Contacts of the helix formed by residues 376 - 396 (chain A) in PDB entry 3HYW
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 LYS 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A GLU* 3.4 50.5 + - + +
354A ASP* 3.8 11.9 + - + +
375A GLY* 1.3 69.1 - - - -
377A TRP* 1.3 66.2 + - - +
379A HIS* 2.9 16.1 + - - +
380A TYR* 3.0 29.6 - - + +
434A SO4 3.0 22.6 + - - +
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Residues in contact with TRP 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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357A PHE* 3.7 40.2 - + + -
373A LYS* 3.9 23.5 - - + +
374A MET 4.2 3.8 + - - +
375A GLY* 3.8 15.4 - - - +
376A LYS* 1.3 79.5 - - - +
378A ALA* 1.3 76.0 + - + +
380A TYR* 3.2 11.9 + - - +
381A PHE* 3.0 38.6 + + + +
434A SO4 3.2 29.2 + - - +
600A LMT 3.6 78.7 + - + +
410B PHE* 4.7 7.4 - - + -
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ILE* 3.4 20.9 - - + +
355A ALA* 3.6 31.9 - - + +
357A PHE* 4.4 9.0 - - + -
375A GLY 3.4 3.1 + - - +
376A LYS 3.1 1.0 - - - -
377A TRP* 1.3 105.1 - - + +
379A HIS* 1.3 59.4 + - - +
381A PHE* 3.5 4.3 + - - +
382A LYS 3.0 21.8 + - - -
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Residues in contact with HIS 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A HIS* 6.2 0.2 - - - -
350A ASP* 2.9 36.4 + - - +
352A GLY 3.1 22.4 + - - -
353A GLU* 3.7 21.3 + - + +
354A ASP 3.9 9.0 - - - -
355A ALA* 3.5 9.1 - - - +
376A LYS 2.9 10.3 + - - +
378A ALA* 1.3 78.3 - - - +
380A TYR* 1.3 89.6 + + - +
382A LYS* 3.3 3.7 + - - +
383A THR* 3.1 36.1 + - - -
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Residues in contact with TYR 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLU* 4.5 14.2 + - - +
376A LYS* 3.0 44.8 - - + +
377A TRP* 3.2 7.6 + - - +
379A HIS* 1.3 98.5 - + - +
381A PHE* 1.3 60.8 - - - +
383A THR* 3.4 2.5 + - - +
384A ALA* 2.9 25.3 + - - +
409B ILE* 3.1 42.0 - - + +
410B PHE* 3.6 25.8 - + + -
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Residues in contact with PHE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 5.4 0.9 - - + -
348A ILE* 3.4 21.8 - - + -
357A PHE* 5.6 2.9 - + - -
377A TRP* 3.0 26.2 + + + +
378A ALA* 3.8 7.2 - - - +
379A HIS 3.3 0.2 - - - -
380A TYR* 1.3 74.3 - - - +
382A LYS* 1.3 55.3 + - - +
384A ALA* 3.7 1.7 - - - +
385A PHE* 2.8 36.8 + - + +
500A DCQ 3.1 41.3 - + + -
600A LMT 3.7 44.4 - - + -
410B PHE* 3.8 8.2 - + + -
600B LMT 3.7 36.1 - - + -
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Residues in contact with LYS 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 5.6 1.2 - - - -
43A PRO* 3.9 21.8 + - - +
47A HIS* 4.1 9.2 - - + +
53A ARG* 6.0 0.9 - - - +
162A GLU* 3.0 20.8 + - - -
348A ILE* 2.7 44.3 + - + +
350A ASP* 4.1 17.5 - - + +
378A ALA 3.0 14.5 + - - +
379A HIS* 3.3 12.7 + - - +
381A PHE* 1.3 77.5 - - - +
383A THR* 1.3 62.1 + - - +
385A PHE* 3.3 6.6 + - - +
386A GLU* 3.1 24.6 + - - +
441A FAD 2.5 31.1 + - - -
500A DCQ 5.0 8.5 - - - -
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Residues in contact with THR 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ARG* 4.2 21.2 + - - +
350A ASP* 5.0 1.4 + - - -
379A HIS* 3.1 28.8 + - - -
380A TYR* 3.8 7.9 - - - -
382A LYS* 1.3 78.7 - - - +
384A ALA* 1.3 62.8 + - - +
386A GLU* 3.3 9.5 + - - +
