Contacts of the helix formed by residues 388 - 406 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A PHE* 1.3 113.9 - - + +
389A TYR* 1.3 83.2 + - + +
390A ASP* 3.2 4.9 - - - -
391A TRP* 3.0 7.7 + - + +
392A ILE* 2.9 36.2 + - + +
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Residues in contact with TYR 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ARG* 6.0 0.4 - - - +
379A TRP* 3.6 27.9 - + - -
380A VAL* 4.7 7.0 - - + +
383A GLN* 3.8 34.3 + - + -
384A GLN* 3.4 29.6 - - + +
386A THR* 3.1 27.6 + - - +
387A PHE 4.2 1.8 - - - -
388A PRO* 1.3 94.1 - - + +
390A ASP* 1.3 55.9 + - - +
392A ILE* 2.8 19.1 + - + +
393A SER* 2.7 37.0 + - - -
114B MET* 5.5 1.9 + - - +
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Residues in contact with ASP 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA* 5.1 3.6 - - - +
384A GLN 4.9 0.2 + - - -
385A THR* 3.6 19.2 + - + +
386A THR* 3.2 3.7 + - - -
387A PHE* 3.0 34.2 + - - +
388A PRO* 3.2 4.0 - - - +
389A TYR* 1.3 74.2 - - - +
391A TRP* 1.3 83.7 + - - -
393A SER* 2.7 22.5 + - - -
394A LEU* 3.1 17.5 + - - +
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Residues in contact with TRP 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TRP* 6.4 2.7 - + - -
387A PHE* 3.6 35.3 - + + -
388A PRO* 3.2 9.9 - - + +
389A TYR 3.0 0.2 - - - -
390A ASP* 1.3 91.6 + - - +
392A ILE* 1.3 68.0 + - + +
394A LEU* 2.8 29.3 + - + +
395A ILE* 2.9 33.9 + - + +
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Residues in contact with ILE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A ILE* 4.0 19.5 - - + -
379A TRP* 4.3 12.1 - - + -
380A VAL* 3.8 17.5 - - + -
388A PRO* 2.9 36.4 + - + +
389A TYR* 2.8 27.8 + - + +
391A TRP* 1.3 72.5 - - + +
393A SER* 1.3 64.5 + - - +
395A ILE* 3.1 11.1 + - + +
396A ALA* 2.8 24.9 + - + +
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Residues in contact with SER 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA* 4.7 11.9 - - - -
306A ARG* 6.1 3.4 - - - -
307A ALA* 3.6 21.9 - - - +
377A LEU* 5.0 1.3 - - - +
380A VAL* 4.6 20.1 - - - +
389A TYR 2.7 16.6 + - - -
390A ASP* 2.7 27.0 + - - -
392A ILE* 1.3 73.5 - - - +
394A LEU* 1.3 57.9 + - - +
396A ALA* 3.1 7.5 + - - +
397A SER* 2.8 36.1 + - - -
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ALA* 4.2 14.6 - - + +
308A PHE* 3.8 32.8 - - + -
312A VAL* 4.0 28.0 - - + -
314A VAL* 6.3 0.4 - - + -
390A ASP* 3.4 12.1 - - + +
391A TRP* 2.8 27.6 + - + +
393A SER* 1.3 80.1 + - - +
395A ILE* 1.3 67.6 + - + +
397A SER* 3.4 1.7 + - - -
398A ALA* 2.8 26.2 + - + +
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Residues in contact with ILE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A TRP* 2.9 37.7 + - + +
392A ILE* 3.7 8.5 - - + +
394A LEU* 1.3 73.9 - - + +
396A ALA* 1.3 53.2 + - - +
398A ALA* 3.0 9.6 - - + +
399A TYR* 2.7 37.2 + - + +
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Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ASP* 2.8 41.8 - - - +
376A ILE* 4.9 9.2 - - + -
377A LEU* 4.0 22.7 - - + -
380A VAL* 5.6 0.4 - - + -
392A ILE* 2.8 13.8 + - + +
393A SER* 3.3 13.0 - - - +
395A ILE* 1.3 77.0 - - - +
397A SER* 1.3 64.1 + - - +
399A TYR* 3.1 3.1 + - - -
400A TRP* 3.0 8.5 + - - +
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Residues in contact with SER 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 3.7 37.8 + - - +
307A ALA* 3.8 4.7 - - - +
308A PHE* 4.1 23.8 - - - -
377A LEU* 4.5 2.3 - - - +
393A SER 2.8 21.8 + - - -
394A LEU* 3.8 3.8 - - - -
396A ALA* 1.3 72.6 - - - +
