Contacts of the helix formed by residues 360 - 382 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LYS* 3.0 31.1 - - - +
350A ASP* 3.1 14.1 + - - -
352A SER* 3.2 29.0 + - - +
354A VAL* 4.0 18.4 - - + -
355A ARG 5.0 0.2 + - - -
356A SER 3.9 17.5 - - - +
357A GLY* 3.3 12.9 + - - +
358A ARG 3.5 1.6 + - - -
359A TYR* 1.3 85.3 - - - +
361A PRO* 1.3 59.5 - - - +
363A PHE* 3.2 37.3 + - + -
364A LYS* 2.9 32.5 + - - +
408A LEU* 4.9 3.8 + - - +
411A LEU* 4.2 17.0 - - - +
412A GLY 4.8 0.4 - - - +
415A GLU* 2.9 27.1 + - - +
417A PRO* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A TYR 3.8 5.8 - - - +
360A ARG* 1.3 86.1 - - - +
362A MET* 1.3 62.2 + - + +
364A LYS* 3.7 22.7 - - + +
365A ILE* 4.0 10.4 + - - +
415A GLU* 3.3 9.9 - - + +
416A LYS 4.2 17.7 - - - +
417A PRO* 4.5 0.2 - - + -
418A VAL* 3.9 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PRO* 1.3 75.1 - - + +
363A PHE* 1.3 68.5 + - - +
365A ILE* 2.9 21.7 + - - +
366A TYR* 3.5 19.7 + - + +
411A LEU* 3.5 32.8 - - + -
414A ILE* 3.8 22.0 - - + +
415A GLU* 2.5 41.3 + - + +
416A LYS 4.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU 3.6 20.4 - - - -
117A TYR* 4.3 16.6 - + - -
121A TYR* 4.5 2.5 - - - -
122A LYS* 6.0 0.2 - - - -
350A ASP* 4.1 3.8 - - - -
357A GLY* 4.4 13.2 - - - -
360A ARG* 3.2 62.4 - - + +
362A MET* 1.3 77.5 - - - +
364A LYS* 1.3 70.2 + - - +
365A ILE 2.7 2.4 + - - -
366A TYR* 2.9 12.6 + - - +
367A PHE* 2.9 35.5 + + + -
403A TYR* 3.3 26.0 - + - -
408A LEU* 3.8 16.2 - - + -
411A LEU* 3.5 12.6 - - + +
415A GLU* 3.0 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TYR* 4.1 14.0 + - + +
357A GLY 3.6 14.4 - - - +
358A ARG* 2.8 39.2 + - - +
360A ARG 2.9 25.4 + - - +
361A PRO* 3.7 15.3 - - + +
363A PHE* 1.3 80.7 - - - +
365A ILE* 1.3 67.0 + - + +
367A PHE* 3.3 3.0 + - - +
368A TRP* 3.0 43.1 + - + +
503A LOP 4.8 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PRO 4.0 13.0 - - - +
362A MET* 2.9 12.1 + - - +
363A PHE 2.7 4.0 + - - -
364A LYS* 1.3 80.8 - - + +
366A TYR* 1.3 76.0 + - + +
368A TRP* 3.5 6.2 + - + +
369A LEU* 3.1 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A MET* 3.5 25.5 + - + +
363A PHE* 2.9 7.0 + - - +
365A ILE* 1.3 81.4 - - + +
367A PHE* 1.3 66.8 + - - +
369A LEU* 3.1 11.8 + - + -
370A LEU* 2.8 16.3 + - - +
399A TYR* 2.8 32.1 + + - +
403A TYR* 3.9 11.8 - - + -
407A ILE* 3.3 44.4 - - + -
411A LEU* 3.7 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 3.8 24.9 - + - -
116A LEU* 4.0 9.0 - - + -
117A TYR* 3.3 54.7 - + + -
363A PHE* 2.9 36.9 + + + +
364A LYS* 3.5 8.1 - - - +
366A TYR* 1.3 75.3 - - - +
368A TRP* 1.3 96.2 + + - +
370A LEU* 2.7 29.5 + - + +
371A ALA* 3.0 7.1 + - + -
403A TYR* 4.0 19.3 - + - -
503A LOP 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TYR* 4.2 11.5 - + - -
364A LYS* 3.0 35.4 + - + +
365A ILE* 4.0 7.2 - - + +
367A PHE* 1.3 103.4 - + - +
369A LEU* 1.3 57.8 + - - +
371A ALA* 3.3 14.7 + - + +
372A ALA* 2.8 29.3 + - - +
503A LOP 3.8 66.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 3.1 27.0 + - + +
366A TYR* 3.1 17.7 + - + +
367A PHE 3.0 0.8 + - - -
368A TRP* 1.3 74.4 - - - +
370A LEU* 1.3 56.5 + - - +
372A ALA* 3.5 9.3 - - + +
373A ASP* 2.6 36.9 + - - +
399A TYR* 3.2 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 4.1 21.1 - - + -
116A LEU* 4.2 8.1 - - + -
366A TYR 2.8 11.7 + - - +
367A PHE* 2.7 18.1 + - + +
369A LEU* 1.3 77.0 - - - +
371A ALA* 1.3 60.6 + - - +
373A ASP* 3.0 4.8 + - - +
374A PHE* 2.8 22.5 + - - +
399A TYR* 3.6 13.2 - - + -
400A TRP* 3.5 33.9 - - + -
403A TYR* 3.3 49.6 - - + +
404A PHE* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 4.2 16.5 - - + -
