Contacts of the helix formed by residues 360 - 382 (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 ARG 360 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P LYS* 2.6 33.5 - - - +
350P ASP* 3.1 19.4 + - - -
352P SER* 3.2 27.0 + - - +
354P VAL* 3.9 17.7 - - + -
356P SER 3.8 17.0 - - - +
357P GLY* 3.3 12.2 + - - +
358P ARG 3.5 1.8 + - - -
359P TYR* 1.3 84.1 - - - +
361P PRO* 1.3 58.9 - - - +
363P PHE* 3.2 34.6 + - + +
364P LYS* 2.9 36.1 + - - +
408P LEU* 4.4 3.6 + - - +
411P LEU* 4.1 18.4 - - - +
412P GLY 4.7 0.4 - - - +
415P GLU* 2.8 32.2 + - - +
417P PRO* 5.3 1.6 - - + -
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Residues in contact with PRO 361 (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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359P TYR 3.8 6.1 - - - +
360P ARG* 1.3 87.3 - - - +
362P MET* 1.3 64.2 + - + +
364P LYS* 3.7 22.5 - - + +
365P ILE* 3.9 9.4 + - - +
415P GLU* 3.9 5.2 - - + +
416P LYS 4.3 15.7 - - - +
417P PRO* 4.8 0.2 - - + -
418P VAL* 3.9 23.6 - - + -
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Residues in contact with MET 362 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361P PRO* 1.3 76.2 - - + +
363P PHE* 1.3 65.4 + - - +
365P ILE* 2.9 23.9 + - - +
366P TYR* 3.5 34.0 + - + +
411P LEU* 3.7 24.5 - - + -
414P ILE* 4.1 21.8 - - + -
415P GLU* 2.8 28.4 + - + +
416P LYS 6.1 0.2 - - - +
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Residues in contact with PHE 363 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P LEU 3.6 20.2 - - - -
117P TYR* 4.4 16.6 - + - -
121P TYR* 4.4 2.2 - - - -
122P LYS* 5.1 0.7 - - - -
350P ASP* 4.0 3.6 - - - -
357P GLY* 4.4 13.2 - - - -
360P ARG* 3.2 59.2 - - + +
362P MET* 1.3 75.3 - - - +
364P LYS* 1.3 70.4 + - - +
365P ILE 2.8 1.6 + - - -
366P TYR* 2.9 14.4 + - - +
367P PHE* 3.0 35.2 + + + -
403P TYR* 3.3 17.2 - + - -
408P LEU* 3.5 28.5 - - + -
411P LEU* 4.0 12.1 - - + +
415P GLU* 2.8 7.3 + - - +
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Residues in contact with LYS 364 (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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117P TYR* 3.6 19.6 + - + +
357P GLY 3.6 8.5 - - - +
358P ARG* 2.8 43.2 + - - +
360P ARG 2.9 24.9 + - - +
361P PRO* 3.7 15.3 - - + +
363P PHE* 1.3 82.8 - - - +
365P ILE* 1.3 68.0 + - + +
367P PHE* 3.2 2.5 + - - +
368P TRP* 3.0 40.7 + - + +
504P LOP 4.3 4.6 + - - -
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Residues in contact with ILE 365 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361P PRO 4.0 10.1 - - - +
362P MET* 2.9 14.3 + - - +
363P PHE 2.8 4.0 + - - -
364P LYS* 1.3 78.4 - - + +
366P TYR* 1.3 75.3 + - + +
368P TRP* 3.5 6.9 + - + +
369P LEU* 3.2 35.9 + - + +
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Residues in contact with TYR 366 (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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362P MET* 3.6 30.6 - - + +
363P PHE 2.9 7.0 + - - +
365P ILE* 1.3 80.2 - - + +
367P PHE* 1.3 59.8 + - - +
369P LEU* 3.2 12.7 + - + -
370P LEU* 2.8 22.0 + - - +
399P TYR* 2.7 34.7 + + - +
403P TYR* 3.9 11.1 - - + -
407P ILE* 3.3 43.3 - - + -
411P LEU* 3.4 29.2 - - + -
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Residues in contact with PHE 367 (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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113P PHE* 3.8 27.4 - + - -
116P LEU* 4.0 9.2 - - + -
117P TYR* 3.3 52.3 - + + -
