Contacts of the helix formed by residues 388 - 406 (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 PRO 388 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387J PHE* 1.3 110.2 - - + +
389J TYR* 1.3 82.2 + - + +
390J ASP* 3.2 5.2 - - - +
391J TRP* 3.0 8.4 + - + +
392J ILE* 2.9 36.5 + - + +
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Residues in contact with TYR 389 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379J TRP* 3.6 29.4 - + - -
380J VAL* 4.8 7.6 - - + +
383J GLN* 3.8 34.9 + - + -
384J GLN* 3.4 28.9 - - + +
386J THR* 3.1 31.0 + - - +
387J PHE 4.2 1.8 - - - -
388J PRO* 1.3 94.1 - - + +
390J ASP* 1.3 57.5 + - - +
392J ILE* 2.8 18.3 + - + +
393J SER* 2.7 36.3 + - - -
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Residues in contact with ASP 390 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307J ALA* 5.2 3.4 - - - +
309J THR* 6.4 2.0 - - + -
385J THR* 3.6 20.4 + - + +
386J THR 3.3 3.2 + - - -
387J PHE* 3.0 34.8 + - - +
388J PRO* 3.2 4.7 - - - +
389J TYR* 1.3 74.6 - - - +
391J TRP* 1.3 83.3 + - - -
393J SER* 2.8 21.4 + - - -
394J LEU* 3.2 17.9 + - + +
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Residues in contact with TRP 391 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387J PHE* 3.4 38.5 - + + -
388J PRO* 3.2 9.9 - - + +
390J ASP* 1.3 90.3 + - - +
392J ILE* 1.3 68.8 + - + +
394J LEU* 2.7 29.9 + - + +
395J ILE* 2.9 34.7 + - + +
320M PHE* 6.5 1.6 - + - -
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Residues in contact with ILE 392 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376J ILE* 4.0 20.4 - - + -
379J TRP* 4.4 11.0 - - + -
380J VAL* 3.8 16.8 - - + -
388J PRO* 2.9 34.9 + - + +
389J TYR* 2.8 29.0 + - + +
391J TRP* 1.3 73.0 - - + +
393J SER* 1.3 64.5 + - - +
395J ILE* 3.1 11.6 + - + +
396J ALA* 2.9 24.4 + - + +
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Residues in contact with SER 393 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303J ALA* 4.7 11.2 - - - -
306J ARG* 6.1 3.4 - - - -
307J ALA* 3.5 21.3 - - - +
377J LEU* 4.9 1.7 - - - +
380J VAL* 4.6 19.4 - - - +
389J TYR 2.7 16.2 + - - -
390J ASP* 2.8 26.7 + - - -
392J ILE* 1.3 74.5 - - - +
394J LEU* 1.3 54.7 + - - +
396J ALA* 3.3 6.6 + - - +
397J SER* 2.6 39.8 + - - -
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Residues in contact with LEU 394 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307J ALA* 4.2 16.8 - - + +
308J PHE* 3.7 32.1 - - + -
312J VAL* 3.9 29.2 - - + -
390J ASP* 3.4 12.3 - - + +
391J TRP* 2.7 32.3 + - + +
393J SER* 1.3 78.8 + - - +
395J ILE* 1.3 58.8 + - + +
397J SER* 3.3 1.4 + - - -
398J ALA* 2.8 32.0 + - + +
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Residues in contact with ILE 395 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391J TRP* 2.9 37.6 + - + +
392J ILE* 3.6 9.2 - - + +
394J LEU* 1.3 72.9 - - + +
396J ALA* 1.3 53.9 + - - +
398J ALA* 3.0 9.1 - - + +
399J TYR* 2.7 37.7 + - + +
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Residues in contact with ALA 396 (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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373J ASP* 2.7 41.8 - - - +
376J ILE* 5.0 9.6 - - + -
377J LEU* 3.9 22.4 - - + -
380J VAL* 5.6 0.2 - - + -
392J ILE* 2.9 17.4 + - + +
393J SER* 3.4 8.5 - - - +
395J ILE* 1.3 77.6 - - - +
397J SER* 1.3 63.3 + - - +
399J TYR* 3.1 2.8 + - - -
400J TRP* 3.0 9.4 + - - +
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Residues in contact with SER 397 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304J ILE* 3.7 40.5 + - - +
307J ALA* 3.8 4.9 - - - +
308J PHE* 4.1 24.2 - - - -
377J LEU* 4.4 1.4 - - - +
393J SER 2.6 26.8 + - - -
394J LEU* 3.7 4.7 - - - -
396J ALA* 1.3 73.4 - - - +
398J ALA* 1.3 64.1 + - - +
400J TRP* 3.1 12.1 + - - +
401J PHE* 3.1 25.8 - - - -
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Residues in contact with ALA 398 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308J PHE* 5.7 1.0 - - - -
