Contacts of the helix formed by residues 319 - 334 (chain Z) in PDB entry 5JPQ
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 319 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316Z GLU 4.4 9.6 - - - +
317Z GLN 3.0 10.7 + - - +
318Z ILE* 1.3 74.7 - - - +
320Z GLU* 1.3 65.6 + - - +
321Z ARG* 3.2 9.0 - - + +
322Z PHE* 3.2 4.3 + - - +
323Z ILE* 3.1 21.6 + - - +
37a PRO 6.0 0.2 - - - -
41a ILE* 5.9 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319Z ASP* 1.3 75.0 - - - +
321Z ARG* 1.3 56.7 + - - +
323Z ILE* 3.3 4.1 + - - +
324Z ILE* 3.0 29.5 + - - +
37a PRO* 4.0 31.0 - - + +
38a GLU* 4.8 7.4 - - + +
41a ILE* 5.8 2.6 - - - +
83a VAL* 4.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 321 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319Z ASP* 3.2 6.0 - - + +
320Z GLU* 1.3 75.7 - - - +
322Z PHE* 1.4 63.6 + - - +
324Z ILE* 3.5 4.7 + - - +
325Z LEU* 3.1 24.1 + - - +
83a VAL* 4.9 20.2 - - - +
84a ASP 5.0 8.1 - - - +
85a LEU* 5.7 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 322 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317Z GLN 3.4 25.6 - - - +
318Z ILE* 4.2 5.6 - - + -
319Z ASP* 3.2 11.1 + - - +
321Z ARG* 1.4 77.6 - - - +
323Z ILE* 1.3 62.5 + - - +
325Z LEU* 3.4 8.4 - - - +
326Z LEU* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 323 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319Z ASP 3.1 12.4 + - - +
320Z GLU* 3.6 8.3 - - - +
321Z ARG 3.3 0.6 - - - -
322Z PHE* 1.3 75.4 - - - +
324Z ILE* 1.3 57.6 + - - +
326Z LEU* 3.2 8.1 + - - +
327Z ARG* 3.0 27.4 + - - +
30a ILE* 5.3 20.5 - - + +
37a PRO* 4.0 23.3 - - + +
40a CYS* 5.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 324 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Z ASN* 6.4 2.7 - - + -
320Z GLU 3.0 15.7 + - - +
321Z ARG* 4.2 4.5 - - - +
323Z ILE* 1.3 71.6 - - - +
325Z LEU* 1.3 66.0 + - - +
327Z ARG* 3.3 8.3 + - - +
328Z ASP* 3.0 25.4 + - - +
37a PRO* 5.0 5.2 - - + +
83a VAL 5.8 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295Z PRO* 5.5 12.8 - - + -
298Z ILE* 6.4 2.0 - - + -
321Z ARG 3.1 14.3 + - - +
322Z PHE* 3.4 12.8 - - - +
323Z ILE 3.3 0.2 - - - -
324Z ILE* 1.3 74.8 - - - +
326Z LEU* 1.3 57.1 + - - +
328Z ASP* 3.3 7.5 + - - +
329Z ILE* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322Z PHE 3.1 10.7 + - - +
323Z ILE* 3.6 9.0 - - - +
325Z LEU* 1.3 75.4 - - - +
327Z ARG* 1.3 64.6 + - - +
329Z ILE* 3.4 7.1 + - - +
330Z LYS* 3.1 24.6 + - - +
335Z THR 4.7 2.1 - - - +
337Z VAL* 5.4 13.9 - - + +
30a ILE* 5.3 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 327 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323Z ILE 3.0 13.2 + - - +
324Z ILE* 3.3 11.2 + - - +
326Z LEU* 1.3 76.8 - - - +
328Z ASP* 1.4 56.2 + - - +
330Z LYS* 3.5 6.0 + - - +
331Z LYS* 3.1 27.7 + - - +
30a ILE 5.1 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 328 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Z ASN* 5.6 10.3 - - + -
19Z LEU* 5.9 5.8 - - + -
20Z ARG* 6.0 8.3 - - + -
23Z LEU* 5.4 3.1 - - - +
324Z ILE 3.0 16.8 + - - +
325Z LEU* 3.3 7.2 + - - +
327Z ARG* 1.4 73.2 - - - +
329Z ILE* 1.4 63.4 + - - +
331Z LYS* 3.3 8.2 + - - +
332Z ILE* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Z LEU* 5.9 4.0 - - - -
302Z VAL* 5.6 10.8 - - + -
325Z LEU 3.0 16.7 + - - +
326Z LEU* 3.8 8.1 - - - +
328Z ASP* 1.4 75.9 - - - +
330Z LYS* 1.3 53.1 + - - +
332Z ILE* 3.2 3.6 + - - +
333Z PHE* 2.7 42.6 + - + +
335Z THR* 4.4 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 330 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326Z LEU 3.1 16.4 + - - +
327Z ARG* 3.9 6.3 - - - +
329Z ILE* 1.3 75.4 - - - +
331Z LYS* 1.3 61.0 + - - +
334Z ASN* 2.8 31.4 + - - +
335Z THR 3.6 22.8 + - - +
336Z GLU* 5.4 2.7 - - + -
31a TYR* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 331 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Z THR* 4.9 14.3 - - - -
327Z ARG 3.1 14.3 + - - +
328Z ASP* 3.6 11.9 - - - +
329Z ILE 3.3 0.2 - - - -
330Z LYS* 1.3 76.2 - - - +
332Z ILE* 1.3 60.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 332 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Z LEU* 4.2 29.4 - - + +
24Z ALA* 5.3 1.8 - - - +
27Z SER* 4.8 13.8 - - - -
29Z LYS* 5.0 10.2 - - + +
328Z ASP 3.2 13.6 + - - +
329Z ILE* 3.9 2.2 - - - +
331Z LYS* 1.3 80.7 - - - +
333Z PHE* 1.3 58.5 + - + +
334Z ASN 3.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 333 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Z SER* 5.7 4.9 - - - -
302Z VAL* 5.6 7.4 - - + +
329Z ILE* 2.7 20.1 + - + +
332Z ILE* 1.3 75.0 - - + +
334Z ASN* 1.4 60.8 + - - +
335Z THR* 3.1 20.7 + - - +
357Z ILE* 5.6 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 334 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330Z LYS* 2.8 30.3 + - - +
332Z ILE 3.7 0.8 - - - -
333Z PHE* 1.4 71.2 - - - +
335Z THR* 1.3 60.2 + - - +
336Z GLU* 3.8 2.8 + - - +
----------------------------------------------------------
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