363P PHE* 3.0 40.6 + + + +
364P LYS* 3.4 7.9 - - - +
366P TYR* 1.3 75.9 - - - +
368P TRP* 1.3 94.3 + + - +
370P LEU* 2.7 29.1 + - + +
371P ALA* 3.0 7.0 + - + +
403P TYR* 3.9 19.4 - + - -
504P LOP 4.2 10.8 - - + -
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Residues in contact with TRP 368 (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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117P TYR* 4.2 10.4 + + - -
364P LYS* 3.0 35.7 + - + +
365P ILE* 4.0 6.7 - - + +
367P PHE* 1.3 95.8 - + - +
369P LEU* 1.3 57.0 + - - +
371P ALA* 3.3 15.2 + - + +
372P ALA* 2.8 29.7 + - - +
504P LOP 3.5 72.2 - - + -
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Residues in contact with LEU 369 (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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365P ILE* 3.2 27.2 + - + +
366P TYR* 3.2 17.7 + - + +
367P PHE 3.1 0.8 - - - -
368P TRP* 1.3 72.6 - - - +
370P LEU* 1.3 57.0 + - - +
372P ALA* 3.5 10.1 - - + +
373P ASP* 2.7 36.6 + - - +
399P TYR* 3.3 36.5 - - + +
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Residues in contact with LEU 370 (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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113P PHE* 4.1 17.5 - - + -
116P LEU* 4.3 7.9 - - + -
366P TYR 2.8 12.1 + - - +
367P PHE* 2.7 18.6 + - + +
369P LEU* 1.3 75.5 - - - +
371P ALA* 1.3 54.4 + - - +
373P ASP* 3.1 4.3 + - - +
374P PHE* 2.9 28.8 + - - +
399P TYR* 3.6 12.8 - - + -
400P TRP* 3.5 35.9 - - + -
403P TYR* 3.3 50.7 - - + +
404P PHE* 3.9 13.7 - - + -
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Residues in contact with ALA 371 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P PHE* 4.2 18.1 - - + -
367P PHE* 3.0 12.3 + - + +
368P TRP* 3.4 26.5 - - + +
370P LEU* 1.3 73.3 - - - +
372P ALA* 1.3 68.7 + - - +
374P PHE* 3.0 4.7 + - - +
375P VAL* 3.0 27.4 + - + +
504P LOP 4.7 23.3 - - + +
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Residues in contact with ALA 372 (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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368P TRP 2.8 20.4 + - - +
369P LEU* 3.5 13.2 - - + +
371P ALA* 1.3 73.6 - - - +
373P ASP* 1.3 53.1 + - - +
375P VAL* 3.1 9.6 + - - +
376P ILE* 2.8 47.2 + - + +
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Residues in contact with ASP 373 (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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369P LEU 2.7 22.2 + - - +
370P LEU* 3.2 10.8 - - + +
371P ALA 3.0 0.2 - - - -
372P ALA* 1.3 70.7 - - - +
374P PHE* 1.3 55.7 + - - +
376P ILE* 2.9 13.9 + - - +
377P LEU* 2.6 46.3 + - - +
396P ALA* 2.7 51.4 - - - +
399P TYR* 3.9 13.2 - - + +
400P TRP* 3.6 15.6 + - + +
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Residues in contact with PHE 374 (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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109P TYR* 3.7 47.8 - + - -
113P PHE* 3.7 25.4 - + + -
300P PRO* 4.0 24.4 - - + +
301P PHE* 4.7 10.1 - + - -
370P LEU 2.9 15.3 + - - +
371P ALA 3.4 8.1 - - - +
373P ASP* 1.3 73.2 + - - +
375P VAL* 1.3 60.8 + - - +
377P LEU* 3.4 11.1 - - + +
378P THR* 2.9 33.0 + - - -
400P TRP* 4.0 25.1 - + + -
504P LOP 3.5 40.2 - - + -
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Residues in contact with VAL 375 (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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371P ALA* 3.0 17.4 + - + +
372P ALA* 3.2 9.6 - - - +
