Contacts of the helix formed by residues 376 - 396 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C GLU* 3.5 50.3 + - - +
354C ASP* 4.0 8.9 + - + +
375C GLY* 1.3 70.5 - - - -
377C TRP* 1.3 65.2 + - - +
379C HIS* 3.0 15.8 + - - +
380C TYR* 3.1 31.7 - - + +
434C SO4 2.8 25.5 + - - +
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Residues in contact with TRP 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C PHE* 3.5 44.6 - + + -
373C LYS* 3.8 24.5 - - + -
374C MET 4.0 4.5 + - - -
375C GLY* 3.9 14.5 - - - -
376C LYS* 1.3 77.7 - - - +
378C ALA* 1.3 76.4 + - + +
380C TYR* 3.4 9.5 + - - +
381C PHE* 3.0 41.9 + + + +
434C SO4 2.9 27.1 + - - +
600C LMT 3.3 78.9 + - + +
410D PHE* 4.5 10.7 - - + -
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Residues in contact with ALA 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C ILE* 3.4 17.3 - - + +
355C ALA* 3.5 31.9 - - + +
357C PHE* 4.2 18.8 - - + -
375C GLY 3.4 3.3 + - - +
376C LYS 3.1 0.8 - - - -
377C TRP* 1.3 99.5 - - + +
379C HIS* 1.3 60.2 + - - +
381C PHE* 3.5 4.4 + - - +
382C LYS 3.0 21.7 + - - -
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Residues in contact with HIS 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C HIS* 6.2 0.2 - - - -
350C ASP* 2.9 36.4 + - - +
352C GLY 3.2 18.8 + - - -
353C GLU* 3.5 28.0 + - - +
354C ASP* 3.9 5.6 - - - -
355C ALA* 3.4 8.9 - - - +
376C LYS 3.0 10.9 + - - +
378C ALA* 1.3 76.7 - - - +
380C TYR* 1.3 87.3 + + - +
382C LYS* 3.3 4.3 + - - +
383C THR* 3.1 36.0 + - - -
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Residues in contact with TYR 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C GLU 4.7 2.2 + - - -
376C LYS* 3.1 45.2 + - + +
377C TRP* 3.9 6.7 - - - +
378C ALA 3.4 0.2 - - - -
379C HIS* 1.3 96.0 - + - +
381C PHE* 1.3 60.0 + - - +
383C THR* 3.4 6.4 + - - +
384C ALA* 2.8 30.3 + - - +
409D ILE* 3.7 33.8 - - + +
410D PHE* 3.8 22.1 - + + -
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Residues in contact with PHE 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C ILE* 5.4 1.8 - - + -
348C ILE* 3.4 20.6 - - + -
357C PHE* 5.5 3.4 - + - -
377C TRP* 3.0 29.3 + + + +
378C ALA* 3.6 8.3 - - - +
380C TYR* 1.3 73.8 - - - +
382C LYS* 1.3 59.0 + - - +
384C ALA* 4.2 1.3 - - - -
385C PHE* 2.8 35.0 + + + +
500C DCQ 3.4 32.8 - - + -
600C LMT 3.7 44.0 - - + -
410D PHE* 3.7 11.3 - + + -
500D DCQ 4.9 0.2 - - + -
600D LMT 3.6 35.4 - - + -
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Residues in contact with LYS 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 5.7 0.4 - - - -
43C PRO* 3.9 22.5 + - - +
47C HIS* 4.0 10.5 - - + +
53C ARG* 5.9 0.9 - - - +
162C GLU* 2.9 19.9 + - - -
348C ILE* 2.7 44.6 + - + +
350C ASP* 3.9 18.6 - - + +
378C ALA 3.0 14.4 + - - +
379C HIS* 3.3 13.7 + - - +
381C PHE* 1.3 76.8 - - - +
383C THR* 1.3 63.2 + - - +
385C PHE* 3.7 5.5 - - - +
386C GLU* 3.0 23.8 + - - +
441C FAD 2.5 30.9 + - - -
500C DCQ 5.1 7.8 - - - -
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Residues in contact with THR 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C ARG* 4.2 22.7 + - - +
