Contacts of the helix formed by residues 362 - 382 (chain J) in PDB entry 2QJK
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 MET 362 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361J PRO* 1.3 76.9 - - + +
363J PHE* 1.3 70.5 + - - +
365J ILE* 2.9 23.4 + - - +
366J TYR* 3.5 25.1 + - + +
411J LEU* 3.9 26.2 - - + -
414J ILE* 4.2 26.5 - - + +
415J GLU* 3.0 25.1 + - + +
416J LYS 5.1 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 363 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J LEU 3.6 20.4 - - - -
117J TYR* 4.3 16.6 - + - -
121J TYR* 4.4 2.5 - - - -
350J ASP* 4.1 2.9 - - - -
357J GLY* 4.4 12.8 - - - -
360J ARG* 3.2 61.0 - - + +
362J MET* 1.3 71.3 - - - +
364J LYS* 1.3 59.3 + - + +
365J ILE 2.7 12.1 + - - -
366J TYR* 2.9 14.8 + - - +
367J PHE* 2.9 35.6 + + + -
403J TYR* 3.3 26.0 - + - -
408J LEU* 3.6 16.8 - - + -
411J LEU* 4.0 11.8 - - + +
415J GLU* 2.7 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 364 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117J TYR* 3.6 17.6 + - + +
357J GLY 3.3 16.4 - - - +
358J ARG* 2.8 42.4 + - - +
360J ARG 2.9 23.6 + - - +
361J PRO* 3.9 11.7 - - + +
362J MET 3.3 0.2 - - - -
363J PHE* 1.3 79.4 - - - +
365J ILE* 1.3 63.9 + - + +
367J PHE* 4.0 4.0 - - - -
368J TRP* 2.8 41.0 + - + +
504J LOP 5.1 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 365 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361J PRO 4.0 13.5 - - - +
362J MET* 2.9 12.0 + - - +
363J PHE 2.7 4.9 + - - -
364J LYS* 1.3 77.3 - - + +
366J TYR* 1.3 78.2 + - + +
368J TRP* 3.5 5.6 + - + +
369J LEU* 3.2 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 366 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362J MET* 3.6 25.4 - - + +
363J PHE 2.9 6.4 + - - +
365J ILE* 1.3 80.8 - - + +
367J PHE* 1.3 59.9 + - - +
369J LEU* 3.2 13.0 + - + -
370J LEU* 2.9 21.3 + - - +
399J TYR* 2.7 33.6 + + - +
403J TYR* 3.9 17.1 - - + -
407J ILE* 3.3 38.6 - - + -
411J LEU* 3.5 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 367 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J PHE* 3.8 27.6 - + - -
116J LEU* 4.0 8.7 - - + -
117J TYR* 3.3 54.5 - + + -
363J PHE* 2.9 44.7 + + + +
364J LYS* 4.0 3.4 - - - +
366J TYR* 1.3 76.8 - - - +
368J TRP* 1.3 93.8 + + - +
370J LEU* 2.7 29.4 + - + +
371J ALA* 3.0 7.7 + - + -
403J TYR* 3.9 19.8 - + - -
504J LOP 4.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 368 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117J TYR* 4.2 9.6 - + - -
364J LYS* 2.8 35.1 + - + +
365J ILE* 4.0 6.3 - - + +
366J TYR 3.4 0.2 - - - -
367J PHE* 1.3 99.6 - + - +
369J LEU* 1.3 55.8 + - - +
371J ALA* 3.5 17.0 - - + +
372J ALA* 2.8 29.3 + - - +
504J LOP 3.7 61.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365J ILE* 3.2 27.8 + - + +
366J TYR* 3.3 17.3 - - + +
367J PHE 3.1 0.8 - - - -
368J TRP* 1.3 73.2 - - - +
370J LEU* 1.3 56.6 + - - +
372J ALA* 3.2 9.6 + - + +
373J ASP* 2.6 37.1 + - - +
399J TYR* 3.2 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J PHE* 4.0 20.6 - - + -
116J LEU* 4.3 7.9 - - + -
366J TYR 2.9 12.1 + - - +
367J PHE* 2.7 17.7 + - + +
369J LEU* 1.3 75.6 - - - +
371J ALA* 1.3 54.9 - - - +
373J ASP* 3.1 4.5 + - - +
374J PHE* 2.9 28.4 + - - +
399J TYR* 3.6 11.9 - - + -
400J TRP* 3.5 35.0 - - + -
403J TYR* 3.3 50.3 - - + +
404J PHE* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J PHE* 4.1 17.9 - - + -
367J PHE* 3.0 14.0 + - + +
368J TRP* 3.5 26.5 - - + +
370J LEU* 1.3 73.7 - - - +
372J ALA* 1.3 68.7 + - - +
374J PHE* 3.0 5.0 + - - +
375J VAL* 3.0 26.2 + - + +
504J LOP 4.4 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 372 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368J TRP 2.8 20.2 + - - +
369J LEU* 3.5 12.3 - - + +
371J ALA* 1.3 73.4 - - - +
373J ASP* 1.3 58.4 + - - +
375J VAL* 3.2 9.8 + - - +
