Contacts of the helix formed by residues 362 - 376 (chain J) in PDB entry 4DVQ
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 LEU 362 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343J GLU* 3.1 34.8 - - + +
344J SER* 3.6 28.0 - - - +
347J ALA* 4.3 7.4 - - + -
351J ILE* 3.4 26.0 - - + -
358J ALA* 3.1 22.8 + - + +
359J THR 4.6 2.5 - - - -
360J THR 3.4 0.8 - - - -
361J GLU* 1.3 85.4 - - - +
363J PRO* 1.3 56.7 - - - +
364J LEU 3.3 0.3 + - - -
365J LEU* 3.3 12.6 + - + -
366J ARG* 3.0 28.3 + - - +
461J LEU* 4.3 9.9 - - + +
465J HIS* 3.5 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 363 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343J GLU* 3.1 8.3 - - + +
359J THR 4.7 0.9 - - - +
360J THR 3.7 11.2 - - - +
361J GLU 3.3 9.2 - - - +
362J LEU* 1.3 89.1 - - - +
364J LEU* 1.3 57.7 + - + +
366J ARG* 3.4 14.7 - - + +
367J ALA* 2.9 26.2 + - - +
429J LEU* 4.6 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336J VAL* 5.2 2.5 - - + +
339J ILE* 3.4 38.1 - - + +
340J LEU* 3.4 22.9 - - + +
343J GLU* 2.7 26.7 + - + +
363J PRO* 1.3 73.0 - - + +
365J LEU* 1.3 57.8 + - - +
367J ALA* 3.1 7.4 - - + +
368J ALA* 3.0 21.1 + - - +
425J PRO* 3.8 16.8 - - + +
426J GLN* 3.2 30.3 - - + +
429J LEU* 3.4 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 365 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326J THR* 5.6 0.2 - - + -
330J LEU* 5.1 4.3 - - + -
340J LEU* 3.4 24.5 - - + +
343J GLU* 3.3 14.4 + - - +
344J SER* 4.5 5.4 - - - +
362J LEU* 3.3 10.3 + - + +
364J LEU* 1.3 74.2 - - - +
366J ARG* 1.3 66.8 + - - +
367J ALA 3.1 1.3 - - - -
368J ALA* 3.0 16.8 + - + +
369J LEU* 3.1 17.8 + - - +
461J LEU* 3.7 35.4 - - + +
464J LEU* 4.0 22.9 - - + -
465J HIS* 3.9 22.4 - - + +
468J LEU* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 366 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359J THR* 3.3 43.7 + - - +
362J LEU 3.0 9.9 + - - +
363J PRO* 3.4 17.3 - - - +
365J LEU* 1.3 76.6 - - - +
367J ALA* 1.3 60.8 + - - +
369J LEU* 3.5 9.9 + - + +
370J LYS* 3.3 42.7 + - - +
453J ARG* 4.8 4.0 - - - +
454J ARG* 3.9 22.6 - - - +
457J GLU* 4.8 19.9 + - + +
461J LEU* 3.5 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 367 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363J PRO 2.9 15.2 + - - +
364J LEU* 3.1 18.2 - - + +
365J LEU 3.1 0.2 - - - -
366J ARG* 1.3 74.6 - - - +
368J ALA* 1.3 61.5 + - - +
370J LYS* 3.0 17.4 + - - +
371J GLU* 3.0 18.2 + - - +
425J PRO* 3.5 26.5 - - + +
428J TRP* 3.6 16.1 - - + -
429J LEU* 5.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 368 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326J THR* 4.7 6.3 - - + -
340J LEU* 4.0 18.6 - - + -
364J LEU 3.0 13.2 + - - +
365J LEU* 3.0 14.7 + - + +
367J ALA* 1.3 74.5 - - - +
369J LEU* 1.3 56.9 + - - +
371J GLU* 3.0 2.9 + - - +
372J THR* 2.8 25.9 + - - -
423J TYR* 2.9 22.2 + - + +
425J PRO* 3.6 22.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
326J THR* 4.1 7.9 - - + +
365J LEU 3.1 14.1 + - - +
366J ARG* 3.5 11.4 - - + +
368J ALA* 1.3 77.7 - - + +
370J LYS* 1.3 60.0 + - - +
372J THR* 3.4 4.8 + - - -
373J LEU* 3.1 32.6 + - + +