350C ASP* 5.0 0.9 + - - -
379C HIS* 3.1 28.8 + - - -
380C TYR* 3.7 9.4 - - - -
381C PHE 3.4 0.2 - - - -
382C LYS* 1.3 78.1 - - - +
384C ALA* 1.3 62.3 + - - +
386C GLU* 3.2 9.6 + - + +
387C LYS* 3.2 33.9 + - - +
409D ILE* 3.9 21.1 - - + -
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Residues in contact with ALA 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C TYR 2.8 21.5 + - - +
381C PHE* 3.7 4.3 - - - +
383C THR* 1.3 72.4 - - - +
385C PHE* 1.3 58.7 + - - +
387C LYS* 3.2 5.5 + - - +
388C TYR* 3.0 27.8 + - - +
406D VAL* 3.8 22.0 - - + +
409D ILE* 4.1 12.5 - - + +
410D PHE* 3.7 22.7 - - + -
500D DCQ 4.5 1.3 - - - -
600D LMT 4.3 9.0 - - + -
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Residues in contact with PHE 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 4.1 19.3 - + - -
43C PRO* 6.0 0.7 - - + -
318C GLU* 4.1 1.1 - - - -
381C PHE* 2.8 26.2 + + + +
382C LYS 3.7 4.5 - - - +
384C ALA* 1.3 70.0 - - - +
386C GLU* 1.3 61.3 + - - +
388C TYR* 4.0 24.2 - + - -
389C PHE* 2.8 52.1 + + + +
392C LYS* 5.1 0.2 - - - -
403C GLU* 5.1 0.4 - - - -
500C DCQ 3.3 102.3 - + + -
500D DCQ 4.6 4.8 - - + +
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Residues in contact with GLU 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 3.6 31.6 - - + -
43C PRO 5.6 0.2 - - - -
44C ALA* 3.6 17.9 - - - +
47C HIS* 5.2 1.9 + - - -
53C ARG* 2.8 46.9 + - - -
57C ASP* 4.7 1.9 - - - +
58C ILE* 3.4 12.9 - - - +
382C LYS* 3.0 16.2 + - + +
383C THR* 3.2 11.5 + - - +
385C PHE* 1.3 77.5 - - - +
387C LYS* 1.3 75.6 + - + +
389C PHE* 4.1 0.7 - - - +
390C LEU* 3.1 39.6 + - + +
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Residues in contact with LYS 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ARG* 6.3 0.4 - - - +
57C ASP* 5.4 12.1 + - - +
383C THR* 3.2 26.5 + - - +
384C ALA* 3.2 7.2 + - - +
386C GLU* 1.3 90.2 + - + +
388C TYR* 1.3 63.5 + - - +
390C LEU* 3.9 6.4 - - + +
391C TRP* 3.1 23.4 + - - +
394C ARG* 4.7 3.0 + - - +
402D PHE* 3.9 10.5 - - + +
405D LYS* 3.7 46.7 - - + +
406D VAL* 5.2 0.9 - - + -
409D ILE* 4.4 11.0 - - + -
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Residues in contact with TYR 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C ALA 3.0 16.6 + - - +
385C PHE* 3.6 22.9 - + - +
387C LYS* 1.3 76.0 - - - +
389C PHE* 1.3 63.2 + - - +
391C TRP* 3.2 9.6 + + - +
392C LYS* 3.1 47.9 + - + +
400C PRO* 3.9 3.5 - - - +
402C PHE* 3.5 26.3 - + - -
403C GLU* 2.5 43.2 + - - +
500C DCQ 3.6 25.8 - - + -
402D PHE* 3.6 39.4 - + + +
500D DCQ 3.9 14.4 - - + -
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Residues in contact with PHE 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 4.2 26.0 - - + -
15C ILE* 6.2 0.7 - - + -
39C PHE* 3.5 25.8 - + - -
41C PHE* 3.6 31.6 - + + -
318C GLU* 3.6 19.5 - - + -
385C PHE* 2.8 41.3 + + + +
388C TYR* 1.3 75.1 - - - +
390C LEU* 1.3 62.3 + - - +
392C LYS* 3.1 31.2 + - - +
393C VAL* 3.1 24.1 + - + +
398C ILE* 3.9 31.2 - - + -
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Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C PHE* 3.9 13.5 - - + -
