Contacts of the helix formed by residues 333 - 354 (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 ASN 333 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329J GLU* 2.8 46.5 + - - +
330J LEU* 3.2 8.4 + - - +
332J ARG* 1.3 85.7 - - - +
334J PRO* 1.4 64.9 - - - +
335J ASP* 3.2 4.3 - - + -
336J VAL* 3.1 20.9 + - + +
337J GLN 3.1 16.1 + - - -
423J TYR* 3.5 33.1 + - + +
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Residues in contact with PRO 334 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330J LEU 3.5 7.3 - - - +
331J ALA 4.0 8.1 - - - +
332J ARG 3.1 15.5 - - - +
333J ASN* 1.4 84.4 - - - +
335J ASP* 1.3 64.0 + - - +
337J GLN* 3.0 9.8 + - + +
338J GLN* 2.8 30.4 + - - +
341J ARG* 5.0 1.4 + - - -
473J VAL 5.9 2.5 - - - +
478J GLN* 5.3 3.1 - - - +
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Residues in contact with ASP 335 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333J ASN* 3.2 1.7 + - - -
334J PRO* 1.3 82.1 - - - +
336J VAL* 1.3 69.0 + - + +
338J GLN* 3.2 16.5 + - - +
339J ILE* 3.2 19.9 + - - +
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Residues in contact with VAL 336 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330J LEU* 4.7 5.6 - - + -
333J ASN* 3.1 19.7 + - + +
335J ASP* 1.3 84.6 - - + +
337J GLN* 1.3 56.8 + - - +
339J ILE* 3.3 11.3 + - + +
340J LEU* 2.9 45.1 + - + +
364J LEU* 5.9 2.2 - - + -
423J TYR* 4.1 23.6 - - + +
424J ASN* 5.4 2.5 - - - +
425J PRO* 4.0 26.9 - - + -
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Residues in contact with GLN 337 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330J LEU* 3.1 43.3 - - + +
333J ASN 3.1 4.8 + - - -
334J PRO* 3.0 15.4 + - + +
336J VAL* 1.3 77.3 - - - +
338J GLN* 1.3 54.9 + - - +
340J LEU* 3.3 4.5 + - - +
341J ARG* 2.8 61.7 + - - +
468J LEU* 3.7 17.7 - - + +
471J PHE 4.1 1.0 + - - -
472J LEU* 3.7 2.0 - - - +
473J VAL* 3.0 52.9 + - - +
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Residues in contact with GLN 338 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334J PRO 2.8 11.5 + - - +
335J ASP* 3.2 10.3 + - - +
337J GLN* 1.3 73.2 - - - +
339J ILE* 1.3 70.3 + - + +
341J ARG* 2.9 41.5 + - - +
342J GLN* 2.9 57.5 + - - +
345J LEU* 5.9 2.0 - - - +
472J LEU* 5.1 1.9 - - - +
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Residues in contact with ILE 339 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335J ASP 3.2 17.9 + - - +
336J VAL* 3.6 8.3 - - - +
338J GLN* 1.3 79.6 - - + +
340J LEU* 1.3 63.7 + - - +
342J GLN* 3.1 22.3 + - - +
343J GLU* 3.1 19.6 + - + +
364J LEU* 3.4 25.1 - - + -
426J GLN* 4.6 9.9 - - - +
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Residues in contact with LEU 340 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330J LEU* 3.4 31.4 - - + -
336J VAL* 2.9 29.2 + - + +
337J GLN* 3.6 4.9 - - - +
339J ILE* 1.3 76.4 - - - +
341J ARG* 1.3 57.8 + - - +
343J GLU* 3.5 14.7 + - - +
344J SER* 3.1 27.0 + - - -
364J LEU* 3.4 21.1 - - + +
365J LEU* 3.3 49.5 - - + +
368J ALA* 4.0 11.2 - - + -
425J PRO* 5.1 0.2 - - + -
468J LEU* 3.8 15.4 - - + +
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Residues in contact with ARG 341 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334J PRO 5.0 1.2 + - - -
337J GLN* 2.8 47.6 + - - +
338J GLN* 2.9 40.5 + - - +
340J LEU* 1.3 75.3 - - - +
342J GLN* 1.3 66.4 + - - +
344J SER* 3.0 3.9 + - - +
345J LEU* 2.8 44.5 + - + +
468J LEU* 3.0 39.8 + - + +
471J PHE 3.0 24.5 + - - -
472J LEU* 3.4 21.7 - - - +
502J ILE* 3.7 18.8 - - - -
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Residues in contact with GLN 342 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338J GLN* 2.9 39.4 + - - +
339J ILE* 3.1 26.4 + - - +
341J ARG* 1.3 73.7 - - - +
343J GLU* 1.3 62.0 + - - +
345J LEU* 3.5 8.2 + - + +
346J ALA* 2.9 25.8 + - - +
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Residues in contact with GLU 343 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339J ILE 3.1 11.0 + - - +
340J LEU* 3.6 13.8 - - - +
341J ARG 3.1 0.6 - - - -
342J GLN* 1.3 78.3 - - - +
344J SER* 1.3 61.4 + - - +
346J ALA* 3.4 7.0 + - - +
347J ALA* 3.3 22.2 + - - +
361J GLU 4.0 7.2 - - - +
362J LEU* 3.5 20.4 - - + +
363J PRO* 3.0 17.4 - - + +
364J LEU* 2.7 37.8 + - + +
365J LEU* 3.3 27.9 + - - +
