Contacts of the helix formed by residues 388 - 406 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387M PHE* 1.3 112.9 - - + +
389M TYR* 1.3 83.6 + - + +
390M ASP* 3.2 5.2 - - - +
391M TRP* 3.0 7.8 + - + +
392M ILE* 2.9 40.3 + - + +
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Residues in contact with TYR 389 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306M ARG* 5.4 1.8 - - - +
379M TRP* 3.6 29.6 - + - -
380M VAL* 4.8 6.1 - - + +
383M GLN* 3.8 34.5 + - + -
384M GLN* 3.4 28.9 - - + +
386M THR* 3.1 29.0 + - - +
387M PHE 4.3 1.8 - - - -
388M PRO* 1.3 93.0 - - + +
390M ASP* 1.3 56.0 + - - +
392M ILE* 2.8 18.6 + - + +
393M SER* 2.7 36.1 + - - -
114N MET* 5.6 0.9 + - - +
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Residues in contact with ASP 390 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307M ALA* 5.2 3.2 - - - +
385M THR* 3.6 20.2 + - + +
386M THR 3.3 3.6 + - - -
387M PHE* 3.1 34.1 + - - +
388M PRO* 3.2 4.2 - - - +
389M TYR* 1.3 74.9 - - - +
391M TRP* 1.3 85.1 + - - -
393M SER* 2.8 21.1 + - - -
394M LEU* 3.2 17.9 + - + +
164R LYS* 5.7 2.8 + - - -
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Residues in contact with TRP 391 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313M TRP* 6.5 1.1 - + - -
387M PHE* 3.6 35.3 - + + -
388M PRO* 3.2 10.1 - - + +
389M TYR 3.0 0.2 - - - -
390M ASP* 1.3 95.2 + - - +
392M ILE* 1.3 68.4 + - + +
394M LEU* 2.7 29.9 + - + +
395M ILE* 2.9 34.0 + - + +
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Residues in contact with ILE 392 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376M ILE* 4.0 19.7 - - + -
379M TRP* 4.4 11.7 - - + -
380M VAL* 3.8 17.3 - - + -
388M PRO* 2.9 35.6 + - + +
389M TYR* 2.8 29.4 + - + +
391M TRP* 1.3 73.0 - - + +
393M SER* 1.3 63.5 + - - +
395M ILE* 3.1 12.1 + - + +
396M ALA* 2.9 24.9 + - + +
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Residues in contact with SER 393 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303M ALA* 4.7 11.7 - - - -
306M ARG* 5.8 5.4 - - - -
307M ALA* 3.6 22.4 - - - +
377M LEU* 4.9 1.1 - - - +
380M VAL* 4.6 20.1 - - - +
389M TYR 2.7 15.5 + - - -
390M ASP* 2.8 19.1 + - - -
392M ILE* 1.3 72.7 - - - +
394M LEU* 1.3 56.4 + - - +
396M ALA* 3.3 7.7 + - - +
397M SER* 2.6 39.3 + - - -
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Residues in contact with LEU 394 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307M ALA* 4.1 15.7 - - + +
308M PHE* 3.7 33.0 - - + -
312M VAL* 3.9 29.6 - - + -
314M VAL* 6.6 0.2 - - + -
390M ASP 3.4 13.0 - - - +
391M TRP* 2.7 33.5 + - + +
393M SER* 1.3 75.1 + - - +
395M ILE* 1.3 63.9 + - + +
397M SER* 3.4 1.2 + - - -
398M ALA* 2.9 25.7 + - + +
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Residues in contact with ILE 395 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391M TRP* 2.9 37.1 + - + +
392M ILE* 3.7 9.9 - - + +
394M LEU* 1.3 71.0 - - + +
396M ALA* 1.3 53.1 + - - +
398M ALA* 3.1 8.8 - - + +
399M TYR* 2.7 38.3 + - + +
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Residues in contact with ALA 396 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373M ASP* 2.7 43.3 - - - +
376M ILE* 5.0 8.1 - - + -
377M LEU* 3.9 24.5 - - + +
380M VAL* 5.6 0.2 - - + -
392M ILE 2.9 13.3 + - - +
393M SER* 3.4 12.1 - - - +
395M ILE* 1.3 76.7 - - - +
397M SER* 1.3 64.1 + - - +
399M TYR* 3.1 2.8 + - - -
400M TRP* 3.0 9.5 + - - +
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Residues in contact with SER 397 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304M ILE* 3.7 36.9 - - - +
307M ALA* 3.8 4.5 - - - +
308M PHE* 4.1 24.2 - - - -
377M LEU* 4.4 1.6 - - - +
393M SER 2.6 26.9 + - - -
394M LEU* 3.7 4.3 - - - -
396M ALA* 1.3 71.5 - - - +
398M ALA* 1.3 64.1 + - - +
400M TRP* 3.1 13.8 + - - +
401M PHE* 3.0 26.8 - - - -