41C PHE* 3.9 30.1 - - + -
57C ASP 3.9 20.6 - - - +
58C ILE* 4.2 10.5 - - - -
59C SER 5.1 0.4 - - - +
60C VAL* 3.8 24.7 - - + -
386C GLU* 3.1 44.1 + - + +
387C LYS* 3.9 7.2 - - + +
389C PHE* 1.3 75.8 - - - +
391C TRP* 1.3 62.4 + - - +
393C VAL* 3.3 5.4 + - - +
394C ARG* 3.1 40.5 + - - +
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Residues in contact with TRP 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C LYS 3.1 13.9 + - - +
388C TYR* 3.2 15.5 + + - +
390C LEU* 1.3 77.2 - - - +
392C LYS* 1.3 87.6 + - + +
394C ARG* 3.2 13.0 + - - +
395C ASN* 2.8 72.5 + - + +
397C ASN* 5.0 3.1 - - + -
400C PRO* 4.8 6.7 - - + -
402C PHE* 5.6 0.7 - + - -
432C SO4 3.3 16.3 + - - -
391D TRP* 3.4 34.3 - + - -
397D ASN* 4.6 8.5 - - + +
400D PRO* 3.8 26.0 - - + +
401D SER* 3.4 23.7 - - - +
402D PHE* 3.5 29.8 - + + -
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Residues in contact with LYS 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 3.6 2.8 - - - -
318C GLU* 3.6 9.9 + - - -
385C PHE* 5.1 1.2 - - - -
388C TYR* 3.1 47.6 + - + +
389C PHE* 3.1 30.5 + - - +
391C TRP* 1.3 91.9 - - + +
393C VAL* 1.3 63.9 + - - +
395C ASN* 4.8 1.1 - - - -
396C GLY 3.1 19.8 + - - -
397C ASN 3.3 31.0 + - - +
398C ILE* 2.9 28.9 + - + +
400C PRO* 3.7 5.2 - - + -
403C GLU* 2.7 28.7 + - - -
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Residues in contact with VAL 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 4.5 9.9 - - + -
19C TYR* 2.6 40.7 + - - +
39C PHE* 3.8 39.0 - - + -
60C VAL* 4.1 20.9 - - + -
62C LEU* 5.0 2.5 - - + -
65C LEU* 3.4 6.8 - - + +
69C PHE* 4.0 0.3 - - - -
389C PHE* 3.1 36.8 + - + +
390C LEU* 3.6 7.2 - - - +
392C LYS* 1.3 75.2 - - - +
394C ARG* 1.3 61.9 + - - +
396C GLY 3.8 0.3 + - - -
398C ILE* 3.8 8.1 - - + -
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Residues in contact with ARG 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C VAL* 3.7 31.5 - - + +
65C LEU* 3.4 23.5 - - + +
68C LYS* 5.9 0.5 - - - +
69C PHE* 3.5 5.0 - - - -
387C LYS 4.7 2.6 + - - -
390C LEU* 3.1 26.1 + - - +
391C TRP* 3.7 25.1 - - - +
393C VAL* 1.3 76.3 - - - +
395C ASN* 1.3 61.7 + - - +
396C GLY 3.6 0.4 - - - -
432C SO4 2.5 58.4 + - - +
401D SER* 4.6 3.4 + - - -
405D LYS* 5.5 5.9 - - - +
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Residues in contact with ASN 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C PHE* 3.6 10.3 - - - -
391C TRP* 2.8 59.2 + - + +
392C LYS* 3.3 1.8 + - - +
393C VAL 3.2 0.2 - - - -
394C ARG* 1.3 80.0 + - - +
396C GLY* 1.3 60.6 + - - +
397C ASN* 3.4 6.0 + - + +
432C SO4 2.9 34.7 + - - -
397D ASN* 4.9 6.5 - - - +
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Residues in contact with GLY 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 3.5 25.5 - - - +
22C ARG* 5.9 0.9 - - - +
23C ASN* 3.0 23.6 + - - +
69C PHE* 3.3 32.6 - - - +
392C LYS 3.1 4.6 + - - -
394C ARG 3.6 0.2 - - - -
395C ASN* 1.3 76.6 - - - +
397C ASN* 1.3 59.4 + - - +
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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