Contacts of the helix formed by residues 366 - 389 (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 ASN 366 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LEU* 5.2 5.6 - - + +
274A PHE* 6.3 1.6 - - + -
277A ASP* 3.0 18.6 + - - +
364A LEU* 5.2 0.9 - - - -
365A MET* 1.3 77.3 - - + +
367A VAL* 1.3 61.8 + - - +
368A PRO* 3.6 10.0 - - - +
369A ARG* 3.2 38.7 + - + +
370A VAL* 3.2 25.1 + - - +
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLY 3.8 15.0 - - - +
364A LEU* 3.8 38.6 - - + +
365A MET 3.3 4.2 + - - +
366A ASN* 1.3 72.9 - - - +
368A PRO* 1.3 73.4 - - + +
370A VAL* 3.2 2.9 + - - +
371A GLU* 2.9 45.0 + - - +
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Residues in contact with PRO 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A MET 5.0 0.9 - - - +
366A ASN* 3.5 12.3 - - - +
367A VAL* 1.3 95.6 - - + +
369A ARG* 1.3 55.3 + - - +
371A GLU* 3.5 11.5 + - - +
372A ALA* 3.0 29.3 + - - +
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Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A SER* 4.3 23.6 + - - +
272A SER* 4.6 11.9 - - - -
273A LEU* 3.6 22.4 - - + +
366A ASN* 3.2 35.2 + - + +
368A PRO* 1.3 78.6 - - - +
370A VAL* 1.3 61.7 + - - +
372A ALA* 3.3 11.4 + - - +
373A ILE* 3.0 46.2 + - + +
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 4.2 25.8 - - + -
277A ASP* 5.3 1.8 - - - +
281A LEU* 4.1 10.1 - - + -
357A LEU* 3.9 6.3 - - + -
358A CYS 3.6 41.7 - - - +
359A GLY* 3.7 1.1 - - - +
364A LEU* 4.0 24.9 - - + -
366A ASN 3.2 14.3 + - - +
367A VAL 3.2 6.8 + - - +
369A ARG* 1.3 75.2 - - - +
371A GLU* 1.3 59.0 + - - +
373A ILE* 3.1 9.8 + - - +
374A GLN* 2.7 27.9 + - - +
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Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLY* 3.9 21.4 - - - +
360A ASP* 4.8 5.5 - - - +
367A VAL* 2.9 36.1 + - + +
368A PRO* 3.8 9.5 - - - +
370A VAL* 1.3 75.8 - - - +
372A ALA* 1.3 57.7 + - - +
374A GLN* 3.4 13.7 + - - +
375A ASP* 2.9 30.2 + - - +
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Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A PRO 3.0 18.7 + - - +
369A ARG* 3.6 14.1 - - - +
370A VAL 3.2 0.2 - - - -
371A GLU* 1.3 77.5 - - - +
373A ILE* 1.3 61.8 + - + +
375A ASP* 3.4 6.6 + - - +
376A THR* 3.1 26.6 + - - -
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 5.2 2.5 - - + -
269A SER* 3.6 45.5 - - - +
273A LEU* 4.2 8.5 - - + -
357A LEU* 3.6 39.3 - - + -
369A ARG* 3.0 47.8 + - + +
370A VAL* 3.1 6.3 + - - +
372A ALA* 1.3 74.2 - - - +
374A GLN* 1.3 67.4 + - - +
376A THR* 3.1 8.5 + - - -
377A ILE* 3.0 25.6 + - + +
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ALA* 4.1 13.2 + - - +
357A LEU 3.0 24.8 + - - +
358A CYS* 3.8 21.4 - - - +
359A GLY* 3.3 17.0 + - - -
360A ASP* 5.6 2.0 + - - +
370A VAL 2.7 17.6 + - - +
371A GLU* 3.5 11.5 - - - +
373A ILE* 1.3 72.4 - - - +
375A ASP* 1.3 64.2 + - - +
377A ILE* 3.1 11.5 + - - +
378A LEU* 2.9 42.0 + - + +
403A MET* 6.0 2.6 - - - -
407A ARG* 5.2 2.4 - - - +
505A PEG 4.7 10.1 + - - -
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Residues in contact with ASP 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLU 2.9 17.2 + - - +
372A ALA* 3.7 7.6 - - - +
374A GLN* 1.3 76.6 - - - +
376A THR* 1.3 64.5 + - - +
378A LEU* 3.1 12.5 + - - +
379A ARG* 2.5 68.4 + - - +
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Residues in contact with THR 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU* 4.0 16.3 - - + +
178A PHE* 4.2 26.5 - - + -
372A ALA 3.1 13.9 + - - -
373A ILE* 3.1 10.9 + - - -
375A ASP* 1.3 74.9 + - - +
377A ILE* 1.3 58.4 + - - +
379A ARG* 3.3 13.3 + - - +
380A ALA* 2.9 27.4 + - - +
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Residues in contact with ILE 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A PHE* 3.6 27.1 - - + -
182A ILE* 4.4 2.9 - - + -
267A ILE* 5.8 0.4 - - + -
350A LEU* 3.5 33.5 - - + +
353A ALA* 3.9 19.5 - - + +
354A ALA* 3.7 16.4 - - + +
357A LEU* 3.3 37.9 - - + -
373A ILE* 3.0 18.9 + - + +
374A GLN* 3.1 7.4 + - - +
376A THR* 1.3 74.1 - - - +
378A LEU* 1.3 59.4 + - - +
380A ALA* 3.2 3.4 + - - +
381A LEU* 2.7 27.0 + - + +
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ALA* 3.9 11.0 - - + -
374A GLN* 2.9 38.5 + - + +
375A ASP* 3.1 13.9 + - - +
377A ILE* 1.3 72.2 - - - +
379A ARG* 1.3 64.7 + - - +