376J ILE* 2.8 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 373 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369J LEU 2.6 21.5 + - - +
370J LEU* 3.2 10.5 - - + +
371J ALA 3.0 0.2 - - - -
372J ALA* 1.3 71.3 - - - +
374J PHE* 1.3 56.3 + - - +
376J ILE* 2.9 14.4 + - - +
377J LEU* 2.5 46.7 + - - +
396J ALA* 2.7 51.2 - - - +
399J TYR* 3.8 13.5 - - + +
400J TRP* 3.6 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 374 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J TYR* 3.7 50.3 - + - -
113J PHE* 3.6 25.6 - + + -
300J PRO* 4.0 24.9 - - + -
301J PHE* 4.7 9.6 - + - -
370J LEU 2.9 14.8 + - - +
371J ALA 3.4 7.6 - - - +
373J ASP* 1.3 71.5 - - - +
375J VAL* 1.3 61.4 + - - +
377J LEU* 3.4 11.5 - - + +
378J THR* 2.9 32.1 + - - -
400J TRP* 4.0 25.7 - + + -
504J LOP 3.4 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 375 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371J ALA* 3.0 16.9 + - + +
372J ALA* 3.2 9.9 - - - +
374J PHE* 1.3 73.6 - - - +
376J ILE* 1.3 68.9 + - + +
378J THR* 3.0 9.8 + - - -
379J TRP* 2.8 23.9 + - + +
504J LOP 4.3 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 376 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372J ALA* 2.8 36.4 + - + +
373J ASP* 3.3 15.3 - - - +
375J VAL* 1.3 73.7 - - + +
377J LEU* 1.3 65.7 + - - +
379J TRP* 2.9 20.4 + - + +
380J VAL* 2.8 25.4 + - + +
392J ILE* 4.0 27.6 - - + -
396J ALA* 5.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300J PRO* 3.7 16.1 - - + +
303J ALA* 3.3 34.5 - - + +
304J ILE* 3.5 35.9 - - + +
373J ASP* 2.5 35.9 + - - +
374J PHE* 3.4 9.9 - - + +
376J ILE* 1.3 73.3 - - - +
378J THR* 1.3 62.4 + - - +
380J VAL* 2.7 24.9 - - + +
381J GLY 3.2 4.7 + - - -
393J SER* 4.9 1.3 - - - +
396J ALA* 3.9 23.8 - - + +
397J SER* 4.4 4.0 - - - +
400J TRP* 4.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 378 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296J TRP* 4.0 14.4 - - + +
299J LEU* 3.7 31.9 - - + +
300J PRO* 3.3 24.2 - - + +
374J PHE* 2.9 17.6 + - - -
375J VAL* 3.0 10.2 + - - -
377J LEU* 1.3 76.3 - - - +
379J TRP* 1.3 67.8 + - - +
381J GLY 3.0 13.0 + - - -
382J ALA 3.7 4.7 + - - -
504J LOP 4.3 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 379 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299J LEU* 5.7 0.4 - - - -
375J VAL* 2.8 18.6 + - + +
376J ILE* 2.9 20.6 + - + +
378J THR* 1.3 75.3 - - - +
380J VAL* 1.3 92.8 + - + +
382J ALA* 3.4 10.2 - - - +
383J GLN* 3.2 34.3 + - + +
389J TYR* 3.6 29.2 - + - -
392J ILE* 4.4 12.3 - - + -
114K MET* 2.6 67.1 + - + +
115K GLY 3.9 14.6 - - - -
116K THR* 4.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 380 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303J ALA* 4.1 9.6 - - + -
306J ARG* 2.8 11.5 + - - -
376J ILE* 2.8 13.5 + - + +
377J LEU* 2.7 33.4 - - - +
379J TRP* 1.3 95.9 - - + +
381J GLY* 1.3 53.0 + - - +
382J ALA 2.8 5.8 - - - -
383J GLN* 2.7 32.0 + - + +
384J GLN 5.0 0.2 - - - +
389J TYR* 4.8 9.5 - - + +
392J ILE* 3.8 25.6 - - + -
393J SER* 4.6 18.8 - - - +
396J ALA* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 381 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293J VAL* 4.3 4.2 - - - +
299J LEU* 3.9 14.0 - - - +
302J TYR* 3.1 37.0 - - - -
303J ALA* 4.2 9.4 - - - -
306J ARG* 3.2 12.2 + - - -
377J LEU 3.2 7.5 + - - -
378J THR 3.0 10.4 + - - -
380J VAL* 1.3 77.1 - - - +
382J ALA* 1.3 56.5 + - - +
383J GLN 3.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 382 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293J VAL* 4.5 17.9 - - + +
299J LEU* 4.2 17.0 - - + +
378J THR 3.7 1.6 + - - -
379J TRP* 3.4 14.8 + - - +
380J VAL 2.8 0.4 - - - -
381J GLY* 1.3 78.8 - - - +
383J GLN* 1.3 68.8 + - - +
115K GLY* 4.8 8.7 - - - +
----------------------------------------------------------
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