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Residues in contact with ALA 398 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308M PHE* 5.6 1.3 - - - -
394M LEU* 2.9 16.4 + - + +
395M ILE* 3.1 14.8 - - + +
397M SER* 1.3 77.7 - - - +
399M TYR* 1.3 65.1 + - - +
401M PHE* 3.3 4.8 + - - +
402M ALA* 3.0 22.2 + - - +
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Residues in contact with TYR 399 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366M TYR* 2.7 44.3 + + - +
369M LEU* 3.3 21.9 - - + +
370M LEU* 3.6 25.4 - - + -
373M ASP* 3.8 24.7 - - + +
395M ILE* 2.7 20.1 + - + +
396M ALA* 3.5 7.9 - - - +
398M ALA* 1.3 73.5 - - - +
400M TRP* 1.3 64.9 + - - +
402M ALA* 3.0 10.6 - - + +
403M TYR* 2.9 28.4 + - + +
407M ILE* 3.8 21.3 - - + +
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Residues in contact with TRP 400 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M PHE* 4.7 7.4 - + - -
116M LEU* 6.0 0.4 - - + -
301M PHE* 5.1 9.0 - + - -
304M ILE* 4.4 7.4 - - + -
339M ALA* 2.9 49.1 + - + +
342M VAL* 4.0 8.2 - - + +
343M MET* 4.2 23.6 - - + -
370M LEU* 3.5 32.8 - - + -
373M ASP* 3.6 11.2 + - - +
374M PHE* 4.0 36.6 - + + -
377M LEU* 4.2 12.8 - - + -
396M ALA 3.0 12.2 + - - +
397M SER* 3.1 14.1 - - - +
399M TYR* 1.3 81.0 - - - +
401M PHE* 1.3 72.0 + + + +
403M TYR* 3.2 15.6 + - - +
404M PHE* 3.3 29.4 - + - -
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Residues in contact with PHE 401 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304M ILE* 4.6 11.2 - - + -
308M PHE* 5.3 7.0 - + - -
335M ALA* 3.2 31.9 - - + -
338M GLY* 3.9 7.0 - - - -
339M ALA* 3.6 28.7 - - + -
342M VAL* 4.1 9.9 - - + -
397M SER* 3.0 30.5 - - - -
398M ALA* 3.3 5.5 + - - +
400M TRP* 1.3 83.1 - + - +
402M ALA* 1.3 58.4 + - - +
404M PHE* 3.1 3.7 + - - +
405M LEU* 2.7 62.0 + - + +
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Residues in contact with ALA 402 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398M ALA 3.0 14.7 + - - +
399M TYR* 3.0 24.0 - - + +
401M PHE* 1.3 77.0 - - - +
403M TYR* 1.3 53.6 + - - +
406M VAL* 2.9 35.4 + - + +
407M ILE* 3.0 25.3 + - + -
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Residues in contact with TYR 403 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116M LEU* 4.9 6.9 + - + +
121M TYR* 5.3 0.7 + - - -
346M VAL* 5.8 0.2 - - + -
363M PHE* 3.3 31.2 - + - -
366M TYR* 3.9 45.1 - - + -
367M PHE* 3.9 11.2 - - + -
370M LEU* 3.2 39.9 - - + -
399M TYR* 2.9 16.6 + - + +
400M TRP 3.2 10.3 + - - +
402M ALA* 1.3 76.2 - - - +
404M PHE* 1.3 84.3 + + - +
407M ILE* 3.9 11.6 - - + +
408M LEU* 3.2 53.7 + - + +
411M LEU* 5.9 0.7 - - + -
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Residues in contact with PHE 404 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116M LEU* 4.4 12.8 - - + -
342M VAL* 3.9 32.1 - - + -
343M MET* 4.0 26.2 - - + -
346M VAL* 4.0 30.7 - - + -
349M LEU* 2.8 31.5 - - + +
370M LEU* 3.9 13.9 - - + -
400M TRP* 3.3 44.4 - + - +
401M PHE 3.1 4.2 + - - +
403M TYR* 1.3 106.4 - + - +
405M LEU* 1.3 62.3 + - + +
408M LEU* 4.4 4.7 - - + +
409M PRO* 3.5 7.3 - - - +
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Residues in contact with LEU 405 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342M VAL* 4.3 17.3 - - + -
345M LEU* 6.5 0.9 - - + -
349M LEU* 3.5 23.8 - - + -
401M PHE* 2.7 49.0 + - + +
404M PHE* 1.3 73.7 - - + +
406M VAL* 1.3 66.4 + - + +
409M PRO* 3.6 11.4 - - - +
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Residues in contact with VAL 406 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402M ALA* 2.9 18.9 + - + +
404M PHE 3.4 0.4 - - - -
405M LEU* 1.3 89.6 - - + +
407M ILE* 1.3 66.2 + - + +
409M PRO* 2.7 22.6 - - - +
410M ILE* 3.1 35.1 + - + +
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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