387A LYS* 3.2 37.6 + - + +
409B ILE* 4.2 21.3 - - + -
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A TYR 2.9 18.1 + - - +
381A PHE* 3.7 4.5 - - - +
383A THR* 1.3 76.5 - - - +
385A PHE* 1.3 57.4 + - - +
387A LYS* 3.3 8.4 + - - +
388A TYR* 3.0 28.4 + - - +
406B VAL* 3.8 23.6 - - + +
409B ILE* 4.1 6.2 - - + +
410B PHE* 3.7 22.0 - - + -
600B LMT 3.9 12.6 - - + -
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Residues in contact with PHE 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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41A PHE* 4.1 17.3 - + - -
43A PRO* 6.1 0.2 - - + -
318A GLU* 4.1 2.2 - - - -
381A PHE* 2.8 27.8 + + + +
382A LYS 3.7 4.3 - - - +
383A THR 3.3 0.2 - - - -
384A ALA* 1.3 68.4 - - - +
386A GLU* 1.3 58.4 + - - +
388A TYR* 3.2 26.4 + + - +
389A PHE* 2.8 57.0 + + + +
403A GLU* 4.8 1.3 - - - -
500A DCQ 3.3 100.7 - + + -
600B LMT 4.6 3.9 - - + +
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Residues in contact with GLU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.6 32.8 - - + -
44A ALA* 3.6 16.6 - - - +
47A HIS* 5.2 1.6 + - - -
53A ARG* 2.7 45.9 + - - -
57A ASP 4.6 1.7 - - - +
58A ILE* 3.5 11.5 - - - +
382A LYS* 3.1 14.3 + - - +
383A THR* 3.3 11.9 - - - +
385A PHE* 1.3 76.8 - - - +
387A LYS* 1.3 80.8 + - + +
389A PHE* 4.0 1.0 - - - +
390A LEU* 3.1 37.3 + - + +
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Residues in contact with LYS 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ARG* 5.6 3.0 - - - +
57A ASP* 4.8 15.8 + - - +
383A THR* 3.2 27.9 + - + +
384A ALA* 3.3 8.7 + - - +
386A GLU* 1.3 95.9 + - + +
388A TYR* 1.3 58.1 + - - +
390A LEU* 3.9 6.2 - - + +
391A TRP* 3.1 28.4 + - - +
394A ARG* 4.8 2.9 + - - -
402B PHE* 3.6 13.7 - - + +
405B LYS* 3.6 50.0 - - + +
406B VAL* 5.0 0.9 - - + -
409B ILE* 6.0 4.0 - - + -
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Residues in contact with TYR 388 (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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384A ALA 3.0 16.8 + - - +
385A PHE* 3.6 25.4 - + - +
387A LYS* 1.3 73.8 - - - +
389A PHE* 1.3 65.8 + - - +
391A TRP* 3.3 6.2 + + - +
392A LYS* 3.1 44.5 + - + +
400A PRO* 3.6 10.7 - - + +
402A PHE* 3.3 34.1 - + - -
403A GLU* 2.6 38.8 + - - +
500A DCQ 4.1 8.7 - - + -
402B PHE* 3.5 44.3 - + + +
500B DCQ 4.1 15.9 - - + -
600B LMT 5.2 0.7 - - + -
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Residues in contact with PHE 389 (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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12A VAL* 4.1 25.8 - - + -
15A ILE* 6.1 0.7 - - + -
39A PHE* 3.5 28.5 - + - -
41A PHE* 3.6 31.9 - + + -
318A GLU* 3.2 22.0 - - - -
385A PHE* 2.8 39.3 + + + +
388A TYR* 1.3 73.3 - - - +
390A LEU* 1.3 64.0 + - - +
392A LYS* 3.0 30.4 + - - +
393A VAL* 3.0 21.7 + - + +
398A ILE* 3.8 30.5 - - + -
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Residues in contact with LEU 390 (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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39A PHE* 3.7 29.6 - - + -
41A PHE* 3.8 17.7 - - + -
57A ASP 4.0 20.2 - - - +
58A ILE* 4.0 12.1 - - - -
59A SER 4.9 0.4 - - - +
60A VAL* 3.9 17.6 - - + +
386A GLU* 3.1 43.7 + - + +
387A LYS* 3.9 7.6 - - + +
389A PHE* 1.3 76.2 - - - +
