Contacts of the helix formed by residues 352 - 369 (chain C) in PDB entry 3J8B
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 ASP 352 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350C ARG 3.8 1.2 + - - -
351C THR* 1.3 72.6 - - - +
353C ARG* 1.3 53.7 + - - +
355C ARG* 4.2 6.3 - - - -
356C THR* 2.5 41.9 + - - -
387C ASN* 4.8 18.4 - - + -
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Residues in contact with ARG 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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351C THR* 3.3 5.9 - - - -
352C ASP* 1.3 78.6 - - - +
354C ILE* 1.3 57.0 + - - +
356C THR* 4.8 0.7 - - - -
357C CYS* 2.9 27.2 + - - +
391C ALA 5.8 1.3 - - - +
392C ASP* 3.7 39.9 - - - +
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Residues in contact with ILE 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C CYS* 6.5 0.7 - - + -
345C ILE* 4.4 11.7 - - + +
350C ARG* 5.6 1.6 - - + -
351C THR* 3.3 18.1 + - - +
353C ARG* 1.3 78.1 - - - +
355C ARG* 1.3 59.9 + - - +
357C CYS* 3.2 6.7 - - - +
358C ALA* 2.9 28.4 + - - +
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Residues in contact with ARG 355 (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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345C ILE 4.5 10.7 + - - +
346C TYR* 4.3 21.9 - - + +
347C ALA 4.9 3.1 - - - +
350C ARG* 4.7 6.3 - - + +
351C THR 2.7 24.4 + - - +
352C ASP* 4.0 4.5 - - - +
354C ILE* 1.3 73.3 - - - +
356C THR* 1.3 63.0 + - - +
358C ALA* 3.1 9.5 + - - +
359C ILE* 3.0 21.9 + - - +
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Residues in contact with THR 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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352C ASP* 2.5 26.8 + - - +
353C ARG* 4.5 2.5 - - - -
355C ARG* 1.3 70.1 - - - +
357C CYS* 1.3 64.3 + - - +
359C ILE* 3.4 8.2 + - - +
360C LEU* 2.9 26.6 + - - +
384C LEU* 5.4 7.6 - - - -
387C ASN* 5.0 20.9 - - - -
388C ILE* 5.6 3.4 - - - -
392C ASP* 5.7 3.8 - - - -
395C VAL* 5.8 4.7 - - - -
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Residues in contact with CYS 357 (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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294C LEU* 6.6 0.4 - - + -
353C ARG 2.9 23.7 + - - +
354C ILE* 3.2 9.2 - - - +
355C ARG 3.2 0.2 - - - -
356C THR* 1.3 76.4 - - - +
358C ALA* 1.3 63.2 + - - +
360C LEU* 3.3 5.8 + - - +
361C CYS* 2.9 24.3 + - - +
392C ASP* 5.3 6.0 - - + +
395C VAL* 5.7 4.9 - - + +
398C LEU* 5.6 0.6 - - - +
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Residues in contact with ALA 358 (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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341C LEU 5.7 0.2 - - - -
342C CYS* 4.3 21.7 - - - +
345C ILE* 3.5 32.1 - - + -
346C TYR* 4.9 2.5 - - + +
354C ILE 2.9 7.5 + - - +
355C ARG* 3.2 9.4 - - - +
357C CYS* 1.3 74.3 - - - +
359C ILE* 1.3 64.9 + - - +
361C CYS* 3.0 9.8 + - - +
362C HIS* 2.9 21.5 + - - +
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Residues in contact with ILE 359 (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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355C ARG 3.0 10.4 + - - +
356C THR* 3.5 12.3 - - - +
358C ALA* 1.3 77.6 - - - +
360C LEU* 1.3 64.3 + - - +
362C HIS* 3.0 11.5 + - - +
363C ILE* 2.9 22.7 + - - +
382C SER* 4.8 19.3 - - - -
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Residues in contact with LEU 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C THR 2.9 20.2 + - - +
357C CYS* 3.6 4.9 - - - +
359C ILE* 1.3 73.2 - - - +
361C CYS* 1.3 58.5 + - - +
363C ILE* 3.3 7.5 + - - +
364C TYR* 2.9 30.2 + - - +
395C VAL* 6.3 0.9 - - + -
398C LEU* 3.3 38.4 - - + +
399C TYR* 5.1 0.7 - - - +
402C THR* 4.5 5.9 - - - -