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Residues in contact with SER 344 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340J LEU 3.1 15.7 + - - -
341J ARG* 3.0 4.7 + - - -
343J GLU* 1.3 73.5 + - - +
345J LEU* 1.3 64.2 + - - +
347J ALA 3.6 0.5 + - - -
348J ALA* 3.2 19.2 + - - +
362J LEU* 3.6 13.3 - - - +
365J LEU* 4.5 3.5 - - - +
465J HIS* 2.7 53.3 + - - -
468J LEU* 4.2 15.0 - - - +
469J LYS* 4.1 6.6 - - - +
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Residues in contact with LEU 345 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338J GLN* 5.9 2.5 - - - +
341J ARG* 2.8 44.4 + - + +
342J GLN* 4.0 6.7 - - + +
344J SER* 1.3 70.0 - - - +
346J ALA* 1.3 66.6 + - - +
348J ALA* 3.0 19.7 + - + +
349J ALA 4.7 0.5 + - - -
469J LYS* 3.9 34.1 - - + +
502J ILE* 5.6 4.0 - - + -
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Residues in contact with ALA 346 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342J GLN 2.9 20.7 + - - +
343J GLU* 3.5 8.3 - - - +
344J SER 3.4 0.2 - - - -
345J LEU* 1.3 75.9 - - - +
347J ALA* 1.3 60.3 + - + +
348J ALA 3.7 0.3 + - - -
349J ALA* 4.8 3.6 + - - +
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Residues in contact with ALA 347 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343J GLU 3.3 12.7 + - - +
344J SER 3.6 1.5 + - - +
345J LEU 3.1 0.6 - - - -
346J ALA* 1.3 77.7 - - + +
348J ALA* 1.3 65.9 + - - +
349J ALA 3.0 3.7 + - - -
350J SER* 2.9 24.4 + - - +
351J ILE* 3.1 13.6 + - + +
361J GLU* 3.6 40.4 - - + +
362J LEU* 4.3 11.4 - - + -
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Residues in contact with ALA 348 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344J SER 3.2 8.8 + - - +
345J LEU* 3.0 19.6 + - + +
347J ALA* 1.3 76.1 - - - +
349J ALA* 1.3 56.5 + - - +
351J ILE* 3.6 1.6 + - - +
352J SER* 3.0 30.9 + - - -
465J HIS* 4.5 6.9 + - - -
469J LYS* 3.5 37.3 + - + +
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Residues in contact with ALA 349 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345J LEU 4.7 1.0 + - - -
346J ALA 4.8 3.8 + - - +
347J ALA 3.0 1.2 + - - -
348J ALA* 1.3 77.2 - - - +
350J SER* 1.3 63.6 + - - +
352J SER* 3.2 8.7 + - - -
353J GLU* 3.1 30.6 + - - +
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Residues in contact with SER 350 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347J ALA* 2.9 17.4 + - - -
349J ALA* 1.3 78.2 - - - +
351J ILE* 1.3 50.8 + - - +
353J GLU* 3.0 12.3 + - - +
354J HIS* 2.7 39.4 + - - +
357J LYS* 4.5 19.1 - - - -
361J GLU* 3.9 23.6 + - - +
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Residues in contact with ILE 351 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162J ASP* 4.4 13.7 - - - +
166J ARG* 5.8 0.2 + - - -
347J ALA* 3.1 18.4 + - + +
348J ALA 4.0 2.9 - - - +
350J SER* 1.3 80.1 + - - +
352J SER* 1.3 67.1 + - - +
354J HIS 3.6 7.0 - - - -
355J PRO* 3.1 32.8 - - + +
357J LYS* 4.4 3.6 - - - -
358J ALA* 3.5 27.4 - - + +
361J GLU* 4.6 2.0 - - + -
362J LEU* 3.4 37.7 - - + -
462J LEU* 4.7 0.7 - - + -
465J HIS* 3.7 31.6 - - + +
466J HIS* 5.1 3.6 - - + +
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Residues in contact with SER 352 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166J ARG* 2.8 33.8 + - - +
348J ALA 3.0 19.7 + - - -
349J ALA* 3.3 9.4 - - - -
350J SER 3.1 0.2 - - - -
351J ILE* 1.3 79.2 - - - +
353J GLU* 1.3 59.9 + - - +
355J PRO* 4.4 5.5 - - - +
469J LYS* 5.6 0.9 - - - -
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Residues in contact with GLU 353 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349J ALA* 3.1 18.4 + - - +
350J SER* 3.0 10.7 + - - +
352J SER* 1.3 80.4 - - - +
354J HIS* 1.3 88.9 + - + +
355J PRO* 3.8 5.2 - - - +
356J GLN* 5.3 0.2 + - - -
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Residues in contact with HIS 354 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350J SER* 2.7 16.4 + - - +
351J ILE* 3.4 4.5 - - - -
353J GLU* 1.3 103.1 + - + +
355J PRO* 1.4 69.2 - - - +
356J GLN* 3.0 21.1 - - - +
357J LYS* 2.9 53.3 + - + +
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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) + - + + + + + -
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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