Contacts of the helix formed by residues 336 - 357 (chain C) in PDB entry 5HJP
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 VAL 336 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294B GLN* 5.6 2.9 - - - +
335C PRO* 1.4 76.3 - - + +
337C THR* 1.4 62.8 + - + +
338C ASN 3.1 5.2 - - - +
339C ILE* 3.2 40.6 + - + +
340C CYS* 3.4 13.5 + - - -
411C ALA* 4.6 10.3 - - + -
413C VAL* 4.7 11.0 - - + -
510C PHE* 3.5 56.1 - - + -
515C ASP* 5.6 2.0 - - - +
516C THR* 4.3 13.0 - - + +
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Residues in contact with THR 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C PRO* 4.6 8.7 - - + -
336C VAL* 1.4 80.8 - - + +
338C ASN* 1.3 63.0 + - - +
339C ILE 3.3 0.2 - - - -
340C CYS* 3.4 3.2 + - - +
341C GLN* 2.8 49.9 + - - +
516C THR* 3.3 44.0 - - + +
517C PRO* 5.2 5.2 - - + -
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Residues in contact with ASN 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C PRO* 3.3 38.2 + - - +
336C VAL 4.8 0.2 - - - -
337C THR* 1.3 83.4 + - - +
339C ILE* 1.4 57.5 + - + +
341C GLN* 4.0 8.4 - - - +
342C ALA* 3.0 29.6 + - - +
397C LEU* 3.7 11.6 - - + +
399C THR* 4.4 3.1 + - - -
401C LEU* 3.3 33.5 - - + +
403C VAL* 5.5 4.3 - - + -
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Residues in contact with ILE 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C PRO 4.8 2.7 - - - +
336C VAL* 3.2 35.6 + - + +
338C ASN* 1.4 74.2 - - + +
340C CYS* 1.3 56.6 + - - +
342C ALA* 3.4 2.1 + - - +
343C ALA* 2.8 39.3 + - + +
384C PHE* 5.8 8.3 - - + -
397C LEU* 4.2 16.0 - - + +
403C VAL* 4.1 35.0 - - + -
408C ALA* 6.2 0.2 - - + -
413C VAL* 5.2 9.2 - - + -
507C LEU* 6.3 3.8 - - + -
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Residues in contact with CYS 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C VAL* 3.4 11.9 + - - +
337C THR* 3.4 10.5 + - - +
339C ILE* 1.3 79.9 - - - +
341C GLN* 1.4 57.4 + - + +
343C ALA* 3.3 3.2 + - - +
344C ASP* 2.9 29.3 + - - +
507C LEU* 4.0 17.9 - - - -
510C PHE* 5.2 13.0 - - - -
516C THR* 4.3 14.6 - - + -
518C ILE* 4.3 18.6 - - + -
519C ASP 5.8 1.5 + - - +
522C LEU* 3.8 26.8 - - + +
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Residues in contact with GLN 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C THR* 2.8 35.2 + - - +
338C ASN* 4.2 7.9 - - - +
340C CYS* 1.4 69.0 - - + +
342C ALA* 1.4 63.7 + - - +
344C ASP* 3.8 6.7 - - - +
345C LYS* 3.3 22.9 + - - +
399C THR* 4.2 8.2 - - + +
517C PRO 5.8 3.6 - - - +
519C ASP* 6.4 2.9 - - + -
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Residues in contact with ALA 342 (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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338C ASN 3.0 20.6 + - - +
339C ILE 3.8 3.1 - - - +
341C GLN* 1.4 73.5 - - - +
343C ALA* 1.4 65.5 + - - +
345C LYS* 3.5 2.3 + - - +
346C GLN* 3.1 30.9 + - + +
397C LEU* 3.8 27.8 - - + -
398C ALA* 4.7 3.4 - - + +
399C THR* 3.7 29.1 - - + +
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Residues in contact with ALA 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ILE* 2.8 27.5 + - + +
340C CYS* 3.5 7.4 - - - +
342C ALA* 1.4 73.5 - - - +
344C ASP* 1.4 60.0 + - - +
346C GLN* 3.6 1.0 + - - -
347C LEU* 3.2 29.3 + - - +
376C TRP* 5.1 1.8 - - + -
380C LEU* 3.6 21.8 - - + +
397C LEU* 5.7 0.2 - - - +
507C LEU* 5.9 3.6 - - + -
522C LEU* 3.8 20.0 - - + -
