Contacts of the helix formed by residues 388 - 406 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387P PHE* 1.3 111.8 - - + +
389P TYR* 1.3 83.4 + - + +
390P ASP* 3.2 5.6 - - - +
391P TRP* 3.0 9.1 + - + +
392P ILE* 2.9 39.5 + - + +
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Residues in contact with TYR 389 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379P TRP* 3.6 28.8 - + - -
380P VAL* 4.8 7.8 - - + +
383P GLN* 3.8 32.5 + - + -
384P GLN* 3.4 29.8 - - + +
386P THR* 3.1 28.8 + - - +
387P PHE 4.2 2.2 - - - -
388P PRO* 1.3 93.4 - - + +
390P ASP* 1.3 55.9 + - - +
392P ILE* 2.8 18.6 + - + +
393P SER* 2.7 36.6 + - - -
114Q MET 5.5 0.7 + - - -
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Residues in contact with ASP 390 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307P ALA* 5.2 3.4 - - - +
385P THR* 3.6 19.4 + - + +
386P THR 3.3 2.9 + - - -
387P PHE* 3.1 33.1 + - - +
388P PRO* 3.2 4.5 - - - +
389P TYR* 1.3 73.8 - - - +
391P TRP* 1.3 85.2 + - - -
393P SER* 2.9 21.1 + - - -
394P LEU* 3.2 18.4 + - + +
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Residues in contact with TRP 391 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313P TRP* 6.3 4.7 - + - -
387P PHE* 3.9 26.2 - + + -
388P PRO* 3.2 10.1 - - + +
389P TYR 3.0 0.2 - - - -
390P ASP* 1.3 100.9 + - - +
392P ILE* 1.3 68.7 + - + +
394P LEU* 2.8 28.5 + - + +
395P ILE* 2.9 33.2 + - + +
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Residues in contact with ILE 392 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376P ILE* 4.1 18.4 - - + -
379P TRP* 4.4 11.2 - - + -
380P VAL* 3.8 18.8 - - + -
388P PRO* 2.9 34.9 + - + +
389P TYR* 2.8 28.9 + - + +
391P TRP* 1.3 73.7 - - + +
393P SER* 1.3 64.9 + - - +
395P ILE* 3.1 12.3 + - + +
396P ALA* 2.9 24.0 + - + +
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Residues in contact with SER 393 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303P ALA* 4.8 11.2 - - - -
306P ARG* 6.2 2.2 - - - -
307P ALA* 3.5 22.1 - - - +
377P LEU* 4.9 1.5 - - - +
380P VAL* 4.6 18.6 - - - +
389P TYR 2.7 16.4 + - - -
390P ASP* 2.9 19.4 + - - -
392P ILE* 1.3 73.7 - - - +
394P LEU* 1.3 56.6 + - - +
396P ALA* 3.3 7.6 + - - +
397P SER* 2.6 39.7 + - - -
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Residues in contact with LEU 394 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307P ALA* 4.1 15.3 - - + +
308P PHE* 3.6 33.4 - - + -
312P VAL* 3.8 30.1 - - + -
390P ASP 3.4 13.7 - - - +
391P TRP* 2.8 30.3 + - + +
393P SER* 1.3 74.2 + - - +
395P ILE* 1.3 65.2 + - + +
397P SER* 3.4 0.6 + - - -
398P ALA* 2.9 26.2 + - + +
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Residues in contact with ILE 395 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391P TRP* 2.9 37.5 + - + +
392P ILE* 3.7 9.4 - - + +
394P LEU* 1.3 72.7 - - + +
396P ALA* 1.3 53.4 + - - +
398P ALA* 3.0 9.4 - - + +
399P TYR* 2.7 38.7 + - + +
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Residues in contact with ALA 396 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373P ASP* 2.7 42.7 - - - +
376P ILE* 5.0 7.6 - - + -
377P LEU* 3.9 23.1 - - + +
380P VAL* 5.6 0.2 - - + -
392P ILE* 2.9 13.0 + - + +
393P SER* 3.3 12.8 - - - +
395P ILE* 1.3 78.0 - - - +
397P SER* 1.3 62.9 + - - +
399P TYR* 3.1 2.8 + - - -
400P TRP* 3.0 9.7 + - - +
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Residues in contact with SER 397 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304P ILE* 3.6 39.4 - - - +
307P ALA* 3.8 4.7 - - - +
308P PHE* 4.1 25.1 - - - -
377P LEU* 4.4 1.6 - - - +
393P SER 2.6 26.1 + - - -
394P LEU* 3.7 4.3 - - - -
396P ALA* 1.3 72.4 - - - +
398P ALA* 1.3 63.4 + - - +
400P TRP* 3.1 11.9 + - - +
401P PHE* 3.1 26.1 - - - -
