Contacts of the helix formed by residues 388 - 406 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387G PHE* 1.3 114.8 - - + +
389G TYR* 1.3 83.2 + - + +
390G ASP* 3.2 4.3 - - - -
391G TRP* 3.0 8.0 + - + +
392G ILE* 2.9 38.7 + - + +
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Residues in contact with TYR 389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G ARG* 5.6 0.4 - - - +
379G TRP* 3.6 29.3 - + - -
380G VAL* 4.8 6.8 - - + +
383G GLN* 3.8 34.5 + - + -
384G GLN* 3.4 28.5 - - + +
386G THR* 3.1 29.2 + - - +
387G PHE 4.2 2.0 - - - -
388G PRO* 1.3 93.4 - - + +
390G ASP* 1.3 56.7 + - - +
392G ILE* 2.9 18.0 + - + +
393G SER* 2.7 36.9 + - - -
114H MET* 5.3 3.8 + - - +
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Residues in contact with ASP 390 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G ALA* 5.1 4.2 - - - +
384G GLN 4.9 0.2 + - - -
385G THR* 3.6 20.3 + - + +
386G THR* 3.3 3.1 + - - -
387G PHE* 3.0 34.1 + - - +
388G PRO* 3.2 4.3 - - - +
389G TYR* 1.3 74.3 - - - +
391G TRP* 1.3 83.1 + - - -
393G SER* 2.7 21.2 + - - -
394G LEU* 3.2 18.4 + - - +
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Residues in contact with TRP 391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G TRP* 6.1 7.0 - + - -
387G PHE* 3.7 32.1 - + + -
388G PRO* 3.2 9.6 - - + +
389G TYR 3.0 0.2 - - - -
390G ASP* 1.3 92.3 + - - +
392G ILE* 1.3 69.1 + - + +
394G LEU* 2.7 29.3 + - + +
395G ILE* 2.9 33.9 + - + +
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Residues in contact with ILE 392 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376G ILE* 4.0 20.6 - - + -
379G TRP* 4.3 12.1 - - + -
380G VAL* 3.8 16.6 - - + -
388G PRO* 2.9 35.2 + - + +
389G TYR* 3.3 24.5 - - + +
391G TRP* 1.3 77.6 - - + +
393G SER* 1.3 65.8 + - - +
395G ILE* 3.0 11.4 + - + +
396G ALA* 2.8 24.0 + - - +
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Residues in contact with SER 393 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G ALA* 4.7 11.2 - - - -
306G ARG* 5.9 4.0 - - - -
307G ALA* 3.6 21.5 - - - +
377G LEU* 4.9 1.2 - - - +
380G VAL* 4.6 19.2 - - - +
389G TYR 2.7 16.5 + - - -
390G ASP* 2.7 27.3 + - - -
392G ILE* 1.3 73.5 - - - +
394G LEU* 1.3 54.8 + - - +
396G ALA* 3.2 6.9 + - - +
397G SER* 2.7 39.2 + - - -
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Residues in contact with LEU 394 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G ALA* 4.2 14.4 - - + +
308G PHE* 3.7 33.9 - - + -
312G VAL* 4.0 28.7 - - + -
390G ASP* 3.2 12.3 + - + +
391G TRP* 2.7 33.0 + - + +
393G SER* 1.3 75.1 + - - +
395G ILE* 1.3 61.2 + - + +
397G SER* 3.7 1.2 - - - -
398G ALA* 2.8 32.9 + - + +
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Residues in contact with ILE 395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391G TRP* 2.9 38.0 + - + +
392G ILE* 3.6 9.6 - - + +
394G LEU* 1.3 72.5 - - + +
396G ALA* 1.3 53.1 + - - +
398G ALA* 3.0 9.6 - - + +
399G TYR* 2.7 37.4 + - + +
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Residues in contact with ALA 396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373G ASP* 2.7 41.3 - - - +
376G ILE* 4.9 8.7 - - + -
377G LEU* 3.9 24.5 - - + +
380G VAL* 5.6 0.2 - - + -
392G ILE* 2.8 16.9 + - + +
393G SER* 3.3 8.7 - - - +
395G ILE* 1.3 78.2 - - - +
397G SER* 1.3 62.8 + - - +
399G TYR* 3.1 3.4 + - - -
400G TRP* 3.0 9.7 + - - +
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Residues in contact with SER 397 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304G ILE* 3.6 40.0 - - - +
307G ALA* 3.8 4.7 - - - +
308G PHE* 4.1 23.8 - - - -
377G LEU* 4.4 1.8 - - - +
393G SER 2.7 26.8 + - - -
394G LEU* 3.7 4.0 - - - -
396G ALA* 1.3 72.4 - - - +
398G ALA* 1.3 65.0 + - - +
400G TRP* 3.1 14.3 + - - +
