Contacts of the helix formed by residues 376 - 396 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D GLU* 3.4 45.0 + - + +
354D ASP* 3.9 9.2 + - + +
375D GLY* 1.3 69.2 - - - -
377D TRP* 1.3 65.7 + - - +
379D HIS* 3.1 13.5 + - - +
380D TYR* 3.1 32.8 + - + +
434D SO4 2.9 27.6 + - - +
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Residues in contact with TRP 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410C PHE* 4.5 11.3 - + + -
357D PHE* 3.6 42.4 - + + -
373D LYS* 3.9 27.0 - - + +
374D MET 4.2 4.6 + - - -
375D GLY* 3.9 15.2 - - - +
376D LYS* 1.3 78.4 - - - +
378D ALA* 1.3 69.8 + - + +
380D TYR* 3.4 10.6 + - - +
381D PHE* 3.0 39.7 + + + +
434D SO4 3.8 13.2 + - - -
600D LMT 3.5 91.8 + - + +
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Residues in contact with ALA 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D ILE* 3.4 18.7 - - + +
355D ALA* 3.6 24.0 - - + +
357D PHE* 4.3 13.5 - - + -
375D GLY 3.2 12.5 + - - +
376D LYS 3.1 1.0 - - - -
377D TRP* 1.3 102.9 - - + +
379D HIS* 1.3 63.3 + - - +
381D PHE* 3.5 3.8 + - - +
382D LYS 3.2 16.6 + - - -
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Residues in contact with HIS 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ARG* 6.0 0.8 + - - -
350D ASP* 2.9 38.8 + - - +
352D GLY 3.2 20.7 + - - -
353D GLU* 3.5 20.9 + - - +
354D ASP 3.8 8.5 - - - -
355D ALA* 3.4 9.1 - - - +
375D GLY 3.8 0.2 + - - -
376D LYS 3.1 9.7 + - - +
378D ALA* 1.3 78.5 - - - +
380D TYR* 1.3 88.3 + + - +
382D LYS* 3.2 4.1 + - - +
383D THR* 3.1 37.9 + - - -
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Residues in contact with TYR 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C ILE* 3.7 38.2 - - + +
410C PHE* 3.9 21.5 - + + -
353D GLU 4.8 2.7 + - - -
376D LYS* 3.1 42.3 + - + +
377D TRP* 3.4 8.7 + - - +
379D HIS* 1.3 97.4 - + - +
381D PHE* 1.3 56.9 + - - +
383D THR* 3.4 5.5 + - - -
384D ALA* 2.9 29.5 + - - +
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Residues in contact with PHE 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C PHE* 3.8 17.1 - + + -
500C DCQ 6.1 0.7 - - + -
600C LMT 4.5 12.8 - - + -
346D ILE* 5.5 2.7 - - + -
348D ILE* 3.5 20.4 - - + -
357D PHE* 5.5 2.0 - + - -
377D TRP* 3.0 30.7 + + + +
378D ALA* 3.7 8.1 - - - +
379D HIS 3.3 0.2 - - - -
380D TYR* 1.3 78.3 - - - +
382D LYS* 1.3 56.3 + - - +
384D ALA* 3.3 4.0 + - + +
385D PHE* 2.8 34.3 + + + +
500D DCQ 3.3 42.0 - - + -
600D LMT 3.6 48.7 - - + -
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Residues in contact with LYS 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PHE* 5.4 2.4 - - + -
43D PRO* 3.7 24.4 - - + +
47D HIS* 3.9 7.6 - - + +
162D GLU* 3.2 15.3 + - - +
348D ILE* 2.8 40.9 + - + +
350D ASP* 3.6 26.5 - - + +
378D ALA 3.2 14.1 + - - +
379D HIS* 3.2 9.8 + - - +
381D PHE* 1.3 76.5 - - - +
383D THR* 1.3 58.0 + - - +
385D PHE* 3.5 8.3 + - + +
386D GLU* 3.0 27.8 + - - +
441D FAD 2.5 31.3 + - - -
500D DCQ 5.9 3.8 - - - -
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Residues in contact with THR 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C ILE* 3.8 16.4 - - + -
53D ARG* 4.1 20.3 + - - +