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Residues in contact with ALA 398 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308P PHE* 5.6 0.9 - - - -
394P LEU* 2.9 16.2 + - + +
395P ILE* 3.0 15.5 - - + +
397P SER* 1.3 79.2 - - - +
399P TYR* 1.3 62.6 + - - +
401P PHE* 3.3 4.6 + - - +
402P ALA* 3.0 22.7 + - - +
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Residues in contact with TYR 399 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366P TYR* 2.7 43.5 + + - +
369P LEU* 3.3 23.1 - - + +
370P LEU* 3.6 25.4 - - + -
373P ASP* 3.9 21.3 - - + +
395P ILE* 2.7 19.3 + - + +
396P ALA* 3.5 7.6 - - - +
398P ALA* 1.3 74.4 - - - +
400P TRP* 1.3 66.3 + - - +
402P ALA* 3.0 9.4 - - + +
403P TYR* 2.9 30.5 + - + +
407P ILE* 3.9 20.2 - - + -
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Residues in contact with TRP 400 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P PHE* 4.7 7.2 - + - -
116P LEU* 6.0 0.7 - - + -
301P PHE* 5.1 9.4 - + - -
304P ILE* 4.5 7.2 - - + -
339P ALA* 2.9 48.5 + - + +
342P VAL* 4.1 8.0 - - + +
343P MET* 4.2 23.3 - - + -
370P LEU* 3.5 34.1 - - + -
373P ASP* 3.6 10.1 + - - +
374P PHE* 4.0 36.3 - + + -
377P LEU* 4.3 10.8 - - + -
396P ALA 3.0 12.0 + - - +
397P SER* 3.1 15.0 + - - +
399P TYR* 1.3 80.5 - - - +
401P PHE* 1.3 74.0 + + + +
403P TYR* 3.2 8.0 + - - +
404P PHE* 3.3 36.8 - + - -
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Residues in contact with PHE 401 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304P ILE* 4.7 10.8 - - + -
308P PHE* 5.3 5.4 - + - -
335P ALA* 3.3 32.8 - - + -
338P GLY* 3.9 7.6 - - - -
339P ALA* 3.6 28.3 - - + -
342P VAL* 4.1 9.6 - - + -
397P SER* 3.1 23.9 + - - -
398P ALA* 4.1 4.0 - - - +
400P TRP* 1.3 82.8 - + + +
402P ALA* 1.3 58.1 + - - +
404P PHE* 3.1 3.8 + - - +
405P LEU* 2.7 62.3 + - + +
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Residues in contact with ALA 402 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398P ALA 3.0 15.5 + - - +
399P TYR* 3.0 23.6 - - + +
401P PHE* 1.3 76.0 - - - +
403P TYR* 1.3 57.1 + - - +
406P VAL* 2.9 36.7 + - + +
407P ILE* 3.0 19.5 + - + -
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Residues in contact with TYR 403 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P LEU* 4.9 7.4 + - + +
121P TYR* 5.3 0.3 + - - -
363P PHE* 3.3 31.4 - + - -
366P TYR* 3.9 45.5 - - + -
367P PHE* 3.9 11.4 - - - -
370P LEU* 3.3 37.0 - - + -
399P TYR* 2.9 17.0 + - + +
400P TRP 3.4 9.4 - - - +
401P PHE 3.2 0.2 - - - -
402P ALA* 1.3 76.5 - - - +
404P PHE* 1.3 78.3 + + - +
407P ILE* 3.9 10.5 - - + +
408P LEU* 3.0 60.2 + - + +
411P LEU* 6.0 0.4 - - + -
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Residues in contact with PHE 404 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P LEU* 4.4 12.3 - - + -
342P VAL* 3.9 32.5 - - + -
343P MET* 3.9 32.3 - - + -
346P VAL* 4.0 28.9 - - + -
349P LEU* 2.8 23.4 - - + +
370P LEU* 3.9 13.7 - - + -
400P TRP* 3.3 39.5 - + - -
401P PHE 3.1 4.6 + - - +
403P TYR* 1.3 107.3 - + - +
405P LEU* 1.3 61.3 + - - +
408P LEU* 4.3 4.6 - - + +
409P PRO* 3.2 16.3 - - - +
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Residues in contact with LEU 405 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342P VAL* 4.3 18.4 - - + -
345P LEU* 6.5 0.9 - - + -
349P LEU* 3.5 23.8 - - + -
401P PHE* 2.7 49.1 + - + +
404P PHE* 1.3 73.1 - - + +
406P VAL* 1.3 64.8 + - + +
409P PRO* 3.4 11.5 - - - +
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Residues in contact with VAL 406 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402P ALA* 2.9 19.2 + - - +
404P PHE 3.5 0.8 - - - -
405P LEU* 1.3 90.4 - - + +
407P ILE* 1.3 58.6 + - + +
409P PRO* 2.7 20.7 - - - +
410P ILE* 2.8 47.1 + - + +
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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