Contacts of the helix formed by residues 394 - 424 (chain A) in PDB entry 5U3Y
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 TYR 394 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ALA 3.8 0.8 + - - -
393A GLN* 1.3 105.0 + - + +
395A LEU* 1.3 62.3 + - - +
396A PHE 3.4 2.5 - - - -
397A PRO* 3.2 23.7 - - + +
398A LYS* 3.0 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU* 4.1 41.1 - - + +
343A LEU* 4.3 8.3 - - + -
385A LEU* 3.9 28.5 - - + -
389A HIS* 3.9 31.6 - - + +
392A ALA* 3.9 27.2 + - + +
393A GLN 3.1 3.4 + - - +
394A TYR* 1.3 78.7 - - - +
396A PHE* 1.3 63.4 + - - +
397A PRO* 4.1 0.2 - - - +
398A LYS* 3.4 5.4 + - + +
399A LEU* 3.0 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 3.4 37.0 - - + -
381A LEU* 4.2 15.7 - - + -
382A GLU* 3.5 48.2 - - + +
385A LEU* 4.0 19.6 - - + +
395A LEU* 1.3 78.5 - - - +
397A PRO* 1.3 72.1 - - + +
399A LEU* 3.1 5.5 + - + +
400A LEU* 3.1 55.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 3.2 40.2 - - + +
396A PHE* 1.3 98.4 - - + +
398A LYS* 1.3 60.4 + - - +
400A LEU* 3.3 15.6 + - + +
401A GLN* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU* 4.1 29.8 - - + +
393A GLN 3.4 16.8 + - - -
394A TYR* 3.0 38.5 + - + +
395A LEU* 3.4 9.8 - - + +
396A PHE 3.2 0.2 - - - -
397A PRO* 1.3 76.8 - - - +
399A LEU* 1.3 56.9 + - - +
401A GLN* 3.2 9.3 + - - +
402A LYS* 3.0 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A PHE* 4.2 5.6 - - + -
341A LEU* 3.5 27.4 - - + -
343A LEU* 3.8 34.5 - - + -
347A ASP* 5.8 0.2 - - + -
351A PHE* 3.5 30.7 - - + -
381A LEU* 4.4 13.7 - - + -
385A LEU* 3.7 30.5 - - + -
395A LEU* 3.0 18.3 + - + +
396A PHE* 3.1 6.7 + - + +
398A LYS* 1.3 73.8 - - - +
400A LEU* 1.3 68.8 + - + +
402A LYS* 3.1 4.5 + - + +
403A MET* 3.0 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 3.9 31.6 - - + -
381A LEU* 5.9 0.4 - - + -
396A PHE* 3.1 47.2 + - + +
397A PRO* 3.3 13.2 + - + +
399A LEU* 1.3 75.4 - - + +
401A GLN* 1.3 63.0 + - - +
403A MET* 3.2 26.5 + - + +
404A ALA* 3.2 10.7 + - - +
505A PEG 3.6 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A PRO 3.1 13.1 + - - +
398A LYS* 3.4 11.9 - - - +
400A LEU* 1.3 77.4 - - - +
402A LYS* 1.3 58.1 + - + +
404A ALA* 3.1 14.8 + - - +
405A ASP* 2.8 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PHE* 4.2 11.9 - - + -
337A LYS* 4.0 31.0 + - - +
338A PHE* 4.0 39.4 - - + +
341A LEU* 4.0 27.8 - - + -
351A PHE* 4.2 2.7 - - + -
398A LYS* 3.0 21.1 + - - +
399A LEU* 3.1 9.4 + - - +
401A GLN* 1.3 76.8 - - + +
403A MET* 1.3 57.2 + - - +
405A ASP* 3.2 20.4 + - - +
406A LEU* 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLU* 4.5 3.0 - - - +
351A PHE* 3.6 36.6 - - + +
354A ALA* 3.6 32.1 - - + +
355A ILE* 4.4 13.2 - - + -
374A GLN* 6.0 2.9 - - - -
378A LEU* 3.8 15.5 - - + -
381A LEU* 4.3 8.1 - - + -
399A LEU 3.0 13.7 + - - +
400A LEU* 3.2 28.5 + - + +
402A LYS* 1.3 75.9 - - - +
404A ALA* 1.3 61.7 + - - +
406A LEU* 3.4 10.4 + - - +
407A ARG* 3.3 24.7 + - - +
