Contacts of the helix formed by residues 388 - 406 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D PHE* 1.3 115.6 - - + +
389D TYR* 1.3 83.0 + - + +
390D ASP* 3.2 5.2 - - - +
391D TRP* 3.0 9.2 + - + +
392D ILE* 2.9 36.8 + - + +
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Residues in contact with TYR 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D TRP* 3.6 28.5 - + - -
380D VAL* 4.8 6.9 - - + +
383D GLN* 3.8 34.1 + - + -
384D GLN* 3.4 28.7 - - + +
386D THR* 3.1 30.1 + - - +
387D PHE 4.2 2.0 - - - -
388D PRO* 1.3 93.2 - - + +
390D ASP* 1.3 56.1 + - - +
392D ILE* 2.8 18.6 + - + +
393D SER* 2.7 37.8 + - - -
114E MET* 5.5 1.4 + - - +
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Residues in contact with ASP 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D ALA* 5.1 3.4 - - - +
309D THR* 6.4 1.8 - - + -
384D GLN 4.9 0.2 + - - -
385D THR* 3.6 19.1 + - + +
386D THR 3.2 8.7 + - - -
387D PHE* 3.1 28.4 + - - +
388D PRO* 3.2 4.5 - - - +
389D TYR* 1.3 73.6 - - - +
391D TRP* 1.3 82.5 + - - -
393D SER* 2.8 21.2 + - - -
394D LEU* 3.2 18.7 + - - +
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Residues in contact with TRP 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D TRP* 6.4 3.4 - + - -
387D PHE* 4.1 23.6 - + + -
388D PRO* 3.2 9.4 - - + +
389D TYR 3.0 0.2 - - - -
390D ASP* 1.3 101.4 + - - +
392D ILE* 1.3 69.5 + - + +
394D LEU* 2.7 29.6 + - + +
395D ILE* 2.9 34.0 + - + +
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Residues in contact with ILE 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D ILE* 4.0 19.7 - - + -
379D TRP* 4.3 11.4 - - + -
380D VAL* 3.9 16.8 - - + -
388D PRO* 2.9 34.3 + - + +
389D TYR* 2.8 30.3 + - + +
391D TRP* 1.3 74.1 - - + +
393D SER* 1.3 64.3 + - - +
395D ILE* 3.1 11.5 + - + +
396D ALA* 2.9 24.8 + - + +
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Residues in contact with SER 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D ALA* 4.8 12.1 - - - -
306D ARG* 6.2 1.6 - - - -
307D ALA* 3.6 21.9 - - - +
377D LEU* 5.6 0.9 - - - -
380D VAL* 4.6 18.5 - - - +
389D TYR 2.7 16.8 + - - -
390D ASP* 2.8 26.5 + - - -
392D ILE* 1.3 73.7 - - - +
394D LEU* 1.3 58.7 + - - +
396D ALA* 3.3 6.6 - - - +
397D SER* 2.7 35.4 + - - -
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Residues in contact with LEU 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D ALA* 4.2 15.9 - - + +
308D PHE* 3.7 32.5 - - + -
312D VAL* 4.0 28.0 - - + -
390D ASP 3.4 12.6 - - - +
391D TRP* 2.7 31.5 + - + +
393D SER* 1.3 78.5 + - - +
395D ILE* 1.3 57.7 + - + +
397D SER* 3.4 0.6 + - - -
398D ALA* 2.9 31.5 + - + +
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Residues in contact with ILE 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D TRP* 2.9 38.2 + - + +
392D ILE* 3.7 8.7 - - + +
394D LEU* 1.3 72.9 - - + +
396D ALA* 1.3 53.6 + - - +
398D ALA* 3.0 9.2 - - + +
399D TYR* 2.7 37.2 + - + +
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Residues in contact with ALA 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D ASP* 2.7 41.9 - - - +
376D ILE* 5.0 9.6 - - + -
377D LEU* 3.9 23.3 - - + -
380D VAL* 5.6 0.2 - - + -
392D ILE* 2.9 17.7 + - + +
393D SER* 3.3 8.3 - - - +
395D ILE* 1.3 74.3 - - - +
397D SER* 1.3 66.5 + - - +
399D TYR* 3.2 2.0 + - - -
400D TRP* 3.1 9.2 + - - +
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Residues in contact with SER 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D ILE* 3.6 37.9 + - - +
307D ALA* 3.8 4.7 - - - +
308D PHE* 4.1 23.1 - - - -
377D LEU* 4.4 1.4 - - - +
393D SER* 2.7 26.2 + - - -
394D LEU* 3.7 4.3 - - - -
396D ALA* 1.3 71.5 - - - +
398D ALA* 1.3 66.1 + - - +
400D TRP* 3.0 16.3 + - - +
401D PHE* 3.1 22.6 - - - -