374P PHE* 1.3 76.8 - - + +
376P ILE* 1.3 68.0 + - + +
378P THR* 3.0 9.9 + - - -
379P TRP* 2.8 23.2 + - + +
504P LOP 4.4 31.2 - - + -
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Residues in contact with ILE 376 (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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372P ALA* 2.8 36.9 + - + +
373P ASP* 3.3 14.6 - - - +
375P VAL* 1.3 72.8 - - + +
377P LEU* 1.3 56.3 + - - +
379P TRP* 2.9 19.9 + - + +
380P VAL* 2.8 35.7 + - + +
392P ILE* 4.1 26.5 - - + -
396P ALA* 5.0 6.5 - - + -
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Residues in contact with LEU 377 (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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300P PRO* 3.8 15.6 - - + +
303P ALA* 3.3 28.6 - - + +
304P ILE* 3.4 41.5 - - + +
373P ASP* 2.6 37.9 + - - +
374P PHE* 3.4 9.6 - - + +
376P ILE* 1.3 72.4 - - - +
378P THR* 1.3 62.2 + - - +
380P VAL* 2.7 24.3 - - + +
381P GLY* 3.2 4.9 + - - -
393P SER 4.9 1.6 - - - +
396P ALA* 3.9 23.1 - - + +
397P SER* 4.4 3.6 - - - +
400P TRP* 4.3 15.9 - - + -
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Residues in contact with THR 378 (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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296P TRP* 4.0 16.4 - - + +
299P LEU* 3.7 32.1 - - + +
300P PRO* 3.3 27.6 - - + +
374P PHE* 2.9 21.9 + - - -
375P VAL* 3.0 11.7 + - - -
377P LEU* 1.3 75.2 - - - +
379P TRP* 1.3 66.9 + - - +
381P GLY 3.0 13.0 + - - -
382P ALA 3.6 4.7 + - - -
504P LOP 4.6 10.2 - - + +
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Residues in contact with TRP 379 (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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375P VAL* 2.8 15.0 + - + +
376P ILE* 3.2 20.9 - - + +
378P THR* 1.3 79.0 - - - +
380P VAL* 1.3 92.3 + - + +
382P ALA* 3.3 18.5 - - + +
383P GLN* 3.3 24.6 + - + +
389P TYR* 3.6 27.6 - + - -
392P ILE* 4.4 12.3 - - + -
114Q MET* 3.1 65.1 + - + +
115Q GLY 4.0 9.9 + - - -
116Q THR* 4.1 10.0 + - + -
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Residues in contact with VAL 380 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303P ALA* 4.1 9.0 - - + -
306P ARG* 2.9 10.8 + - - -
376P ILE* 2.8 13.2 + - + +
377P LEU* 2.7 29.4 - - - +
379P TRP* 1.3 94.6 - - + +
381P GLY* 1.3 53.4 + - - +
382P ALA 2.8 6.1 - - - -
383P GLN* 2.6 34.1 + - + +
389P TYR* 4.8 8.6 - - + +
392P ILE* 3.8 25.8 - - + -
393P SER* 4.6 19.1 - - - +
396P ALA* 5.6 0.7 - - + -
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Residues in contact with GLY 381 (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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293P VAL* 4.4 3.8 - - - +
299P LEU* 4.0 12.4 - - - +
302P TYR* 3.1 32.8 - - - -
303P ALA* 4.2 10.1 - - - -
306P ARG* 3.1 18.8 + - - -
377P LEU 3.2 7.9 + - - -
378P THR 3.0 8.9 + - - -
380P VAL* 1.3 78.1 - - - +
382P ALA* 1.3 56.9 + - - +
383P GLN 3.2 0.9 - - - +
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Residues in contact with ALA 382 (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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293P VAL* 4.6 18.1 - - + +
299P LEU* 4.2 17.5 - - + +
378P THR 3.6 1.6 + - - -
379P TRP* 3.3 15.5 - - - +
380P VAL 2.8 0.2 - - - -
381P GLY* 1.3 79.5 - - - +
383P GLN* 1.3 67.6 + - - +
115Q GLY* 4.7 7.1 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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