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Residues in contact with ASP 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C CYS 2.9 16.7 + - - +
341C GLN* 3.8 7.9 - - - +
342C ALA 3.3 0.2 - - - -
343C ALA* 1.4 72.6 - - - +
345C LYS* 1.3 66.6 + - - +
347C LEU* 3.1 15.9 + - - +
348C PHE* 3.3 26.7 - - - -
519C ASP* 2.9 45.4 - - + +
521C PHE* 3.3 6.8 - - - +
522C LEU* 3.1 34.4 + - + +
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Residues in contact with LYS 345 (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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312C GLU* 5.4 5.9 + - - -
341C GLN 3.3 15.0 + - - +
342C ALA 3.5 4.2 + - - +
344C ASP* 1.3 78.4 - - - +
346C GLN* 1.4 74.8 + - - +
348C PHE* 3.4 20.3 + - - +
349C THR* 3.1 24.5 + - - +
398C ALA* 4.2 21.0 - - + +
399C THR* 4.0 22.2 - - + +
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Residues in contact with GLN 346 (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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311C VAL 5.7 2.4 + - - -
342C ALA* 3.1 22.8 + - + +
343C ALA 3.8 2.7 - - - +
345C LYS* 1.4 82.6 + - - +
347C LEU* 1.3 57.8 + - - +
348C PHE 3.3 0.9 - - - -
349C THR* 3.3 27.0 + - - +
350C LEU* 2.9 29.3 + - - +
380C LEU* 3.6 26.1 - - + +
383C SER* 4.9 7.9 + - - -
387C ARG* 3.8 27.8 - - - +
398C ALA* 3.3 29.9 - - + +
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Residues in contact with LEU 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C ALA 3.2 17.8 + - - +
344C ASP* 3.1 11.3 + - - +
346C GLN* 1.3 75.7 - - - +
348C PHE* 1.4 61.5 + - - +
350C LEU* 3.7 14.0 + - + +
351C VAL* 3.4 19.2 + - - +
376C TRP* 3.7 38.6 - - + -
380C LEU* 4.3 5.8 - - + -
521C PHE* 3.2 26.4 - - + -
522C LEU* 3.6 44.4 - - + +
525C MET* 3.7 23.1 - - + -
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Residues in contact with PHE 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ASP* 3.3 42.0 - - - -
345C LYS* 3.7 12.6 - - - +
346C GLN 3.3 0.6 - - - -
347C LEU* 1.4 73.9 - - - +
349C THR* 1.3 64.5 + - - +
351C VAL* 3.5 5.5 + - - +
352C GLU* 3.5 25.6 + - - +
519C ASP* 5.1 2.9 - - - -
520C THR* 6.1 0.2 - - - -
521C PHE* 3.6 28.7 - + + -
542C ILE* 4.2 11.7 - - + -
546C LEU* 3.7 28.0 - - + +
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Residues in contact with THR 349 (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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311C VAL* 3.6 36.2 - - + +
345C LYS* 3.1 25.7 + - - +
346C GLN* 3.4 30.7 + - - +
348C PHE* 1.3 77.6 - - - +
350C LEU* 1.3 56.2 + - - +
352C GLU* 3.4 8.6 + - + +
353C TRP* 2.9 27.3 + - - +
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Residues in contact with LEU 350 (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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346C GLN 2.9 17.1 + - - +
347C LEU* 3.9 16.2 - - + +
348C PHE 3.3 0.2 - - - -
349C THR* 1.3 74.7 - - - +
351C VAL* 1.3 60.1 + - + +
353C TRP* 3.2 18.7 + - + +
354C ALA* 2.8 28.9 + - - +
372C LEU* 4.1 18.6 - - + -
376C TRP* 3.8 39.0 - - + +
379C LEU* 3.7 16.4 - - + -
380C LEU* 4.5 7.4 - - + -
442C ARG* 3.4 29.2 - - - +
525C MET* 5.6 0.7 - - + -
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Residues in contact with VAL 351 (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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347C LEU 3.4 17.5 - - - +
