Contacts of the helix formed by residues 376 - 396 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B GLU* 3.6 38.8 + - - +
354B ASP* 3.8 8.1 + - + +
375B GLY* 1.3 68.6 - - - -
377B TRP* 1.3 66.3 + - - +
379B HIS* 3.0 14.6 + - - +
380B TYR* 3.0 30.6 - - + -
434B SO4 3.0 26.7 + - - +
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Residues in contact with TRP 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A PHE* 4.7 9.1 - - + -
357B PHE* 3.6 40.6 - + + -
373B LYS* 3.8 27.1 - - + +
374B MET 4.1 7.4 + - - -
375B GLY* 3.8 17.7 - - - -
376B LYS* 1.3 75.8 - - - +
378B ALA* 1.3 75.1 + - + +
380B TYR* 3.2 10.6 + - - +
381B PHE* 2.9 45.5 + + - +
434B SO4 2.9 27.6 + - - +
600B LMT 3.5 80.6 + - + +
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Residues in contact with ALA 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ILE* 3.3 20.4 - - + +
355B ALA* 3.6 26.5 - - + +
357B PHE* 4.3 9.2 - - + -
375B GLY 3.3 8.2 + - - +
376B LYS 3.2 0.8 - - - -
377B TRP* 1.3 105.4 - - + +
379B HIS* 1.3 58.9 - - - +
381B PHE* 3.6 5.3 - - - +
382B LYS 3.0 21.5 + - - -
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Residues in contact with HIS 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B HIS* 6.0 0.4 - - - -
52B TRP* 6.2 0.6 - - - -
53B ARG* 5.8 1.4 + - - -
350B ASP* 2.9 32.0 + - - +
352B GLY 2.9 27.2 + - - -
353B GLU* 3.5 24.2 + - + +
354B ASP* 3.9 4.3 - - - -
355B ALA* 3.5 8.6 - - - +
375B GLY 3.8 0.2 + - - -
376B LYS 3.0 10.1 + - - +
378B ALA* 1.3 78.8 - - - +
380B TYR* 1.3 87.6 + + - +
382B LYS* 3.3 5.2 + - - +
383B THR* 3.1 42.5 + - - -
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Residues in contact with TYR 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ILE* 3.5 35.5 - - + +
410A PHE* 3.8 24.5 - + + -
353B GLU* 4.5 10.1 + - - +
376B LYS* 3.0 43.0 - - + +
377B TRP* 3.2 8.5 + - - +
379B HIS* 1.3 96.3 + + - +
381B PHE* 1.3 59.6 + - - +
383B THR* 3.5 4.8 + - - -
384B ALA* 2.9 29.5 + - - +
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Residues in contact with PHE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A PHE* 3.9 9.5 - + + -
500A DCQ 5.5 3.6 - - + -
600A LMT 4.0 21.5 - - + -
348B ILE* 3.5 18.8 - - + -
357B PHE* 5.3 3.8 - + - -
377B TRP* 2.9 29.6 + + - +
378B ALA* 3.6 12.8 - - - +
380B TYR* 1.3 75.1 - - - +
382B LYS* 1.3 59.0 + - - +
384B ALA* 3.3 3.9 + - + +
385B PHE* 2.8 32.9 + + + +
500B DCQ 3.2 42.2 - + + -
600B LMT 3.6 48.2 - - + -
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Residues in contact with LYS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 5.6 1.0 - - - -
43B PRO* 4.0 21.5 + - - +
47B HIS* 4.2 8.5 - - + +
53B ARG* 6.3 0.4 - - - +
162B GLU* 3.1 18.1 + - - -
348B ILE* 2.6 46.3 + - + +
350B ASP* 4.0 17.7 - - + +
378B ALA 3.0 15.9 + - - +
379B HIS* 3.3 11.9 + - - +
381B PHE* 1.3 76.4 - - - +
383B THR* 1.3 62.4 + - - +
385B PHE* 3.5 6.5 + - - +
386B GLU* 3.1 23.6 + - - +
441B FAD 2.5 31.8 + - - -
500B DCQ 4.3 9.0 - - - -
