Contacts of the helix formed by residues 362 - 371 (chain A) in PDB entry 5JJA
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 ASN 362 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PHE* 3.7 13.7 - - - -
321A VAL* 3.8 15.1 - - - +
324A MET* 3.8 28.4 - - + +
358A LEU* 3.0 21.8 + - - +
359A ILE 3.0 5.5 + - - -
361A ASP* 1.3 86.3 + - - +
363A ALA* 1.3 64.4 + - - +
364A ALA* 3.2 3.1 - - - -
365A LYS* 3.0 17.6 + - + +
366A ILE* 3.2 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ILE* 2.9 11.3 + - + +
360A SER* 3.6 20.0 + - - +
361A ASP 3.6 0.6 - - - -
362A ASN* 1.3 77.1 - - - +
364A ALA* 1.3 59.6 + - - +
366A ILE* 4.5 1.8 - - - +
367A LEU* 2.9 56.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ASN 3.1 1.4 + - - -
363A ALA* 1.3 78.4 - - - +
365A LYS* 1.3 63.5 + - + +
367A LEU* 5.6 0.4 - - - -
368A PRO* 3.2 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A MET* 4.3 23.5 - - + +
325A GLU* 3.5 26.8 + - + +
362A ASN* 3.0 9.6 + - + +
364A ALA* 1.3 84.0 - - + +
366A ILE* 1.3 62.4 + - + +
368A PRO* 3.7 7.4 - - - +
369A ILE* 3.4 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PHE* 4.0 13.0 - - + -
324A MET* 3.9 21.5 - - + +
325A GLU* 6.2 0.4 - - + -
328A PHE* 4.0 37.5 - - + -
350A TRP* 5.3 0.7 - - + -
359A ILE* 3.8 39.5 - - + +
362A ASN* 3.2 31.8 + - + +
363A ALA 4.5 0.4 - - - +
365A LYS* 1.3 78.6 - - - +
367A LEU* 1.3 66.6 + - - +
368A PRO 3.3 0.4 - - - -
369A ILE* 3.0 19.5 + - + +
370A MET* 3.0 20.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A TRP* 4.3 17.3 - - + -
359A ILE* 5.1 6.3 - - + -
363A ALA* 2.9 38.3 + - + +
364A ALA* 5.9 0.2 - - - -
366A ILE* 1.3 77.8 - - - +
368A PRO* 1.4 58.2 - - + +
370A MET* 4.5 1.3 - - - +
371A PHE* 2.8 53.7 + - + -
375A TYR* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ALA 3.8 0.2 - - - +
364A ALA 3.2 26.7 - - - +
365A LYS* 3.7 7.4 - - - +
366A ILE 3.4 3.6 - - - -
367A LEU* 1.4 94.7 - - + +
369A ILE* 1.3 57.0 + - + +
371A PHE 4.1 1.3 - - - +
372A PRO* 3.3 26.7 - - - +
375A TYR* 3.7 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A MET 5.1 0.2 - - - +
325A GLU* 4.0 38.4 - - + +
328A PHE* 3.4 38.8 - - + +
329A ARG* 3.5 25.8 - - + +
332A ALA* 3.6 11.1 - - + +
365A LYS 3.4 20.6 - - - +
366A ILE* 3.0 11.1 + - + +
368A PRO* 1.3 80.7 - - + +
370A MET* 1.3 61.5 + - - +
372A PRO* 3.6 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 3.7 38.1 - - + +
331A LEU* 3.9 21.5 - - + -
332A ALA* 3.9 15.6 - - - +
335A VAL* 4.0 25.1 - - + -
350A TRP* 4.1 25.6 - - + +
366A ILE* 3.0 31.9 + - + +
367A LEU* 4.8 0.7 - - - -
369A ILE* 1.3 75.3 - - - +
371A PHE* 1.3 90.3 + - + +
372A PRO* 3.5 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A TRP* 4.0 26.2 - + - -
367A LEU* 2.8 33.6 + - + +
368A PRO 3.8 3.5 - - - +
370A MET* 1.3 93.3 - - + +
372A PRO* 1.4 61.7 - - - +
373A SER 3.3 2.7 - - - -
374A LEU* 3.0 23.6 + - + -
375A TYR* 2.9 54.3 + + + -
----------------------------------------------------------
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