391A TRP* 1.3 62.7 + - - +
393A VAL* 3.3 4.5 + - - +
394A ARG* 3.1 47.4 + - - +
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Residues in contact with TRP 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LYS 3.1 14.9 + - - +
388A TYR* 3.4 11.2 - + - +
389A PHE 3.2 0.2 - - - -
390A LEU* 1.3 77.1 - - - +
392A LYS* 1.3 76.4 + - + +
394A ARG* 3.1 11.4 + - - +
395A ASN* 2.9 69.3 + - + +
397A ASN* 5.2 4.0 - - + -
400A PRO* 5.3 2.0 - - + -
402A PHE* 6.0 0.4 - + - -
432A SO4 3.2 26.0 + - - +
391B TRP* 3.6 35.7 - + - -
397B ASN* 4.3 13.2 - - + +
400B PRO* 3.4 28.3 - - + +
401B SER* 3.4 22.0 - - - +
402B PHE* 3.6 29.8 - + + -
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Residues in contact with LYS 392 (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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19A TYR* 3.7 2.3 - - - -
318A GLU* 3.9 6.1 + - - -
385A PHE* 5.2 0.6 - - - -
388A TYR* 3.1 48.0 + - + +
389A PHE* 3.0 37.5 + - - +
391A TRP* 1.3 92.9 - - + +
393A VAL* 1.3 62.9 + - - +
395A ASN* 4.4 0.4 - - - +
396A GLY 3.1 20.4 + - - -
397A ASN 3.3 29.1 + - - +
398A ILE* 2.7 33.0 + - + +
400A PRO* 3.7 5.4 - - + -
403A GLU* 2.9 21.8 + - - -
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Residues in contact with VAL 393 (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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15A ILE* 4.5 8.5 - - + -
19A TYR* 2.6 40.3 + - - +
39A PHE* 3.8 42.0 - - + -
60A VAL* 4.0 30.1 - - + -
62A LEU* 4.9 2.2 - - + -
65A LEU* 3.5 5.9 - - + +
69A PHE* 4.0 0.5 - - - -
389A PHE* 3.0 27.8 + - + +
390A LEU* 3.6 7.9 - - - +
392A LYS* 1.3 75.0 - - - +
394A ARG* 1.3 62.1 + - - +
396A GLY 3.8 0.7 + - - -
398A ILE* 3.9 7.2 - - + -
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Residues in contact with ARG 394 (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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57A ASP 5.7 2.0 + - - -
59A SER 5.2 2.8 + - - -
60A VAL* 3.8 30.1 - - + +
65A LEU* 3.5 22.7 - - + +
69A PHE* 3.5 6.4 - - - -
387A LYS 4.8 2.4 + - - -
390A LEU* 3.1 33.8 + - - +
391A TRP* 3.1 20.4 + - - +
393A VAL* 1.3 74.8 - - - +
395A ASN* 1.3 65.7 + - - +
396A GLY 3.7 0.2 - - - -
432A SO4 2.6 42.5 + - - +
401B SER* 3.8 10.3 + - - -
405B LYS* 5.0 10.7 - - - +
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Residues in contact with ASN 395 (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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69A PHE* 3.6 11.6 - - - -
391A TRP* 2.9 65.7 + - + +
392A LYS 4.4 0.4 - - - +
393A VAL 3.2 0.2 - - - -
394A ARG* 1.3 82.9 + - - +
396A GLY* 1.3 60.3 + - - +
397A ASN* 3.4 6.4 + - + +
432A SO4 3.0 28.0 + - - -
397B ASN* 4.5 9.1 - - - +
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Residues in contact with GLY 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.4 27.6 - - - +
22A ARG* 5.9 1.6 - - - +
23A ASN* 3.0 21.8 + - - +
69A PHE* 3.4 27.1 - - - +
392A LYS 3.1 4.6 + - - -
393A VAL 3.8 1.0 + - - -
394A ARG 3.7 0.4 - - - -
395A ASN* 1.3 76.8 - - - +
397A ASN* 1.3 60.1 + - - +
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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
------------------------------------------------------------
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