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Residues in contact with ALA 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D PHE* 5.6 1.1 - - - -
394D LEU* 2.9 16.3 + - + +
395D ILE* 3.0 15.5 - - + +
397D SER* 1.3 79.0 - - - +
399D TYR* 1.3 64.0 + - - +
401D PHE* 3.3 5.9 + - - +
402D ALA* 2.9 21.3 + - - +
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Residues in contact with TYR 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D TYR* 2.7 43.0 + + - +
369D LEU* 3.2 23.9 - - + +
370D LEU* 3.6 25.6 - - + -
373D ASP* 3.8 22.0 - - + +
395D ILE* 2.7 18.7 + - + +
396D ALA* 3.2 8.0 + - - +
398D ALA* 1.3 72.8 - - - +
400D TRP* 1.3 66.0 - - - +
402D ALA* 3.0 10.5 - - + +
403D TYR* 2.9 29.2 + - + +
407D ILE* 3.9 20.8 - - + +
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Residues in contact with TRP 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PHE* 4.7 6.5 - + - -
116D LEU* 6.0 0.9 - - + -
301D PHE* 5.1 9.4 - + - -
304D ILE* 4.5 7.2 - - + -
339D ALA* 2.9 49.6 + - + +
342D VAL* 4.0 7.5 - - + +
343D MET* 4.2 23.1 - - + -
370D LEU* 3.5 33.2 - - + -
373D ASP* 3.6 10.1 + - - +
374D PHE* 4.0 37.2 - + + -
377D LEU* 4.3 11.2 - - + -
396D ALA 3.1 11.3 + - - +
397D SER* 3.0 15.6 + - - +
399D TYR* 1.3 81.9 - - - +
401D PHE* 1.3 73.9 + + + +
403D TYR* 3.1 15.8 + - - +
404D PHE* 3.4 28.8 - + - -
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Residues in contact with PHE 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D ILE* 4.6 12.3 - - + -
308D PHE* 5.3 5.2 - + - -
335D ALA* 3.2 32.3 - - + -
338D GLY* 4.0 6.5 - - - -
339D ALA* 3.6 28.7 - - + -
342D VAL* 4.1 10.5 - - + -
397D SER* 3.1 23.8 - - - -
398D ALA* 3.3 4.7 + - - +
400D TRP* 1.3 82.1 - + - +
402D ALA* 1.3 59.3 + - - +
404D PHE* 3.2 3.9 + - - +
405D LEU* 2.7 62.1 + - + +
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Residues in contact with ALA 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398D ALA 2.9 15.1 + - - +
399D TYR* 3.0 26.9 - - + +
401D PHE* 1.3 77.2 - - - +
403D TYR* 1.3 54.7 + - - +
406D VAL* 2.9 36.8 + - + +
407D ILE* 3.0 19.5 + - + -
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Residues in contact with TYR 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LEU* 4.9 7.9 + - + +
121D TYR* 5.4 0.7 + - - -
363D PHE* 3.4 30.7 - + - -
366D TYR* 3.9 44.4 - - + -
367D PHE* 3.9 11.3 - - + -
370D LEU* 3.3 38.3 - - + +
399D TYR* 2.9 16.6 + - + +
400D TRP 3.3 9.4 - - - +
402D ALA* 1.3 77.8 - - - +
404D PHE* 1.3 78.6 + + - +
407D ILE* 3.9 11.2 - - + +
408D LEU* 3.2 60.0 + - + +
411D LEU* 6.0 0.4 - - + -
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Residues in contact with PHE 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LEU* 4.3 13.0 - - + -
342D VAL* 3.9 30.7 - - + -
343D MET* 3.9 29.8 - - + -
346D VAL* 4.1 27.6 - - + -
349D LEU* 2.9 31.0 - - + +
370D LEU* 3.9 13.5 - - + -
400D TRP* 3.4 44.9 - + - -
401D PHE 3.2 4.8 + - - +
403D TYR* 1.3 105.6 - + - +
405D LEU* 1.3 63.6 + - + +
408D LEU* 4.3 5.0 - - + +
409D PRO* 3.4 7.4 - - - +
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Residues in contact with LEU 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D VAL* 4.3 17.0 - - + -
349D LEU* 3.6 23.3 - - + -
401D PHE* 2.7 48.3 + - + +
404D PHE* 1.3 74.7 - - + +
406D VAL* 1.3 66.8 + - + +
409D PRO* 3.6 12.2 - - - +
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Residues in contact with VAL 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D ALA* 2.9 20.2 + - + +
404D PHE 3.4 0.6 - - - -
405D LEU* 1.3 90.2 - - + +
407D ILE* 1.3 65.6 + - + +
409D PRO* 2.7 22.7 - - - +
410D ILE* 3.0 38.0 + - + +
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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