Contacts of the helix formed by residues 379 - 395 (chain J) in PDB entry 5GJQ
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 THR 379 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339J THR* 4.7 14.8 - - + +
340J ARG 5.4 3.6 - - - -
342J ILE* 5.3 2.0 - - - -
375J ARG* 3.4 29.6 + - - +
377J HIS* 5.7 2.5 - - + -
378J VAL* 1.3 81.9 - - - +
380J GLN* 1.3 65.5 + - - +
381J GLU* 3.2 22.6 + - - +
382J ASP* 3.7 19.0 + - - +
383J PHE* 3.9 4.9 - - - -
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Residues in contact with GLN 380 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340J ARG 5.4 0.4 + - - -
341J GLY 3.3 25.1 + - - +
342J ILE* 4.7 7.7 - - - +
343J ASN* 3.2 32.1 + - - +
346J LYS* 2.9 45.0 + - - +
347J ILE* 4.3 11.6 - - + +
379J THR* 1.3 73.0 - - - +
381J GLU* 1.3 69.6 + - - +
382J ASP 3.1 0.9 + - - -
383J PHE* 3.1 16.8 + - - +
384J GLU* 3.0 39.2 + - + +
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Residues in contact with GLU 381 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375J ARG* 4.1 10.2 + - - -
379J THR* 3.2 11.1 + - - +
380J GLN* 1.3 78.0 - - - +
382J ASP* 1.3 75.6 + - - +
384J GLU* 2.9 26.4 + - - +
385J MET* 3.0 26.8 + - + +
187Q ARG* 3.5 18.5 + - - -
191Q THR* 2.7 41.9 + - + +
194Q ARG* 3.5 27.1 + - - -
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Residues in contact with ASP 382 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366J ALA* 3.8 20.6 - - - +
369J TYR* 4.2 8.5 - - + +
370J ALA* 3.1 33.9 + - - +
373J GLU* 6.1 0.2 - - - +
375J ARG* 4.4 14.0 + - - -
378J VAL* 3.6 16.7 - - + +
379J THR* 3.7 18.8 + - - +
380J GLN 3.1 0.2 + - - -
381J GLU* 1.3 89.3 - - - +
383J PHE* 1.3 57.4 + - - +
385J MET* 2.7 33.4 + - - +
386J ALA* 3.0 10.9 + - - +
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Residues in contact with PHE 383 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329J LEU* 4.4 7.9 - - + -
333J SER* 4.0 6.1 - - - -
336J MET* 4.1 9.0 - - - -
338J LEU* 2.9 50.9 - - + -
342J ILE* 3.8 9.6 - - + -
344J LEU* 5.2 0.2 - - + -
347J ILE* 3.1 31.9 - - + -
362J VAL* 4.0 15.1 - - + +
363J CYS* 3.5 33.7 - - - -
366J ALA* 3.7 21.5 - - + +
378J VAL* 3.9 1.8 - - + -
379J THR 3.9 11.2 - - - -
380J GLN 3.1 3.9 + - - +
382J ASP* 1.3 78.8 - - - +
384J GLU* 1.3 63.4 + - - +
385J MET 3.1 0.2 + - - -
386J ALA* 3.1 4.7 + - - +
387J VAL* 3.0 28.5 + - - +
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Residues in contact with GLU 384 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346J LYS* 4.1 8.0 + - - +
347J ILE* 4.3 12.1 - - + -
350J LEU* 4.6 17.4 - - + +
380J GLN* 3.0 47.8 + - + +
381J GLU* 2.9 20.4 + - - +
383J PHE* 1.3 77.1 - - - +
385J MET* 1.3 59.4 + - - +
387J VAL* 3.4 20.9 - - - +
388J ALA 4.0 1.6 + - - -
191Q THR* 4.4 12.3 - - - +
195Q THR* 3.2 24.3 - - + +
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Residues in contact with MET 385 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369J TYR* 3.7 22.7 - - + +
381J GLU* 3.2 33.7 - - + +
382J ASP* 2.7 12.2 + - - +
384J GLU* 1.3 74.0 - - - +
386J ALA* 1.3 60.5 + - - +
387J VAL 3.0 1.8 - - - -
388J ALA* 2.8 25.3 + - - +
389J LYS 2.9 8.7 + - - -
194Q ARG* 5.1 6.7 - - + +
195Q THR* 3.7 23.6 - - + +
198Q ASN* 3.8 4.6 + - - +
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Residues in contact with ALA 386 (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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362J VAL* 3.1 33.9 - - + +
365J GLU* 3.5 15.9 - - + -
366J ALA* 3.7 7.4 - - - +
369J TYR* 3.7 3.7 - - - -
382J ASP 3.0 5.1 + - - +
383J PHE 3.1 8.3 + - - +
385J MET* 1.3 75.9 - - - +
387J VAL* 1.3 59.3 + - - +
389J LYS* 3.9 10.8 - - - -
390J VAL* 2.4 40.1 + - - +
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Residues in contact with VAL 387 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347J ILE* 4.0 21.8 - - + +