394J LEU* 2.8 16.2 + - + +
395J ILE* 3.0 16.2 - - + +
397J SER* 1.3 79.4 - - - +
399J TYR* 1.3 65.1 + - - +
401J PHE* 3.3 5.1 + - - +
402J ALA* 3.0 21.7 + - - +
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Residues in contact with TYR 399 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366J TYR* 2.7 43.1 + + - +
369J LEU* 3.2 24.2 - - + +
370J LEU* 3.6 26.0 - - + -
373J ASP* 3.8 21.3 - - + +
395J ILE* 2.7 18.7 + - + +
396J ALA* 3.6 7.2 - - - +
398J ALA* 1.3 73.4 - - - +
400J TRP* 1.3 67.8 + - - +
402J ALA* 3.0 11.2 - - + +
403J TYR* 2.8 30.1 + - + +
407J ILE* 3.9 20.6 - - + -
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Residues in contact with TRP 400 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J PHE* 4.7 7.4 - + - -
116J LEU* 6.0 0.7 - - + -
301J PHE* 5.0 8.7 - + - -
304J ILE* 4.5 8.3 - - + -
339J ALA* 2.9 49.3 + - + +
342J VAL* 4.0 8.6 - - + +
343J MET* 4.2 23.3 - - + -
370J LEU* 3.5 33.4 - - + -
373J ASP* 3.6 11.6 + - - +
374J PHE* 4.0 35.9 - + + -
377J LEU* 4.3 11.2 - - + -
396J ALA 3.0 11.8 + - - +
397J SER* 3.1 14.8 + - - +
399J TYR* 1.3 80.9 - - - +
401J PHE* 1.3 73.9 + + + +
403J TYR* 3.1 15.1 + - - +
404J PHE* 3.4 28.3 - + - -
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Residues in contact with PHE 401 (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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304J ILE* 4.6 11.7 - - + -
308J PHE* 5.3 7.6 - + - -
335J ALA* 3.3 31.0 - - + -
338J GLY* 4.0 6.5 - - - -
339J ALA* 3.6 28.9 - - + -
342J VAL* 4.1 9.6 - - + -
397J SER* 3.1 30.9 + - - -
398J ALA* 4.0 4.0 - - - +
400J TRP* 1.3 81.7 - + - +
402J ALA* 1.3 59.6 + - - +
404J PHE* 3.2 3.7 + - - +
405J LEU* 2.7 62.5 + - + +
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Residues in contact with ALA 402 (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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398J ALA 3.0 15.7 + - - +
399J TYR* 3.0 27.4 - - + +
401J PHE* 1.3 77.2 - - - +
403J TYR* 1.3 53.8 + - - +
406J VAL* 2.9 37.8 + - + +
407J ILE* 3.0 20.1 + - + -
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Residues in contact with TYR 403 (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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116J LEU* 4.9 6.4 + - + +
121J TYR* 5.3 0.9 + - - -
363J PHE* 3.3 32.0 - + - -
366J TYR* 3.9 45.1 - - + -
367J PHE* 3.9 11.3 - - - -
370J LEU* 3.3 33.8 - - + +
399J TYR* 2.8 17.1 + - + +
400J TRP 3.1 9.6 + - - +
402J ALA* 1.3 76.4 - - - +
404J PHE* 1.3 84.4 + + - +
407J ILE* 3.8 11.5 - - + +
408J LEU* 3.1 58.2 + - + +
411J LEU* 6.2 0.4 - - + -
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Residues in contact with PHE 404 (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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116J LEU* 4.4 12.1 - - + -
342J VAL* 3.9 31.6 - - + -
343J MET* 3.9 33.0 - - + -
346J VAL* 4.0 28.5 - - + -
349J LEU* 2.9 31.5 - - + +
370J LEU* 3.9 13.9 - - + -
400J TRP* 3.4 41.1 - + - -
401J PHE 3.2 3.8 + - - +
403J TYR* 1.3 104.8 - + - +
405J LEU* 1.3 63.8 + - + +
408J LEU* 4.3 4.4 - - + +
409J PRO* 3.4 7.8 - - - +
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Residues in contact with LEU 405 (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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342J VAL* 4.3 18.4 - - + -
345J LEU* 6.5 0.4 - - + -
349J LEU* 3.5 24.0 - - + -
401J PHE* 2.7 49.0 + - + +
404J PHE* 1.3 73.3 - - - +
406J VAL* 1.3 66.0 + - + +
409J PRO* 3.6 12.1 - - - +
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Residues in contact with VAL 406 (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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402J ALA* 2.9 20.4 + - + +
404J PHE 3.4 0.6 - - - -
405J LEU* 1.3 90.1 - - + +
407J ILE* 1.3 67.5 + - + +
409J PRO* 2.7 21.9 - - - +
410J ILE* 3.0 37.0 + - + +
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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