401G PHE* 3.1 22.8 - - - -
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Residues in contact with ALA 398 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G PHE* 5.6 1.5 - - - -
394G LEU* 2.8 16.0 + - + +
395G ILE* 3.0 15.5 - - + +
397G SER* 1.3 78.1 - - - +
399G TYR* 1.3 64.8 + - - +
401G PHE* 3.3 5.2 + - - +
402G ALA* 3.0 22.0 + - - +
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Residues in contact with TYR 399 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G TYR* 2.7 43.0 + + - +
369G LEU* 3.3 24.7 - - + +
370G LEU* 3.6 25.6 - - + -
373G ASP* 3.8 22.2 - - + +
395G ILE* 2.7 18.4 + - + +
396G ALA* 3.1 7.8 + - - +
398G ALA* 1.3 72.3 - - - +
400G TRP* 1.3 67.3 + - - +
402G ALA* 2.9 10.3 - - + +
403G TYR* 2.9 30.1 + - + +
407G ILE* 3.9 21.2 - - + +
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Residues in contact with TRP 400 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G PHE* 4.7 7.6 - + - -
301G PHE* 5.0 9.2 - + - -
304G ILE* 4.5 7.0 - - + -
339G ALA* 2.9 48.3 + - + +
342G VAL* 4.0 9.2 - - + +
343G MET* 4.2 22.9 - - + -
370G LEU* 3.5 31.9 - - + -
373G ASP* 3.6 10.5 + - - +
374G PHE* 3.9 36.6 - + + -
377G LEU* 4.3 11.2 - - + -
396G ALA 3.0 11.6 + - - +
397G SER* 3.2 14.4 - - - +
399G TYR* 1.3 80.9 - - - +
401G PHE* 1.3 73.7 + + + +
403G TYR* 3.1 15.1 + - - +
404G PHE* 3.4 29.1 - + - -
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Residues in contact with PHE 401 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304G ILE* 4.6 11.9 - - + -
308G PHE* 5.3 7.2 - + - -
335G ALA* 3.3 31.6 - - + -
338G GLY* 3.9 6.7 - - - -
339G ALA* 3.6 30.1 - - + -
342G VAL* 4.1 9.6 - - + -
397G SER* 3.1 30.1 - - - -
398G ALA* 3.3 5.5 + - - +
400G TRP* 1.3 81.8 - + - +
402G ALA* 1.3 59.2 + - - +
404G PHE* 3.2 3.3 + - - +
405G LEU* 2.7 62.2 + - + +
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Residues in contact with ALA 402 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398G ALA 3.0 14.2 + - - +
399G TYR* 2.9 27.6 - - + +
401G PHE* 1.3 76.7 - - - +
403G TYR* 1.3 55.2 + - - +
406G VAL* 2.9 36.9 + - + +
407G ILE* 3.0 19.9 + - + -
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Residues in contact with TYR 403 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 4.9 7.2 + - + +
121G TYR* 5.3 0.3 + - - -
363G PHE* 3.3 31.7 - + - -
366G TYR* 3.9 44.9 - - + -
367G PHE* 3.9 10.7 - - - -
370G LEU* 3.3 38.4 - - + -
399G TYR* 2.9 16.6 + - + +
400G TRP 3.3 9.6 - - - +
402G ALA* 1.3 75.8 - - - +
404G PHE* 1.3 79.7 + + - +
407G ILE* 3.9 9.8 - - + +
408G LEU* 3.1 59.9 + - + +
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Residues in contact with PHE 404 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 4.4 11.4 - - + -
342G VAL* 3.9 32.1 - - + -
343G MET* 3.9 30.7 - - + -
346G VAL* 4.0 32.8 - - + -
349G LEU* 2.9 30.9 - - + +
370G LEU* 3.9 13.5 - - + -
400G TRP* 3.4 40.6 - + - -
401G PHE 3.2 4.6 + - - +
403G TYR* 1.3 105.9 - + - +
405G LEU* 1.3 62.7 + - + +
408G LEU* 4.4 3.8 - - + +
409G PRO* 3.4 7.3 - - - +
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Residues in contact with LEU 405 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G VAL* 4.3 18.4 - - + -
345G LEU* 6.6 0.4 - - + -
349G LEU* 3.5 23.8 - - + -
401G PHE* 2.7 49.2 + - + +
404G PHE* 1.3 73.9 - - + +
406G VAL* 1.3 67.0 + - + +
409G PRO* 3.6 11.4 - - - +
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Residues in contact with VAL 406 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402G ALA* 2.9 20.3 + - + +
404G PHE 3.4 0.4 - - - -
405G LEU* 1.3 89.4 - - + +
407G ILE* 1.3 73.6 + - + +
409G PRO* 2.8 15.3 - - - +
410G ILE* 2.9 37.6 + - + +
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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