29.4 + - + +
392C GLY 3.4 3.4 - - - +
394C THR* 1.3 71.9 - - - +
396C LYS* 1.3 67.3 + - - +
398C MET* 3.3 15.8 + - + +
400C ASP* 3.0 49.6 + - + +
403C GLY* 3.6 29.2 - - - +
404C ALA* 3.5 10.1 - - + +
407C CYS* 4.0 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C GLY 2.8 11.4 + - - +
393C ASN* 3.5 12.3 - - - +
395C LEU* 1.3 75.7 - - - +
397C GLU* 1.3 53.8 + - - +
398C MET 2.7 12.3 + - - -
399C GLN* 2.7 21.5 + - - +
400C ASP 4.4 3.8 - - - -
401C VAL* 5.0 4.7 + - + +
404C ALA* 3.5 8.2 - - + +
408C TYR* 4.0 11.7 - - - +
424C ASN 5.0 0.4 + - - -
427C SER* 3.6 33.7 + - - -
428C ILE* 3.7 24.3 - - + +
431C ASP* 3.3 27.7 + - - -
1399G SER* 4.9 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C GLN* 3.6 24.2 + - - +
367C LEU* 3.9 30.0 - - + +
393C ASN 3.0 15.0 + - - +
394C THR* 3.1 7.1 + - - +
396C LYS* 1.3 74.1 - - - +
398C MET* 1.3 57.8 + - - +
399C GLN* 3.3 12.4 + - - +
524C LYS* 3.4 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C LEU* 3.7 30.3 - - + -
368C GLN* 4.5 11.0 - - - +
371C LEU* 4.1 26.2 - - + -
394C THR* 3.1 20.2 + - - +
395C LEU* 3.7 16.6 - - + +
396C LYS 2.7 4.0 + - - -
397C GLU* 1.3 72.9 - - - +
399C GLN* 1.3 66.6 + - - +
400C ASP* 3.0 14.9 + - + +
----------------------------------------------------------
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