398A ALA* 1.3 63.2 + - - +
400A TRP* 3.1 14.3 + - - +
401A PHE* 3.1 25.7 - - - -
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A PHE* 5.6 0.9 - - - -
394A LEU* 2.8 16.9 + - + +
395A ILE* 3.0 16.6 - - + +
397A SER* 1.3 78.6 - - - +
399A TYR* 1.3 63.8 + - - +
401A PHE* 3.3 5.8 + - - +
402A ALA* 3.0 21.6 + - - +
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Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A TYR* 2.8 43.1 + + - +
369A LEU* 3.2 22.7 - - + +
370A LEU* 3.6 26.0 - - - -
373A ASP* 3.8 24.0 - - + +
395A ILE* 2.7 18.3 + - + +
396A ALA* 3.5 7.6 - - - +
398A ALA* 1.3 73.4 - - - +
400A TRP* 1.3 65.5 + - - +
402A ALA* 2.9 11.3 - - + +
403A TYR* 2.9 28.8 + - + +
407A ILE* 3.9 19.6 - - + +
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Residues in contact with TRP 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 4.7 6.5 - + - -
116A LEU* 6.0 0.9 - - + -
301A PHE* 5.1 9.4 - + - -
304A ILE* 4.5 7.2 - - + -
339A ALA* 2.9 49.3 + - + +
342A VAL* 4.0 8.6 - - + +
343A MET* 4.2 22.4 - - + -
370A LEU* 3.5 32.3 - - + -
373A ASP* 3.6 11.1 + - - +
374A PHE* 4.0 36.8 - + + -
377A LEU* 4.3 11.9 - - + -
396A ALA 3.0 10.9 + - - +
397A SER* 3.1 14.6 + - - +
399A TYR* 1.3 80.2 - - - +
401A PHE* 1.3 73.3 + + + +
403A TYR* 3.1 15.4 + - - +
404A PHE* 3.4 29.2 - + - -
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Residues in contact with PHE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ILE* 4.6 11.9 - - + -
308A PHE* 5.3 5.4 - + - -
335A ALA* 3.2 33.0 - - + -
338A GLY* 4.0 6.7 - - - -
339A ALA* 3.6 29.4 - - + -
342A VAL* 4.1 9.2 - - + -
397A SER* 3.1 30.3 - - - -
398A ALA* 3.3 5.1 + - - +
400A TRP* 1.3 87.7 - + - +
402A ALA* 1.3 56.5 + - - +
404A PHE* 3.2 3.5 + - - +
405A LEU* 2.7 62.1 + - + +
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Residues in contact with ALA 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ALA 3.0 15.3 + - - +
399A TYR* 2.9 27.4 - - + +
401A PHE* 1.3 76.6 - - - +
403A TYR* 1.3 54.1 + - - +
406A VAL* 2.9 35.3 + - + +
407A ILE* 3.0 21.0 + - + -
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Residues in contact with TYR 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.9 7.4 + - + +
121A TYR* 5.3 0.5 + - - -
346A VAL* 5.8 0.2 - - + -
363A PHE* 3.3 32.3 - + - -
366A TYR* 3.9 44.6 - - + -
367A PHE* 4.0 10.1 - - - -
370A LEU* 3.3 31.6 - - + -
399A TYR* 2.9 16.0 + - + +
400A TRP 3.3 9.2 - - - +
402A ALA* 1.3 77.4 - - - +
404A PHE* 1.3 86.6 + + - +
407A ILE* 3.9 10.3 - - + +
408A LEU* 3.1 62.7 + - + +
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Residues in contact with PHE 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.3 12.1 - - + -
342A VAL* 4.0 31.2 - - + -
343A MET* 3.9 28.7 - - + -
346A VAL* 4.0 28.7 - - + -
349A LEU* 2.9 31.2 - - + +
370A LEU* 3.9 14.4 - - + -
400A TRP* 3.4 43.5 - + - -
401A PHE 3.2 4.0 + - - +
403A TYR* 1.3 109.4 - + - +
405A LEU* 1.3 63.6 + - + +
408A LEU* 4.3 3.9 - - + +
409A PRO* 3.4 8.3 - - - +
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A VAL* 4.3 18.2 - - + -
345A LEU* 6.6 0.2 - - + -
349A LEU* 3.5 22.2 - - + -
401A PHE* 2.7 49.2 + - + +
404A PHE* 1.3 73.7 - - + +
406A VAL* 1.3 64.6 + - + +
409A PRO* 3.6 12.3 - - - +
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A ALA* 2.9 20.6 + - + +
404A PHE 3.4 0.6 - - - -
405A LEU* 1.3 90.4 - - + +
407A ILE* 1.3 67.8 + - + +
409A PRO* 2.7 20.8 - - - +
410A ILE* 3.0 35.7 + - + +
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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