367A PHE* 3.0 13.0 + - + +
368A TRP* 3.5 22.7 - - + +
369A LEU 3.2 0.2 - - - -
370A LEU* 1.3 75.6 - - - +
372A ALA* 1.3 65.7 + - - +
373A ASP 3.0 0.9 + - - -
374A PHE* 3.0 13.3 + - - +
375A VAL* 3.0 16.9 + - + +
503A LOP 4.2 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A TRP 2.8 20.7 + - - +
369A LEU* 3.5 13.0 - - + +
371A ALA* 1.3 72.7 - - - +
373A ASP* 1.3 58.6 + - - +
375A VAL* 3.3 9.8 + - - +
376A ILE* 2.8 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU 2.6 16.9 + - - +
370A LEU* 3.1 14.1 - - + +
372A ALA* 1.3 71.4 - - - +
374A PHE* 1.3 56.6 + - - +
376A ILE* 2.8 15.8 + - - +
377A LEU* 2.5 45.0 + - - +
396A ALA* 2.8 50.5 - - - +
399A TYR* 3.8 13.2 - - + +
400A TRP* 3.6 17.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR* 3.7 44.6 - + - -
113A PHE* 3.7 23.6 - + + -
300A PRO* 4.0 25.3 - - + +
301A PHE* 4.7 10.3 - + - -
370A LEU 2.8 13.9 + - - +
371A ALA 3.4 7.9 - - - +
373A ASP* 1.3 71.4 - - - +
375A VAL* 1.3 60.6 + - - +
377A LEU* 3.4 10.9 - - + +
378A THR* 2.8 32.2 + - - -
400A TRP* 4.0 24.6 - + + -
503A LOP 3.3 46.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ALA* 3.0 16.6 + - + +
372A ALA* 3.3 10.5 - - - +
374A PHE* 1.3 74.4 - - - +
376A ILE* 1.3 68.9 + - + +
378A THR* 3.0 9.0 + - - -
379A TRP* 2.8 24.3 + - + +
503A LOP 4.3 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ALA* 2.8 37.0 + - + +
373A ASP* 2.8 19.0 + - - +
375A VAL* 1.3 72.2 - - + +
377A LEU* 1.3 65.6 + - - +
379A TRP* 2.9 19.9 + - + +
380A VAL* 2.9 26.1 + - + +
392A ILE* 4.0 26.9 - - + -
396A ALA* 4.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A PRO* 3.6 15.8 - - + +
303A ALA* 3.4 34.6 - - + +
304A ILE* 3.5 35.7 - - + +
373A ASP* 2.5 35.9 + - - +
374A PHE* 3.4 10.3 - - + +
376A ILE* 1.3 73.2 - - - +
378A THR* 1.3 61.6 + - - +
380A VAL* 2.7 25.1 - - + +
381A GLY 3.2 4.3 + - - -
393A SER* 5.0 1.6 - - - +
396A ALA* 4.0 22.6 - - + +
397A SER* 4.5 3.6 - - - +
400A TRP* 4.3 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TRP* 4.0 14.8 - - + +
299A LEU* 3.6 37.8 - - + +
300A PRO* 3.4 22.6 - - - +
374A PHE* 2.8 22.6 + - - -
375A VAL* 3.0 10.0 + - - -
377A LEU* 1.3 77.4 - - - +
379A TRP* 1.3 66.3 + - - +
381A GLY 3.0 12.8 + - - -
503A LOP 4.4 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL* 2.8 19.7 + - + +
376A ILE* 3.2 20.6 - - + +
378A THR* 1.3 73.5 - - - +
380A VAL* 1.3 93.2 + - + +
382A ALA* 3.2 12.4 - - - +
383A GLN* 3.2 33.8 + - + +
389A TYR* 3.6 24.7 - + - -
392A ILE* 4.3 16.6 - - + -
114B MET* 3.3 62.0 + - + +
115B GLY 3.8 12.7 + - - -
116B THR* 4.2 10.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA* 4.1 9.4 - - + -
306A ARG* 2.7 16.8 + - - +
376A ILE* 2.9 12.6 + - + +
377A LEU* 2.7 33.7 - - - +
379A TRP* 1.3 96.0 - - + +
381A GLY* 1.3 48.7 + - - +
382A ALA 2.8 5.8 - - - -
383A GLN* 2.7 32.7 + - + +
384A GLN 5.1 0.2 - - - +
389A TYR* 4.7 8.4 - - + +
392A ILE* 3.8 26.5 - - + -
393A SER* 4.6 18.8 - - - +
396A ALA* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL* 4.3 4.3 - - - +
299A LEU* 4.0 13.4 - - - +
302A TYR* 3.2 31.8 - - - -
303A ALA* 4.2 8.7 - - - -
306A ARG* 3.2 18.0 + - - -
377A LEU 3.2 7.5 + - - -
378A THR 3.0 10.0 + - - -
380A VAL* 1.3 78.4 - - - +
382A ALA* 1.3 58.4 + - - +
383A GLN 3.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL* 4.6 17.7 - - + +
299A LEU* 4.2 16.3 - - + +
378A THR 3.6 1.4 + - - -
379A TRP* 3.2 15.5 + - + +
380A VAL 2.8 0.4 - - - -
381A GLY* 1.3 78.8 - - - +
383A GLN* 1.3 66.9 + - - +
115B GLY 4.8 6.3 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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