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Residues in contact with THR 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A ILE* 3.9 23.8 - - + -
53B ARG* 3.9 24.0 + - - +
350B ASP* 5.0 1.4 + - - -
379B HIS* 3.1 31.4 + - - -
380B TYR* 3.8 7.9 - - - -
382B LYS* 1.3 74.7 - - - +
384B ALA* 1.3 66.8 + - - +
386B GLU* 3.2 10.3 + - - +
387B LYS* 3.2 32.5 + - - +
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A VAL* 3.8 27.8 - - + +
409A ILE* 4.2 7.9 - - + +
410A PHE* 3.8 17.7 - - + -
500A DCQ 4.4 11.4 - - + -
600A LMT 5.1 1.3 - - + -
380B TYR 2.9 19.2 + - - +
381B PHE* 3.5 5.8 - - - +
383B THR* 1.3 77.0 - - - +
385B PHE* 1.3 62.5 + - - +
387B LYS* 3.1 5.6 + - - +
388B TYR* 3.0 22.5 + - - +
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Residues in contact with PHE 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A DCQ 4.5 3.3 - - - +
41B PHE* 4.0 20.9 - + - -
43B PRO* 6.0 0.4 - - + -
318B GLU* 4.1 3.6 - - - -
381B PHE* 2.8 24.1 + - + +
382B LYS 3.9 4.5 - - - +
383B THR 3.3 0.2 - - - -
384B ALA* 1.3 73.0 - - - +
386B GLU* 1.3 58.2 + - - +
388B TYR* 3.3 21.1 + + - +
389B PHE* 2.8 52.0 + + + +
392B LYS* 5.2 0.4 - - - -
403B GLU* 5.0 1.1 - - - -
500B DCQ 3.4 106.1 - + + +
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.6 31.3 - - + -
44B ALA* 3.7 14.8 - - - +
47B HIS* 5.1 3.5 + - - -
53B ARG* 2.8 48.0 + - - +
57B ASP* 4.9 0.9 - - - +
58B ILE* 3.7 8.0 - - - +
382B LYS* 3.1 14.1 + - - +
383B THR* 3.2 12.3 - - - +
385B PHE* 1.3 77.4 - - - +
387B LYS* 1.3 79.1 + - + +
389B PHE* 3.5 1.2 + - - +
390B LEU* 3.2 34.9 + - + +
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Residues in contact with LYS 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A PHE* 3.7 15.6 - - + +
405A LYS* 3.9 49.3 - - + +
406A VAL* 5.0 1.1 - - + -
409A ILE* 4.7 9.2 - - + -
53B ARG* 6.3 0.2 - - - +
57B ASP* 4.9 17.4 + - - +
383B THR* 3.5 23.6 - - - +
384B ALA* 3.1 8.3 + - - +
386B GLU* 1.3 92.6 + - + +
388B TYR* 1.3 62.2 + - - +
390B LEU* 3.7 7.9 + - + +
391B TRP* 3.1 23.0 + - - +
394B ARG* 4.9 2.8 + - - -
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Residues in contact with TYR 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A PHE* 3.6 43.6 - + + +
500A DCQ 4.0 11.9 - - + -
384B ALA 3.0 12.5 + - - +
385B PHE* 3.5 17.9 - + - +
387B LYS* 1.3 76.9 - - - +
389B PHE* 1.3 58.8 + - - +
391B TRP* 3.2 7.6 + + - +
392B LYS* 3.0 49.3 + - + +
400B PRO* 3.2 18.2 - - + +
402B PHE* 3.3 27.1 - + - -
403B GLU* 2.6 33.7 + - - +
500B DCQ 3.6 28.5 - - + -
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Residues in contact with PHE 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 4.1 26.0 - - + -
15B ILE* 6.2 1.1 - - + -
16B ALA 6.3 0.2 - - - -
39B PHE* 3.5 25.4 - + - -
41B PHE* 3.7 32.3 - + + -
318B GLU* 3.5 26.7 - - + -
385B PHE* 2.8 39.6 + + + +
387B LYS 3.5 0.2 - - - -
388B TYR* 1.3 73.9 - - - +
390B LEU* 1.3 58.3 + - - +
392B LYS* 3.0 22.4 + - - +
393B VAL* 3.0 38.0 + - + +
398B ILE* 3.9 24.5 - - + -