350J LEU* 4.0 29.8 - - + +
351J MET* 5.0 4.3 - - + +
362J VAL* 3.9 13.4 - - + +
383J PHE 3.0 18.9 + - - +
384J GLU* 3.4 18.4 - - - +
386J ALA* 1.3 73.8 - - - +
388J ALA* 1.3 54.2 + - - +
390J VAL* 3.5 0.5 - - - +
391J MET* 2.5 63.8 + - - +
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Residues in contact with ALA 388 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384J GLU 4.0 1.5 + - - +
385J MET 2.8 14.4 + - - +
387J VAL* 1.3 77.7 - - - +
389J LYS* 1.3 53.7 + - - +
391J MET* 4.2 6.3 - - - +
392J GLN* 2.2 42.3 + - - +
195Q THR* 3.4 28.0 - - - +
198Q ASN* 3.6 15.3 - - + -
199Q ALA* 3.8 13.6 - - + +
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Residues in contact with LYS 389 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365J GLU* 2.5 46.5 + - + +
369J TYR* 3.1 25.8 + - + +
372J ARG* 4.1 19.8 - - - +
385J MET 2.9 4.9 + - - -
386J ALA* 2.9 14.4 + - - +
388J ALA* 1.3 76.7 - - - +
390J VAL* 1.3 61.9 + - - +
392J GLN* 3.1 20.0 - - + +
393J LYS* 3.2 15.7 + - + +
175K GLN* 4.5 5.4 - - - +
176K GLU* 5.6 0.8 + - - -
179K GLU* 4.2 9.5 + - - -
329K ARG* 4.9 4.9 - - - +
198Q ASN* 3.4 17.9 - - - +
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Residues in contact with VAL 390 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358J GLU* 4.1 14.6 - - + +
361J GLY* 3.5 10.3 - - - +
362J VAL* 3.3 47.1 - - + +
365J GLU* 4.7 7.2 - - + -
386J ALA 2.4 28.4 + - - +
387J VAL 3.7 2.5 - - - +
389J LYS* 1.3 68.0 - - - +
391J MET* 1.3 49.9 + - + +
392J GLN 2.9 4.0 - - - -
393J LYS* 2.7 14.7 + - + +
394J ASP* 2.4 56.2 + - - +
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Residues in contact with MET 391 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350J LEU 3.7 6.3 - - - +
351J MET* 4.3 6.7 - - - -
352J PRO* 3.1 44.2 - - + +
362J VAL* 6.3 0.7 - - + -
387J VAL* 2.5 47.1 + - - +
388J ALA* 3.0 5.2 - - - +
390J VAL* 1.3 72.5 - - + +
392J GLN* 1.3 55.0 + - - +
394J ASP* 3.5 23.8 - - + +
395J SER* 2.9 33.3 + - - +
199Q ALA* 6.4 0.4 - - - -
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Residues in contact with GLN 392 (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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388J ALA 2.2 29.2 + - - +
389J LYS* 3.1 12.3 - - + +
391J MET* 1.3 70.2 - - - +
393J LYS* 1.3 57.3 + - + +
395J SER* 3.2 7.8 + - - -
396J GLU* 2.8 43.8 + - - +
198Q ASN* 3.2 30.2 + - - +
199Q ALA* 3.5 21.3 + - - +
200Q ILE 3.8 11.3 + - - -
201Q TYR* 5.4 0.8 - - - +
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Residues in contact with LYS 393 (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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389J LYS* 3.2 14.8 + - + +
390J VAL* 2.7 15.0 + - + +
392J GLN* 1.3 70.7 - - + +
394J ASP* 1.3 59.1 + - - +
396J GLU* 2.7 61.1 + - - +
329K ARG* 6.1 1.0 - - - +
330K LYS 5.0 9.9 + - - -
332K GLU* 5.0 11.9 + - - +
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Residues in contact with ASP 394 (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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353J GLY 5.7 1.2 - - - -
354J ALA* 4.8 2.9 - - - +
358J GLU* 3.4 39.9 - - - +
390J VAL* 2.4 50.0 + - - +
391J MET* 3.5 23.8 - - + +
393J LYS* 1.3 68.8 - - - +
395J SER* 1.3 58.1 + - - +
396J GLU 3.5 1.4 + - - -
397J LYS 4.3 7.4 - - - +
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Residues in contact with SER 395 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391J MET* 2.9 22.3 + - - +
392J GLN* 3.3 7.2 - - - -
393J LYS 3.1 0.4 - - - -
394J ASP* 1.3 75.0 - - - +
396J GLU* 1.3 55.9 + - - +
397J LYS 4.1 3.0 + - - -
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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
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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