505A PEG 4.1 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LEU 3.2 8.6 + - - +
401A GLN* 3.1 22.2 + - - +
403A MET* 1.3 75.4 - - - +
405A ASP* 1.3 66.3 + - - +
407A ARG* 3.1 16.7 + - - +
408A GLN* 3.3 11.4 + - - +
505A PEG 4.0 25.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PHE* 4.0 17.1 - - + -
401A GLN* 2.8 45.4 + - - +
402A LYS* 3.2 30.4 + - - +
404A ALA* 1.3 76.1 - - - +
406A LEU* 1.3 57.8 + - - +
408A GLN* 3.1 8.8 + - - +
409A LEU* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLU* 3.7 30.7 - - + +
291A PHE* 4.1 12.6 - - + -
292A ALA* 3.8 17.7 - - + +
334A PHE* 3.4 32.5 - - + -
351A PHE* 3.9 10.5 - - + -
355A ILE* 3.7 29.6 - - + -
402A LYS 2.9 21.0 + - - +
403A MET* 3.7 7.0 - - - +
404A ALA 3.2 0.2 - - - -
405A ASP* 1.3 73.4 - - - +
407A ARG* 1.3 61.8 + - - +
409A LEU* 3.6 8.9 - - + +
410A VAL* 2.8 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLU* 3.3 25.6 + - - +
358A CYS* 3.1 25.0 - - - -
360A ASP* 2.6 40.1 + - - +
361A ARG* 4.3 9.7 - - - +
374A GLN* 5.2 3.2 - - - +
403A MET* 3.3 12.4 + - - +
404A ALA* 3.1 9.1 + - - +
406A LEU* 1.3 78.1 - - - +
408A GLN* 1.3 57.3 + - - +
410A VAL* 3.8 2.0 - - - +
411A THR* 2.8 34.5 + - - +
505A PEG 3.7 45.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ALA 3.3 7.3 + - - +
405A ASP* 3.1 10.4 + - - +
407A ARG* 1.3 77.0 - - - +
409A LEU* 1.3 65.7 + - - +
411A THR* 3.1 15.0 + - - +
412A GLU* 2.9 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 4.0 34.1 - - + -
330A PRO* 4.0 35.4 - - + +
331A LYS* 4.5 15.6 + - + +
334A PHE* 4.0 30.7 - - + -
405A ASP 2.9 16.1 + - - +
406A LEU* 3.3 11.0 + - + +
408A GLN* 1.3 77.0 - - - +
410A VAL* 1.3 57.4 + - - +
412A GLU* 3.3 15.1 + - + +
413A HIS* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TYR 5.7 0.7 - - - +
287A HIS* 3.8 10.8 - - + -
288A GLU* 3.5 42.2 - - + +
291A PHE* 3.7 19.7 - - + -
406A LEU* 2.8 23.3 + - - +
407A ARG 4.0 2.7 - - - +
409A LEU* 1.3 70.5 - - - +
411A THR* 1.3 61.0 + - - +
413A HIS* 3.5 8.4 - - + +
414A ALA* 2.9 29.7 + - + +
437A TYR* 6.2 0.7 - - + -
503A PGO 3.5 31.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ARG* 2.8 25.2 + - - +
408A GLN* 3.1 21.2 + - - +
410A VAL* 1.3 78.9 - - - +
412A GLU* 1.3 62.6 + - - +
414A ALA* 3.3 6.1 + - - +
415A GLN* 3.1 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PRO* 5.2 5.9 - - + +
408A GLN* 2.9 52.4 + - - +
409A LEU* 3.7 18.6 - - + +
411A THR* 1.3 76.1 - - + +
413A HIS* 1.3 61.2 + - - +
415A GLN* 3.3 18.2 + - - +
416A MET* 3.0 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A HIS* 4.1 4.0 - + + -
291A PHE* 3.8 29.2 - + + -
327A ILE* 3.4 27.3 - - + +
331A LYS* 3.0 24.5 + - - +
409A LEU 2.9 17.4 + - - +
410A VAL* 3.5 10.5 - - + +
411A THR 3.2 0.2 - - - -
412A GLU* 1.3 76.6 - - - +
414A ALA* 1.3 57.7 + - - +
416A MET* 3.2 11.7 + - - +
417A MET* 2.9 35.5 + - + +
437A TYR* 3.1 19.0 + + - -
502A 7U7 2.8 40.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A VAL* 2.9 17.5 + - + +