350D ASP* 5.0 1.2 + - - -
379D HIS* 3.1 30.6 + - - -
380D TYR* 3.7 8.8 - - - -
381D PHE 3.3 0.2 - - - -
382D LYS* 1.3 77.1 - - - +
384D ALA* 1.3 61.6 + - - +
386D GLU* 3.3 11.8 - - - +
387D LYS* 3.2 44.1 + - - +
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Residues in contact with ALA 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C VAL* 3.7 26.0 - - + +
409C ILE* 4.0 12.5 - - + +
410C PHE* 3.8 19.7 - - + -
500C DCQ 6.2 1.3 - - + -
600C LMT 5.3 4.7 - - + -
380D TYR 2.9 18.3 + - - +
381D PHE* 3.6 6.3 - - + +
383D THR* 1.3 76.5 - - - +
385D PHE* 1.3 58.0 + - - +
387D LYS* 3.3 6.3 + - - +
388D TYR* 3.0 27.0 + - - +
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Residues in contact with PHE 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C DCQ 5.9 1.6 - - + -
41D PHE* 4.1 12.1 - + - -
43D PRO* 6.2 0.2 - - + -
318D GLU* 4.2 0.9 - - - -
381D PHE* 2.8 28.1 + + + +
382D LYS* 3.8 9.4 - - + +
384D ALA* 1.3 73.7 - - - +
386D GLU* 1.3 57.0 + - - +
388D TYR* 3.2 24.1 + + - +
389D PHE* 2.8 60.9 + + + +
392D LYS* 5.2 0.2 - - - -
403D GLU* 5.1 0.7 - - - -
500D DCQ 3.2 95.3 - + + +
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Residues in contact with GLU 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PHE* 3.6 31.6 - - + -
44D ALA* 3.7 15.4 - - - +
47D HIS* 5.3 1.2 + - - -
53D ARG* 2.8 47.5 + - - -
57D ASP* 4.7 3.6 - - - +
58D ILE* 3.6 10.8 - - - +
382D LYS* 3.0 13.8 + - - +
383D THR* 3.3 11.7 - - - +
385D PHE* 1.3 76.4 - - - +
387D LYS* 1.3 77.4 + - + +
389D PHE* 4.0 1.2 - - - +
390D LEU* 3.1 38.6 + - + +
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Residues in contact with LYS 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C PHE* 3.7 9.8 - - + +
405C LYS* 3.6 56.3 - - + +
406C VAL* 5.3 0.7 - - + -
409C ILE* 4.2 11.9 - - + +
53D ARG* 5.4 1.8 - - - +
57D ASP 6.0 0.7 - - - +
383D THR* 3.2 35.3 + - - +
384D ALA* 3.5 7.4 - - - +
386D GLU* 1.3 91.4 + - + +
388D TYR* 1.3 61.3 + - - +
390D LEU* 3.7 8.6 + - + +
391D TRP* 3.1 24.1 + - - +
394D ARG* 5.1 1.7 + - - -
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Residues in contact with TYR 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C PHE* 3.6 47.7 - + + +
406C VAL* 5.6 0.2 - - + -
500C DCQ 3.7 17.7 - - + -
384D ALA 3.0 14.7 + - - +
385D PHE* 3.2 26.9 + + - +
387D LYS* 1.3 73.3 - - - +
389D PHE* 1.3 67.2 + - - +
391D TRP* 3.2 6.9 + + - +
392D LYS* 3.0 49.1 + - + +
400D PRO* 3.5 11.3 - - - +
402D PHE* 3.6 21.7 - + - -
403D GLU* 2.5 35.0 + - - +
500D DCQ 3.8 15.7 - - + -
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Residues in contact with PHE 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 4.2 26.7 - - + -
15D ILE* 6.2 0.4 - - + -
39D PHE* 3.6 24.9 - + - -
41D PHE* 3.7 31.2 - + + -
318D GLU* 3.4 27.4 - - - -
385D PHE* 2.8 39.8 + + + +
388D TYR* 1.3 74.6 - - - +
390D LEU* 1.3 58.2 + - - +
392D LYS* 3.1 21.5 + - - +
393D VAL* 3.0 36.6 + - + +
398D ILE* 4.0 24.0 - - + -
500D DCQ 6.0 0.9 - - - -
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Residues in contact with LEU 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D PHE* 4.1 18.6 - - + -
