Contacts of the helix formed by residues 360 - 382 (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 ARG 360 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122M LYS* 2.7 32.1 - - - +
350M ASP* 3.1 18.6 + - - -
352M SER* 3.2 26.6 + - - +
354M VAL* 4.0 18.6 - - + -
356M SER 3.8 17.5 - - - +
357M GLY* 3.3 12.9 + - - +
358M ARG 3.5 1.6 + - - -
359M TYR* 1.3 84.7 - - - +
361M PRO* 1.4 56.8 - - - +
363M PHE* 3.2 34.3 + - + -
364M LYS* 2.9 36.7 + - - +
408M LEU* 4.8 3.0 + - - +
411M LEU* 4.1 19.2 - - - +
412M GLY 4.8 0.4 - - - +
415M GLU* 2.9 34.4 + - - +
417M PRO* 5.5 0.2 - - + -
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Residues in contact with PRO 361 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359M TYR 3.8 6.3 - - - +
360M ARG* 1.4 85.5 - - - +
362M MET* 1.3 63.0 + - + +
364M LYS* 3.8 22.3 - - + +
365M ILE* 4.0 10.6 + - - +
415M GLU* 3.2 10.5 - - + +
416M LYS 4.1 13.7 - - - +
418M VAL* 3.7 23.1 - - + -
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Residues in contact with MET 362 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361M PRO* 1.3 78.0 - - + +
363M PHE* 1.3 69.0 + - - +
365M ILE* 2.9 23.8 + - - +
366M TYR* 3.5 25.3 + - + +
411M LEU* 3.4 21.5 - - + -
414M ILE* 3.8 32.8 - - + +
415M GLU* 3.1 22.4 + - + +
416M LYS 5.0 2.0 - - - +
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Residues in contact with PHE 363 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116M LEU 3.6 19.3 - - - -
117M TYR* 4.4 16.6 - + - -
121M TYR* 4.4 2.5 - - - -
350M ASP* 4.0 3.4 - - - -
357M GLY* 4.4 13.5 - - - -
360M ARG* 3.2 61.7 - - + +
362M MET* 1.3 76.4 - - - +
364M LYS* 1.3 71.8 + - - +
365M ILE 2.8 2.3 + - - -
366M TYR* 2.9 14.2 + - - +
367M PHE* 2.9 35.3 + + + -
403M TYR* 3.3 25.8 - + - -
408M LEU* 3.5 17.3 - - + -
411M LEU* 4.1 14.8 - - + +
415M GLU* 3.5 3.5 + - - +
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Residues in contact with LYS 364 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M TYR* 4.1 15.9 + - + +
357M GLY 3.5 9.6 - - - +
358M ARG* 2.8 42.3 + - - +
360M ARG 2.9 30.1 + - - +
361M PRO* 3.8 14.8 - - + +
363M PHE* 1.3 80.4 - - - +
365M ILE* 1.3 64.7 + - + +
367M PHE* 4.0 2.9 - - - -
368M TRP* 2.9 41.7 + - + +
418M VAL* 6.5 0.2 - - - -
504M LOP 4.8 4.4 + - - +
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Residues in contact with ILE 365 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361M PRO 4.0 12.3 - - - +
362M MET* 2.9 12.7 + - - +
363M PHE 2.8 4.2 + - - -
364M LYS* 1.3 80.8 - - + +
366M TYR* 1.3 75.4 + - + +
368M TRP* 3.5 5.7 + - + +
369M LEU* 3.2 36.1 + - + +
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Residues in contact with TYR 366 (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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362M MET* 3.5 24.5 + - + +
363M PHE 2.9 6.1 + - - +
365M ILE* 1.3 79.0 - - + +
367M PHE* 1.3 67.0 - - - +
369M LEU* 3.2 12.5 + - + -
370M LEU* 2.9 15.9 + - - +
399M TYR* 2.7 36.0 + + - +
403M TYR* 3.9 18.1 - - + -
407M ILE* 3.2 38.8 - - + -
411M LEU* 3.5 24.9 - - + -
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Residues in contact with PHE 367 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M PHE* 3.7 23.3 - + - -
116M LEU* 4.0 9.4 - - + -
117M TYR* 3.3 52.5 - + + -
363M PHE* 2.9 44.0 + + + +
364M LYS* 3.7 3.6 - - - +
366M TYR* 1.3 76.0 - - - +
368M TRP* 1.3 90.9 + + - +