411A THR* 3.3 6.0 + - - +
413A HIS* 1.3 76.3 - - - +
415A GLN* 1.3 59.6 + - + +
417A MET* 3.2 3.0 + - - +
418A GLN* 2.9 28.1 + - - +
437A TYR* 4.1 29.4 - - + -
503A PGO 4.4 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A THR* 3.1 28.8 + - + +
412A GLU* 3.6 21.6 - - - +
413A HIS 3.2 0.2 - - - -
414A ALA* 1.3 77.9 - - + +
416A MET* 1.3 62.1 + - + +
418A GLN* 3.2 10.2 + - - +
419A ARG* 3.1 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PRO* 5.4 4.7 - - + +
326A ASP* 3.4 32.3 - - + +
327A ILE* 3.7 25.4 - - + -
330A PRO* 4.5 9.6 - - + -
331A LYS* 3.7 26.0 - - - +
412A GLU* 3.0 31.0 + - + +
413A HIS* 3.7 5.6 - - - +
415A GLN* 1.3 76.8 - - + +
417A MET* 1.3 57.2 + - - +
419A ARG* 3.3 10.8 + - + +
420A ILE* 3.0 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PHE* 3.9 23.6 - - + -
327A ILE* 3.4 19.7 - - + -
413A HIS* 2.9 31.8 + - + +
414A ALA* 3.2 10.1 + - - +
416A MET* 1.3 75.4 - - - +
418A GLN* 1.3 65.1 + - - +
420A ILE* 3.2 8.8 + - + +
421A LYS* 3.0 22.7 + - - +
429A LEU* 3.7 32.1 - - + -
437A TYR* 3.9 26.9 - - + +
502A 7U7 3.7 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ALA 2.9 13.7 + - - +
415A GLN* 3.2 12.8 + - - +
417A MET* 1.3 76.6 - - - +
419A ARG* 1.3 65.8 + - + +
421A LYS* 3.3 23.3 + - - +
422A LYS* 3.1 23.7 + - + +
439A ASP 5.3 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PRO* 5.6 6.5 - - + -
415A GLN 3.1 15.2 + - - +
416A MET* 3.6 10.8 - - + +
417A MET 3.2 0.4 - - - -
418A GLN* 1.3 77.5 - - - +
420A ILE* 1.3 61.8 + - + +
422A LYS* 3.3 19.3 + - - +
423A THR* 2.8 66.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PHE* 3.9 38.4 - - + -
323A PRO* 3.7 26.9 - - + +
324A PHE* 4.3 19.5 - - + -
327A ILE* 4.1 20.0 - - + -
416A MET* 3.0 15.2 + - + +
417A MET* 3.2 10.3 + - + +
419A ARG* 1.3 76.2 - - - +
421A LYS* 1.3 58.7 + - - +
423A THR* 4.2 4.0 - - - -
424A GLU* 2.8 47.7 + - + +
427A THR* 4.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A MET 3.0 12.9 + - - +
418A GLN* 3.3 25.3 + - - +
420A ILE* 1.3 77.3 - - - +
422A LYS* 1.3 60.1 + - - +
424A GLU 5.3 1.1 - - - -
425A THR* 4.5 12.0 - - - +
429A LEU* 6.0 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLN* 3.1 17.8 + - + +
419A ARG* 3.7 26.0 - - - +
420A ILE 3.2 0.2 - - - -
421A LYS* 1.3 80.3 - - - +
423A THR* 1.3 67.3 + - + +
425A THR* 3.8 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PRO* 4.8 5.7 - - - +
419A ARG* 2.8 54.3 + - + +
420A ILE* 4.2 0.2 - - - -
422A LYS* 1.3 82.0 - - + +
424A GLU* 1.3 76.6 + - - +
425A THR* 3.5 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 4.9 0.2 - - - +
321A ARG* 2.7 46.0 + - - -
323A PRO* 3.5 15.0 - - + +
324A PHE* 4.0 15.7 - - + -
420A ILE* 2.8 30.7 + - + +
421A LYS* 5.1 1.3 - - - +
423A THR* 1.3 91.2 + - - +
425A THR* 1.3 58.1 + - - +
426A GLU* 3.1 4.5 - - - +
427A THR* 2.9 40.8 + - - +
----------------------------------------------------------
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