457J GLU* 4.2 16.2 - - + +
460J MET* 3.2 38.0 - - + +
461J LEU* 3.8 38.8 - - + +
464J LEU* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 370 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366J ARG* 3.3 32.7 + - - +
367J ALA* 3.0 13.2 + - - +
369J LEU* 1.3 77.9 - - - +
371J GLU* 1.3 58.1 + - - +
373J LEU* 3.6 2.5 + - - +
374J ARG* 3.0 28.8 + - - +
428J TRP* 3.6 44.6 - - + +
440J HIS* 3.4 53.1 + - + +
457J GLU* 4.9 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 371 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367J ALA 3.0 12.0 + - - +
368J ALA* 3.0 11.2 + - - +
370J LYS* 1.3 74.9 - - - +
372J THR* 1.3 67.0 + - - +
374J ARG* 3.0 34.1 + - - +
375J LEU* 3.3 15.1 + - - +
422J ARG 3.3 8.3 - - - +
423J TYR* 3.5 21.1 - - + -
424J ASN 2.7 39.2 + - - +
425J PRO* 4.2 4.3 - - + -
427J ARG* 2.9 23.8 + - - -
428J TRP* 3.1 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 372 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322J PRO* 3.4 40.2 - - + +
325J MET* 4.2 14.2 - - + -
326J THR* 2.9 22.9 + - - +
368J ALA 2.8 8.6 + - - -
369J LEU* 3.6 9.0 - - - +
371J GLU* 1.3 79.6 - - - +
373J LEU* 1.3 53.9 + - + +
375J LEU 3.0 0.3 + - - -
376J TYR* 2.7 42.7 + - + -
423J TYR* 3.0 27.6 + - - -
460J MET* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322J PRO* 3.7 31.9 - - + -
369J LEU* 3.1 17.3 + - + +
370J LYS* 4.0 4.0 - - - +
372J THR* 1.3 80.6 - - - +
374J ARG* 1.3 62.0 + - - +
375J LEU 3.3 0.2 - - - -
376J TYR 3.7 13.9 - - - +
377J PRO* 3.3 23.8 - - + +
378J VAL 4.4 9.6 - - - +
440J HIS* 4.9 2.2 - - + -
442J PRO* 3.9 32.3 - - + +
443J PHE* 3.9 29.8 - - + -
460J MET* 5.3 5.8 - - + -
601J HEM 4.4 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 374 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370J LYS 3.0 15.4 + - - +
371J GLU* 3.0 35.3 + - - +
372J THR 3.2 0.2 - - - -
373J LEU* 1.3 78.0 - - - +
375J LEU* 1.3 78.0 + - - +
377J PRO* 3.9 9.4 - - - +
407J LEU 4.3 1.6 - - - +
411J GLY* 2.7 60.7 + - - +
412J ARG* 4.1 3.6 + - - -
417J PHE* 3.9 29.8 - - + +
420J PRO* 2.9 37.8 + - - +
422J ARG 3.1 23.8 + - - -
427J ARG* 3.5 12.0 - - - +
428J TRP* 4.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329J GLU* 5.0 2.7 - - - +
371J GLU 3.9 4.9 - - - +
372J THR 3.0 3.1 + - - +
374J ARG* 1.3 101.8 - - - +
376J TYR* 1.3 88.9 + - + +
377J PRO* 3.4 4.0 - - - +
408J TYR* 4.4 2.6 - - - -
412J ARG* 2.8 52.3 + - + +
420J PRO 3.2 26.5 - - - +
421J GLU* 4.6 15.5 - - + +
423J TYR* 4.0 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 376 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322J PRO* 5.2 2.3 - - + +
325J MET* 3.9 38.1 - - + -
328J PHE* 4.6 4.2 - + - -
329J GLU* 2.7 39.3 + - + -
332J ARG* 4.1 6.4 + - - -
372J THR* 2.7 28.1 + - + +
373J LEU* 3.5 18.3 - - - +
375J LEU* 1.3 99.0 - - + +
377J PRO* 1.3 65.5 - - - +
378J VAL* 3.1 7.3 + - - +
412J ARG* 4.3 9.4 + - - -
480J ASP* 5.5 2.4 + - - +
481J ILE* 4.7 11.1 + - + -
483J MET* 3.6 42.8 - - + -
489J LEU* 5.1 1.3 - - - +
----------------------------------------------------------
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