381A LEU* 4.2 9.2 - - + -
382A GLU* 3.0 19.1 + - - +
396A PHE* 3.4 19.6 - - + -
400A LEU* 3.9 22.4 - - + -
403A MET* 3.8 30.3 - - + -
505A PEG 5.0 6.5 - - - +
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Residues in contact with ARG 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLN* 6.2 0.4 - - - +
175A LEU* 4.4 18.0 - - + +
375A ASP* 2.5 43.5 + - - +
376A THR* 3.6 14.1 - - - +
378A LEU* 1.3 73.1 - - + +
380A ALA* 1.3 59.7 + - - +
382A GLU* 3.3 7.5 + - - +
383A PHE* 3.0 28.9 + - - +
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 3.9 21.0 - - + +
178A PHE* 4.0 15.5 - - + -
179A SER* 3.5 21.0 + - - +
350A LEU* 3.9 7.7 - - + +
376A THR 2.9 17.4 + - - +
377A ILE 3.5 4.7 - - - +
379A ARG* 1.3 76.8 - - - +
381A LEU* 1.3 58.2 + - - +
383A PHE* 3.5 5.9 + - - +
384A HIS* 2.8 31.2 + - - +
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A ASP* 4.1 11.9 - - - +
350A LEU* 3.9 30.5 - - + +
351A PHE* 4.4 11.0 - - + +
354A ALA* 5.3 0.7 - - + -
377A ILE* 2.7 20.9 + - + +
378A LEU* 3.6 10.8 - - + +
379A ARG 3.2 0.2 - - - -
380A ALA* 1.3 70.0 - - - +
382A GLU* 1.3 61.5 + - - +
384A HIS* 3.0 2.5 + - + +
385A LEU* 2.8 60.9 + - + +
396A PHE* 4.2 13.7 - - + -
399A LEU* 4.4 18.8 - - + -
400A LEU* 5.9 0.4 - - + -
403A MET* 4.3 24.2 - - + -
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Residues in contact with GLU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A LEU 3.0 17.0 + - - +
379A ARG* 3.7 7.1 - - - +
381A LEU* 1.3 76.2 - - - +
383A PHE* 1.3 64.2 + - - +
385A LEU* 3.2 4.6 + - - +
386A GLN* 3.0 38.9 + - + +
396A PHE* 3.5 44.4 - - + +
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Residues in contact with PHE 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A VAL* 3.3 37.9 - - + -
175A LEU* 4.5 23.3 - - + -
176A LYS* 3.3 38.1 - - + -
179A SER* 5.6 1.8 - - - -
379A ARG 3.0 16.5 + - - +
380A ALA* 3.8 7.4 - - - +
382A GLU* 1.3 77.7 - - - +
384A HIS* 1.3 67.2 + - + +
386A GLN* 3.3 15.7 + - + +
387A ALA* 3.2 28.7 + - + +
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Residues in contact with HIS 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A SER* 4.6 10.9 - - - +
346A SER* 2.9 48.1 + - - -
347A ASP* 3.1 23.7 + - - -
350A LEU* 3.5 18.3 - - + +
380A ALA 2.8 21.9 + - - +
381A LEU* 3.5 4.9 - - + +
383A PHE* 1.3 80.1 - - + +
385A LEU* 1.3 59.0 + - + +
387A ALA* 3.2 6.6 + - + +
388A ASN* 2.8 40.7 + - + +
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Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A LEU* 4.5 0.9 - - + -
347A ASP* 3.6 30.7 - - + +
381A LEU* 2.8 42.6 + - + +
382A GLU 3.9 3.1 - - - +
384A HIS* 1.3 69.2 - - - +
386A GLN* 1.3 61.7 + - - +
388A ASN 4.4 0.7 - - - +
389A HIS* 2.8 38.9 + - + +
395A LEU* 3.9 26.9 - - + -
396A PHE* 4.0 31.0 - - + +
399A LEU* 3.7 26.0 - - + -
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Residues in contact with GLN 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A GLU* 3.0 32.4 + - + +
383A PHE* 3.6 19.7 - - + +
384A HIS 3.3 0.2 - - - -
385A LEU* 1.3 77.3 - - + +
387A ALA* 1.3 60.4 + - - +
389A HIS 4.8 2.2 - - - -
390A PRO* 3.6 22.7 - - - +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A PHE* 3.2 20.2 + - + +
384A HIS* 3.2 11.3 + - - +
386A GLN* 1.3 81.9 - - - +
388A ASN* 1.3 60.9 + - + +
389A HIS 3.5 0.2 - - - -
390A PRO* 4.0 9.2 - - - +
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Residues in contact with ASN 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ASP* 2.7 31.9 + - - +
346A SER* 3.5 7.4 + - - -
347A ASP* 3.0 24.6 + - - +
384A HIS* 2.8 26.2 + - + +
387A ALA* 1.3 77.7 - - + +
389A HIS* 1.3 73.7 + - + +
390A PRO* 3.6 6.9 - - - +
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Residues in contact with HIS 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU 4.9 2.3 + - - -
342A GLU* 3.5 26.5 - - + -
343A LEU* 4.6 0.8 - - - -
344A ASP* 4.9 3.1 - - + -
347A ASP* 2.5 38.0 + - - -
385A LEU* 2.8 33.7 + - + +
386A GLN* 4.8 1.0 - - - -
388A ASN* 1.3 87.9 + - + +
390A PRO* 1.3 67.2 - - - +
391A ASP 3.2 2.7 - - - -
392A ALA* 3.1 34.1 + - + +
395A LEU* 3.9 14.3 - - + +
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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
------------------------------------------------------------
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