41D PHE* 4.1 15.7 - - + -
57D ASP 3.5 22.9 - - - +
58D ILE* 4.1 15.0 - - - -
59D SER 4.3 0.4 - - - +
60D VAL* 3.8 25.4 - - + -
386D GLU* 3.1 39.9 + - + +
387D LYS* 4.0 9.2 - - + +
389D PHE* 1.3 74.5 - - - +
391D TRP* 1.3 62.7 + - - +
393D VAL* 3.3 6.8 + - - +
394D ARG* 3.0 46.7 + - - +
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Residues in contact with TRP 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C TRP* 3.4 34.3 - + - -
397C ASN* 4.7 9.8 - - + +
400C PRO* 3.7 28.1 - - + +
401C SER* 3.2 21.6 - - - +
402C PHE* 3.5 28.7 - + + -
387D LYS 3.1 16.2 + - - +
388D TYR* 3.4 10.5 - + - +
390D LEU* 1.3 76.6 - - - +
392D LYS* 1.3 88.7 + - + +
394D ARG* 3.2 11.0 + - - +
395D ASN* 2.8 66.4 + - + +
397D ASN* 5.2 3.8 - - + -
400D PRO* 4.9 4.9 - - + -
432D SO4 3.1 29.7 + - - +
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Residues in contact with LYS 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D TYR* 3.7 1.9 - - - -
318D GLU* 3.3 17.2 + - - -
385D PHE* 5.2 0.8 - - - -
388D TYR* 3.0 50.9 + - + +
389D PHE* 3.1 30.1 + - - +
391D TRP* 1.3 90.8 - - + +
393D VAL* 1.3 62.1 + - - +
395D ASN* 3.3 0.6 + - - -
396D GLY 3.0 20.4 + - - -
397D ASN 3.3 30.9 + - - +
398D ILE* 2.7 33.4 + - + +
400D PRO* 3.6 4.7 - - + -
403D GLU* 2.8 18.4 + - - -
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Residues in contact with VAL 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ILE* 4.5 10.8 - - + -
19D TYR* 2.6 37.5 + - - +
39D PHE* 3.9 33.9 - - + -
60D VAL* 4.2 11.9 - - + -
62D LEU* 5.1 2.0 - - + -
65D LEU* 3.5 16.7 - - + +
69D PHE* 4.1 0.2 - - - -
389D PHE* 3.0 39.5 + - + +
390D LEU* 3.5 9.4 - - - +
392D LYS* 1.3 75.9 - - - +
394D ARG* 1.3 60.9 + - - +
395D ASN 3.3 1.0 + - - -
396D GLY 3.6 0.7 + - - -
398D ILE* 3.8 9.0 - - + -
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Residues in contact with ARG 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C SER* 4.7 2.0 + - - -
405C LYS* 5.6 5.7 - - - +
56D GLU 5.7 1.2 + - - -
57D ASP* 4.7 7.3 + - - +
59D SER 5.1 3.6 + - - -
60D VAL* 4.0 28.1 - - + +
65D LEU* 3.4 25.4 - - + +
68D LYS* 6.0 0.3 - - - +
69D PHE* 3.6 4.9 - - - -
387D LYS 5.1 1.0 + - - -
390D LEU* 3.0 49.6 + - - +
391D TRP* 3.8 12.2 - - - +
393D VAL* 1.3 74.9 - - - +
395D ASN* 1.3 61.7 + - - +
432D SO4 2.9 43.4 + - - +
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Residues in contact with ASN 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397C ASN* 5.3 5.1 - - - +
69D PHE* 3.6 11.8 - - - -
391D TRP* 2.8 69.5 + - + +
392D LYS* 4.3 1.8 - - - +
393D VAL 3.2 0.2 - - - -
394D ARG* 1.3 84.3 + - - +
396D GLY* 1.3 61.0 + - - +
397D ASN* 3.5 5.9 + - + +
432D SO4 3.3 17.6 + - - -
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Residues in contact with GLY 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D TYR* 3.4 28.1 - - - +
22D ARG* 6.0 0.9 - - - +
23D ASN* 3.0 23.6 + - - +
69D PHE* 3.4 27.4 - - - +
392D LYS 3.0 5.3 + - - -
393D VAL 3.6 1.8 + - - -
395D ASN* 1.3 75.9 - - - +
397D ASN* 1.3 60.9 + - - +
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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