370M LEU* 2.8 29.8 + - + +
371M ALA* 3.0 6.5 + - + +
403M TYR* 3.9 19.8 - + - -
504M LOP 4.0 19.3 - - + -
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Residues in contact with TRP 368 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M TYR* 4.2 9.7 - - - -
364M LYS* 2.9 35.7 + - + +
365M ILE* 4.0 6.3 - - + +
367M PHE* 1.3 92.3 - + - +
369M LEU* 1.3 57.2 + - - +
371M ALA* 3.3 17.3 + - + +
372M ALA* 2.8 29.3 + - - +
504M LOP 3.6 67.5 - - + -
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Residues in contact with LEU 369 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365M ILE* 3.2 28.7 + - + +
366M TYR* 3.4 17.0 - - + +
367M PHE 3.1 0.6 - - - -
368M TRP* 1.3 73.8 - - - +
370M LEU* 1.3 56.6 + - - +
372M ALA* 3.2 9.1 + - + +
373M ASP* 2.6 37.2 + - - +
399M TYR* 3.3 37.1 - - + +
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Residues in contact with LEU 370 (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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113M PHE* 4.1 21.1 - - + -
116M LEU* 4.3 8.1 - - + -
366M TYR 2.9 13.0 + - - +
367M PHE* 2.8 18.3 + - + +
369M LEU* 1.3 76.2 - - - +
371M ALA* 1.3 54.6 + - - +
373M ASP* 3.1 4.5 + - - +
374M PHE* 2.8 29.3 + - - +
399M TYR* 3.6 13.0 - - + -
400M TRP* 3.5 33.7 - - + -
403M TYR* 3.2 49.8 - - + +
404M PHE* 3.9 13.7 - - + -
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Residues in contact with ALA 371 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M PHE* 4.2 15.2 - - + -
367M PHE* 3.0 13.1 + - + +
368M TRP* 3.4 24.9 - - + +
370M LEU* 1.3 73.5 - - - +
372M ALA* 1.3 68.3 + - - +
374M PHE* 3.0 5.0 + - - +
375M VAL* 3.0 27.2 + - + +
504M LOP 4.1 25.7 - - + +
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Residues in contact with ALA 372 (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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368M TRP 2.8 21.2 + - - +
369M LEU* 3.4 13.2 - - + +
371M ALA* 1.3 72.2 - - - +
373M ASP* 1.3 57.1 + - - +
375M VAL* 3.1 11.3 + - - +
376M ILE* 2.8 40.8 + - + +
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Residues in contact with ASP 373 (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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369M LEU 2.6 21.3 + - - +
370M LEU* 3.1 10.5 - - + +
372M ALA* 1.3 70.4 - - - +
374M PHE* 1.3 57.6 + - - +
376M ILE* 2.9 13.7 + - - +
377M LEU* 2.6 46.2 + - - +
396M ALA* 2.7 51.0 - - - +
399M TYR* 3.8 13.2 - - + +
400M TRP* 3.6 15.6 + - + +
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Residues in contact with PHE 374 (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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109M TYR* 3.7 51.4 - + - -
113M PHE* 3.7 24.0 - + + -
296M TRP* 6.1 0.2 - + - -
300M PRO* 4.0 24.6 - - + +
301M PHE* 4.7 10.1 - + - -
370M LEU 2.8 15.5 + - - +
371M ALA 3.4 8.7 - - - +
373M ASP* 1.3 73.3 - - - +
375M VAL* 1.3 61.0 + - - +
377M LEU* 3.4 10.6 - - + +
378M THR* 2.9 33.1 + - - -
400M TRP* 4.0 24.4 - + + -
504M LOP 3.3 39.7 - - + -
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Residues in contact with VAL 375 (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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371M ALA* 3.0 17.2 + - + +
372M ALA* 3.2 10.3 - - - +
374M PHE* 1.3 76.2 - - - +
376M ILE* 1.3 67.4 + - + +
378M THR* 3.0 9.9 + - - -
379M TRP* 2.8 23.7 + - + +
504M LOP 4.1 30.5 - - + -