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PHE* 4.0 10.3 - - + -
41B PHE* 3.9 24.9 - - + -
57B ASP 3.4 25.1 - - - +
58B ILE* 3.8 21.3 - - - +
59B SER 4.1 0.9 - - - +
60B VAL* 4.0 21.8 - - + +
386B GLU* 3.2 33.9 + - + +
387B LYS* 4.0 8.1 - - + +
389B PHE* 1.3 77.0 - - - +
391B TRP* 1.3 61.3 + - - +
393B VAL* 3.5 5.7 + - - +
394B ARG* 3.1 44.4 + - - +
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Residues in contact with TRP 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A TRP* 3.6 35.7 - + - -
397A ASN* 4.4 12.6 - - + +
400A PRO* 3.5 29.0 - - + +
401A SER* 3.4 21.3 - - - +
402A PHE* 3.6 29.4 - + + -
387B LYS 3.1 15.1 + - - +
388B TYR* 3.2 11.2 + + - +
390B LEU* 1.3 77.9 - - - +
392B LYS* 1.3 78.4 + - + +
394B ARG* 3.2 10.5 + - - +
395B ASN* 2.9 67.6 + - + +
397B ASN* 5.2 4.0 - - + -
400B PRO* 5.7 1.8 - - + -
402B PHE* 6.1 0.7 - + - -
432B SO4 3.3 29.4 + - - +
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Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 3.8 1.7 - - - -
318B GLU* 3.5 10.1 + - - -
385B PHE* 5.2 1.0 - - - -
388B TYR* 3.0 50.0 + - + +
389B PHE* 3.0 31.3 + - - +
391B TRP* 1.3 93.0 - - + +
393B VAL* 1.3 57.0 + - - +
395B ASN* 3.2 0.8 + - - +
396B GLY 3.0 25.6 + - - -
397B ASN 3.3 30.3 + - - +
398B ILE* 2.7 34.8 + - + +
400B PRO* 3.7 5.8 - - + -
403B GLU* 2.8 22.6 + - - -
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 4.4 10.5 - - + -
19B TYR* 2.7 40.1 + - - +
39B PHE* 3.8 39.0 - - + -
60B VAL* 4.1 15.7 - - + -
62B LEU* 4.9 2.5 - - + -
65B LEU* 3.4 8.3 - - + +
69B PHE* 4.0 0.2 - - - -
389B PHE* 3.0 37.0 + - + +
390B LEU* 3.7 7.9 - - - +
392B LYS* 1.3 75.1 - - - +
394B ARG* 1.3 61.1 + - - +
395B ASN 3.3 0.7 + - - -
396B GLY 3.7 0.7 + - - -
398B ILE* 3.9 8.3 - - + -
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A SER* 4.0 8.5 + - - -
405A LYS* 5.0 9.7 - - - +
57B ASP 5.5 2.6 + - - -
59B SER 5.1 3.4 + - - -
60B VAL* 3.7 32.5 - - + +
65B LEU* 3.5 22.7 - - + +
68B LYS* 6.1 0.2 - - - +
69B PHE* 3.5 6.8 - - - -
387B LYS 4.9 2.2 + - - -
390B LEU* 3.1 35.7 + - - +
391B TRP* 3.2 17.6 + - - +
393B VAL* 1.3 75.1 - - - +
395B ASN* 1.3 67.4 + - - +
396B GLY 3.6 0.4 - - - -
432B SO4 2.7 42.7 + - - +
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Residues in contact with ASN 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A ASN* 4.5 8.9 - - - +
69B PHE* 3.6 11.0 - - - -
391B TRP* 2.9 60.7 + - + +
392B LYS 4.3 0.9 - - - +
394B ARG* 1.3 83.6 + - - +
396B GLY* 1.3 59.6 + - - +
397B ASN* 3.4 6.3 + - - +
432B SO4 2.9 27.7 + - - -
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Residues in contact with GLY 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 3.5 25.9 - - - +
22B ARG* 6.0 0.9 - - - +
23B ASN* 3.1 23.0 + - - +
69B PHE* 3.3 30.4 - - - +
392B LYS 3.0 4.4 + - - -
393B VAL 3.7 1.0 + - - -
394B ARG 3.6 0.2 - - - -
395B ASN* 1.3 78.8 - - - +
397B ASN* 1.3 57.0 + - - +
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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