Contacts of the helix formed by residues 333 - 364 (chain J) in PDB entry 5KHU
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 TYR 333 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332J THR* 3.8 28.3 - - - +
334J GLY* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 334 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333J TYR* 3.8 29.6 - - - +
335J PRO* 3.8 28.5 - - - -
337J TRP* 4.6 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 335 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334J GLY* 3.8 24.9 - - - -
336J ALA* 3.7 30.1 - - - -
338J ILE* 4.4 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335J PRO* 3.7 29.8 - - - -
337J TRP* 3.8 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 337 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334J GLY* 4.6 13.0 - - - +
336J ALA* 3.8 29.2 - - - +
338J ILE* 3.8 25.4 - - - +
340J TYR* 4.2 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 338 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335J PRO* 4.4 17.7 - - - -
337J TRP* 3.8 24.7 - - - +
339J ALA* 3.7 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338J ILE* 3.7 30.1 - - - +
340J TYR* 3.8 25.8 - - - +
342J HIS* 4.4 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 340 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337J TRP* 4.2 17.9 - - - +
339J ALA* 3.8 23.8 - - - +
341J GLY* 3.7 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 341 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340J TYR* 3.7 29.4 - - - +
342J HIS* 3.8 26.2 - - - +
353J ALA* 4.6 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 342 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339J ALA* 4.4 16.4 - - - +
341J GLY* 3.8 24.0 - - - +
343J SER* 3.8 29.6 - - - +
345J ALA* 4.3 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 343 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342J HIS* 3.8 26.7 - - - +
344J PHE* 3.7 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 344 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343J SER* 3.7 28.7 - - - +
345J ALA* 3.8 25.6 - - - +
347J GLU* 4.1 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 345 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342J HIS* 4.3 19.7 - - - +
344J PHE* 3.8 25.6 - - - +
346J VAL* 3.8 29.4 - - - +
348J SER* 4.5 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 346 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345J ALA* 3.8 24.9 - - - +
347J GLU* 3.8 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 347 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344J PHE* 4.1 19.7 - - - +
346J VAL* 3.8 29.4 - - - +
348J SER* 3.8 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 348 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345J ALA* 4.5 16.8 - - - +
347J GLU* 3.8 28.9 - - - +
349J GLU* 3.8 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 349 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348J SER* 3.8 27.1 - - - +
350J HIS* 3.7 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 350 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349J GLU* 3.7 29.8 - - - +
351J ASP* 3.8 27.6 - - - +
353J ALA* 4.5 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 351 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350J HIS* 3.8 26.7 - - - +
352J GLN* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 352 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351J ASP* 3.8 28.9 - - - +
353J ALA* 3.8 25.6 - - - +
355J ALA* 4.7 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341J GLY* 4.6 20.4 - - - +
350J HIS* 4.5 15.9 - - - +
352J GLN* 3.8 26.0 - - - +
354J MET* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 354 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353J ALA* 3.8 28.9 - - - +
355J ALA* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352J GLN* 4.7 15.7 - - - +
354J MET* 3.8 27.6 - - - +
356J ALA* 3.8 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 356 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355J ALA* 3.8 26.0 - - - +
357J TYR* 3.7 29.6 - - - +
359J THR* 4.3 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 357 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356J ALA* 3.7 29.8 - - - +
358J PHE* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 358 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357J TYR* 3.8 24.7 - - - +
359J THR* 3.8 29.8 - - - +
361J ALA* 4.5 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 359 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356J ALA* 4.3 18.6 - - - +
358J PHE* 3.8 29.4 - - - +
360J ALA* 3.8 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 360 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359J THR* 3.8 25.8 - - - +
361J ALA* 3.8 30.1 - - - +
363J LEU* 4.2 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 361 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358J PHE* 4.5 17.0 - - - +
360J ALA* 3.8 29.4 - - - +
362J GLN* 3.8 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 362 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361J ALA* 3.8 24.2 - - - +
363J LEU* 3.7 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 363 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360J ALA* 4.2 18.4 - - - +
362J GLN* 3.7 28.9 - - - +
364J MET* 3.8 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 364 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363J LEU* 3.8 28.9 - - - +
365J LYS* 3.8 29.4 - - - +
----------------------------------------------------------
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