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Residues in contact with ILE 376 (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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372M ALA* 2.8 36.9 + - + +
373M ASP* 3.3 14.1 - - - +
375M VAL* 1.3 75.6 - - + +
377M LEU* 1.3 65.4 + - - +
379M TRP* 2.9 20.1 + - + +
380M VAL* 2.8 26.0 + - + +
392M ILE* 4.0 26.5 - - + -
396M ALA* 5.0 6.7 - - + -
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Residues in contact with LEU 377 (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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300M PRO* 3.7 16.1 - - + +
303M ALA* 3.3 29.2 - - + +
304M ILE* 3.4 40.6 - - + +
373M ASP* 2.6 36.4 + - - +
374M PHE* 3.4 10.3 - - + +
376M ILE* 1.3 72.6 - - - +
378M THR* 1.3 62.5 + - - +
380M VAL* 2.7 24.6 - - + +
381M GLY 3.2 5.2 + - - -
393M SER* 4.9 1.8 - - - +
396M ALA* 3.9 22.4 - - + +
397M SER* 4.4 3.6 - - - +
400M TRP* 4.2 16.6 - - + -
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Residues in contact with THR 378 (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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296M TRP* 4.0 14.8 - - + +
299M LEU* 3.7 32.0 - - + +
300M PRO* 3.3 23.8 - - + +
374M PHE* 2.9 23.3 + - - -
375M VAL* 3.0 10.7 + - - -
377M LEU* 1.3 75.0 - - - +
379M TRP* 1.3 67.3 + - - +
381M GLY 3.0 12.5 + - - -
382M ALA 3.6 4.5 + - - -
504M LOP 4.5 16.4 - - + +
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Residues in contact with TRP 379 (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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375M VAL* 2.8 18.8 + - + +
376M ILE* 2.9 21.7 + - + +
378M THR* 1.3 75.1 - - - +
380M VAL* 1.3 92.6 + - + +
382M ALA* 3.3 18.7 - - + +
383M GLN* 3.3 26.6 + - + +
389M TYR* 3.6 28.3 - + - -
392M ILE* 4.4 13.0 - - + -
114N MET* 3.3 61.5 + - + +
115N GLY 3.9 9.4 + - - -
116N THR* 4.1 11.7 + - + -
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Residues in contact with VAL 380 (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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303M ALA* 4.1 9.4 - - + -
306M ARG* 2.7 19.5 + - - +
376M ILE* 2.8 13.0 + - + +
377M LEU* 2.7 34.1 - - + +
379M TRP* 1.3 94.8 - - + +
381M GLY* 1.3 48.6 + - - +
382M ALA 2.8 5.8 - - - -
383M GLN* 2.6 31.3 + - + +
389M TYR* 4.8 8.9 - - + +
392M ILE* 3.8 25.6 - - + -
393M SER* 4.6 18.2 - - - +
396M ALA* 5.6 0.4 - - + -
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Residues in contact with GLY 381 (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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293M VAL* 4.4 4.2 - - - +
299M LEU* 4.0 12.4 - - - +
302M TYR* 3.1 39.3 - - - -
303M ALA* 4.2 8.3 - - - -
306M ARG* 3.5 12.4 + - - -
377M LEU 3.2 7.5 + - - -
378M THR 3.0 10.0 + - - -
380M VAL* 1.3 77.5 - - - +
382M ALA* 1.3 57.9 + - - +
383M GLN 3.2 0.4 - - - +
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Residues in contact with ALA 382 (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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293M VAL* 4.6 17.6 - - + +
299M LEU* 4.2 17.4 - - + +
378M THR 3.6 1.4 + - - -
379M TRP* 3.3 15.3 - - - +
380M VAL 2.8 0.6 - - - -
381M GLY* 1.3 79.4 - - - +
383M GLN* 1.3 67.9 + - - +
115N GLY 4.8 6.5 - - - +
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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