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Residues in contact with CYS 361 (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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297C ILE* 5.0 16.6 - - + +
301C TYR* 4.2 15.0 - - + +
357C CYS 2.9 14.2 + - - +
358C ALA* 3.4 11.2 - - - +
360C LEU* 1.3 72.3 - - - +
362C HIS* 1.3 66.0 + - - +
364C TYR* 3.3 6.3 + - - +
365C HIS* 3.0 27.3 + - - +
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Residues in contact with HIS 362 (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 MET* 6.2 4.0 - - - -
342C CYS* 4.9 16.4 - - + -
358C ALA 2.9 11.3 + - - +
359C ILE* 3.1 12.8 - - - +
361C CYS* 1.3 75.7 - - - +
363C ILE* 1.3 58.4 + - - +
365C HIS* 3.9 3.7 - - - +
366C HIS* 2.9 35.3 + - + +
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Residues in contact with ILE 363 (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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359C ILE 2.9 12.2 + - - +
360C LEU* 3.3 11.0 + - - +
362C HIS* 1.3 76.0 - - - +
364C TYR* 1.3 56.2 + - - +
366C HIS* 4.0 4.8 - - - +
367C ALA* 2.9 33.4 + - - +
375C ALA* 4.4 17.6 - - + +
378C LEU* 5.3 9.0 - - + -
379C MET* 5.7 6.5 - - + +
402C THR* 4.5 13.2 - - - -
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Residues in contact with TYR 364 (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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301C TYR* 5.1 9.0 - - + +
302C TYR* 6.4 0.9 - - - -
360C LEU 2.9 18.0 + - - +
361C CYS* 3.7 6.7 - - - +
363C ILE* 1.3 76.3 - - - +
365C HIS* 1.3 63.6 + - - +
367C ALA* 3.3 5.1 + - - +
368C LEU* 3.0 23.6 + - - +
398C LEU* 6.6 0.2 - - - -
401C ARG* 6.1 1.6 - - + -
402C THR* 4.4 16.9 - - - +
405C GLN* 5.0 6.5 - - + +
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Residues in contact with HIS 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C TYR* 4.2 28.9 - - + +
338C MET* 5.3 12.8 - - + -
361C CYS 3.0 17.6 + - - +
362C HIS* 3.9 3.8 - - - +
364C TYR* 1.3 75.8 - - - +
366C HIS* 1.3 58.2 + - - +
368C LEU* 3.1 5.0 + - - +
369C HIS* 2.8 33.1 + - + +
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Residues in contact with HIS 366 (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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362C HIS 2.9 19.4 + - - +
363C ILE* 4.0 4.5 - - - +
365C HIS* 1.3 76.8 - - - +
367C ALA* 1.3 56.7 + - - +
369C HIS* 5.1 0.4 - - - -
370C SER* 2.7 50.0 + - - +
371C ARG 4.3 0.4 - - - +
374C GLN* 5.5 4.0 - - + -
375C ALA* 4.7 15.3 - - + +
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Residues in contact with ALA 367 (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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363C ILE 2.9 21.4 + - - +
364C TYR 3.7 3.6 - - - +
366C HIS* 1.3 76.9 - - - +
368C LEU* 1.3 62.4 + - - +
370C SER 3.9 7.6 - - - +
371C ARG 5.3 0.2 - - - -
372C TRP* 5.6 1.8 - - - +
375C ALA* 4.2 18.1 - - + +
402C THR 5.4 1.1 - - - +
405C GLN* 4.4 19.7 - - + +
406C LEU* 4.4 17.0 - - + +
409C CYS* 3.6 23.0 - - + +
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Residues in contact with LEU 368 (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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301C TYR 5.5 5.2 - - - +
302C TYR 6.5 0.7 - - - -
303C LYS 5.7 3.8 - - - +
364C TYR 3.0 12.9 + - - +
365C HIS* 3.6 8.5 - - - +
367C ALA* 1.3 80.4 - - - +
369C HIS* 1.3 61.3 + - + +
370C SER 3.6 1.3 + - - +
405C GLN* 5.6 2.4 - - + +
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Residues in contact with HIS 369 (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 LYS 6.1 1.6 - - - +
304C PHE* 6.4 0.4 - - - -
305C ASP* 5.4 16.2 - - + +
365C HIS* 2.8 17.4 + - + +
366C HIS* 5.4 0.2 - - - -
368C LEU* 1.3 74.4 - - + +
370C SER* 1.3 60.0 + - - +
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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