Contacts of the helix formed by residues 365 - 372 (chain A) in PDB entry 4JYH
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 HIS 365 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LYS* 3.5 0.4 - - - +
364A PRO* 1.3 98.9 + - + +
366A MET* 1.3 63.9 + - - +
367A PHE 3.2 2.9 - - - -
368A PRO* 3.3 25.6 - - + +
369A LYS* 3.6 10.7 + - - +
346B GLU* 3.1 48.4 + - + +
349B LEU* 5.6 7.2 - - + +
350B GLU* 3.6 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU* 3.5 34.1 - - + -
356A ILE* 3.8 9.0 - - + -
360A ARG* 3.6 38.6 - - - +
363A LYS* 3.3 60.8 - - + +
364A PRO 3.1 2.8 + - - -
365A HIS* 1.3 78.0 - - - +
367A PHE* 1.3 64.6 + - - +
368A PRO 3.6 0.2 - - - -
369A LYS* 3.9 11.4 - - + -
370A ILE* 3.1 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.7 16.6 - - + -
352A LEU* 4.2 15.0 - - + -
353A LYS* 3.4 55.6 - - + +
356A ILE* 3.7 23.9 - - + +
364A PRO 4.3 5.6 + - - +
365A HIS 3.2 0.2 - - - -
366A MET* 1.3 78.6 - - - +
368A PRO* 1.3 71.1 - - + +
369A LYS 3.2 0.3 + - - -
370A ILE* 4.0 0.5 - - - +
371A LEU* 2.9 48.1 + - + +
367B PHE* 4.8 16.8 - + - -
368B PRO* 4.2 28.7 - - + -
371B LEU* 5.9 2.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
364A PRO 4.9 0.9 - - - +
365A HIS* 3.3 26.5 - - + +
367A PHE* 1.3 104.8 - - + +
369A LYS* 1.3 54.8 + - - +
371A LEU* 4.1 6.3 - - + -
372A MET* 2.9 36.9 + - + +
349B LEU* 4.3 28.9 - - + -
367B PHE* 4.8 8.3 - - + -
371B LEU* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU* 5.0 6.1 - - + -
365A HIS 3.6 13.8 + - - +
366A MET* 3.8 20.9 - - + +
367A PHE 3.2 0.4 - - - -
368A PRO* 1.3 82.0 - - - +
370A ILE* 1.3 68.1 + - - +
372A MET* 3.4 7.7 + - - +
373A LYS* 3.5 23.3 + - - +
349B LEU* 5.8 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU* 4.5 13.7 - - + -
314A MET* 4.0 30.5 - - + -
318A GLU* 4.1 15.3 - - - +
322A LEU* 3.8 14.3 - - + +
352A LEU* 4.7 5.6 - - + -
356A ILE* 3.6 27.4 - - + -
360A ARG* 2.9 32.5 - - - +
366A MET* 3.1 20.3 + - + +
369A LYS* 1.3 77.9 - - - +
371A LEU* 1.3 66.0 + - - +
373A LYS* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LEU* 4.1 8.1 - - + -
325A ILE* 4.0 6.5 - - + -
349A LEU* 3.9 22.2 - - + -
352A LEU* 3.8 21.5 - - + +
367A PHE* 2.9 39.3 + - + +
368A PRO* 4.0 4.7 - - + +
370A ILE* 1.3 76.5 - - - +
372A MET* 1.3 78.6 + - + +
373A LYS 3.2 0.2 + - - -
374A ILE* 3.1 33.3 - - + +
368B PRO* 5.1 4.9 - - + +
371B LEU* 5.2 6.3 - - + -
372B MET* 3.8 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A PRO* 2.9 28.7 + - + +
369A LYS* 3.9 4.7 - - - +
370A ILE 3.2 0.6 - - - -
371A LEU* 1.3 94.2 - - + +
373A LYS* 1.3 56.7 + - - +
374A ILE* 2.9 6.1 - - - +
375A THR* 3.0 53.0 + - - +
376A ASP* 4.0 3.1 + - - +
325B ILE* 6.5 0.7 - - + -
349B LEU* 6.1 1.3 - - + -
371B LEU* 3.5 42.2 - - + +
372B MET* 3.9 4.5 - - - -
374B ILE* 3.6 22.7 - - + -
375B THR* 3.8 8.5 - - - +
----------------------------------------------------------
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