348C PHE 3.5 6.2 + - - +
349C THR 3.4 0.4 - - - -
350C LEU* 1.3 75.5 - - + +
352C GLU* 1.4 63.0 + - - +
354C ALA* 3.2 8.2 + - - +
355C LYS* 3.0 31.8 + - - +
372C LEU* 4.4 7.2 - - + -
521C PHE* 4.2 2.7 - - + -
543C LEU* 3.8 22.7 - - + -
546C LEU* 3.8 42.2 - - + +
547C LEU* 3.8 28.5 - - + -
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Residues in contact with GLU 352 (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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311C VAL* 4.8 5.6 - - + -
348C PHE 3.5 13.0 + - - +
349C THR* 3.4 11.1 + - - +
350C LEU 3.3 0.4 - - - -
351C VAL* 1.4 79.2 - - - +
353C TRP* 1.4 61.6 + - - +
355C LYS* 3.4 42.3 + - - +
356C ARG* 3.5 31.4 + - - +
546C LEU* 4.3 9.5 - - - +
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Residues in contact with TRP 353 (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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307C ALA* 3.3 40.4 - - + +
308C GLU* 3.1 18.8 + - - +
311C VAL* 3.7 20.5 - - + +
349C THR 2.9 14.3 + - - +
350C LEU* 3.2 25.8 + - + +
352C GLU* 1.4 75.4 - - - +
354C ALA* 1.4 71.2 + - + +
356C ARG* 3.0 27.9 + - - +
357C ILE* 3.4 31.7 + - + +
379C LEU* 3.9 15.3 - - + -
439C GLY 4.0 5.4 - - - -
442C ARG* 3.2 59.7 - - + +
443C ALA 4.0 0.9 - - - -
446C LEU* 3.9 23.6 - - + -
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Residues in contact with ALA 354 (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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350C LEU 2.8 20.3 + - - +
351C VAL* 3.2 6.3 + - - +
353C TRP* 1.4 85.2 - - + +
355C LYS* 1.4 60.3 + - - +
357C ILE* 3.2 12.6 + - - +
360C PHE* 3.2 46.0 - - + +
372C LEU* 3.9 18.8 - - + -
446C LEU* 4.3 7.4 - - + -
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Residues in contact with LYS 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C VAL* 3.0 17.5 + - - +
352C GLU* 3.6 40.6 + - - +
353C TRP 3.3 0.2 - - - -
354C ALA* 1.4 75.0 - - - +
356C ARG* 1.4 59.3 + - + +
357C ILE 3.5 4.0 - - - +
360C PHE* 4.6 0.7 - - + -
361C SER* 3.6 31.4 + - - +
546C LEU 2.9 27.1 + - - +
547C LEU* 4.1 29.5 + - + +
548C GLN 4.0 11.5 + - - -
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Residues in contact with ARG 356 (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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303C ARG* 3.9 17.0 - - - +
306C GLU* 5.2 5.3 + - + +
307C ALA* 3.7 20.6 - - + +
310C ALA* 3.6 34.8 + - - +
311C VAL* 5.4 2.7 - - - +
352C GLU* 3.6 29.1 + - - +
353C TRP* 3.0 11.5 + - - +
355C LYS* 1.4 77.0 - - + +
357C ILE* 1.4 63.6 + - - +
358C PRO* 3.5 7.1 - - - +
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Residues in contact with ILE 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C MET* 5.0 2.7 - - - -
304C ILE* 4.1 26.9 - - + -
307C ALA* 3.8 17.0 - - + -
353C TRP* 3.7 50.7 - - + +
354C ALA 3.2 10.8 + - - +
355C LYS 4.4 3.5 - - - +
356C ARG* 1.4 76.1 - - - +
358C PRO* 1.4 73.6 - - + +
359C HIS 3.4 0.3 + - - -
360C PHE* 3.2 14.9 + - - +
361C SER 4.7 0.5 + - - -
439C GLY 4.8 1.6 - - - +
443C ALA* 4.4 9.9 - - + -
446C LEU* 4.1 9.2 - - + -
447C PHE* 3.7 33.0 - - + -
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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
------------------------------------------------------------
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