Contacts of the helix formed by residues 370 - 382 (chain C) in PDB entry 1HJX
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 PHE 370 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C ALA 3.8 17.0 - - - -
46C LEU* 4.0 15.0 - - + -
47C ASP* 3.8 24.2 - - + -
50C LEU* 3.5 29.6 - - + -
354C LEU* 3.6 33.0 - - + -
357C ASP* 3.1 23.1 - - + +
358C ASP 2.8 14.7 + - - -
359C PHE* 3.2 38.8 - - + -
369C ARG* 1.3 89.3 - - + +
371C PRO* 1.3 69.2 - - - +
373C THR* 4.2 0.7 - - - -
374C ASN* 2.9 22.2 + - - +
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Residues in contact with PRO 371 (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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296C TYR* 4.3 15.0 - - + -
331C GLN* 4.0 24.6 - - - +
357C ASP* 3.0 16.8 - - - +
358C ASP* 3.5 25.6 - - + +
364C CYS* 4.6 8.7 - - + -
368C LEU* 3.7 32.9 - - + +
369C ARG 3.4 2.0 - - - +
370C PHE* 1.3 88.7 - - - +
372C LEU* 1.3 57.2 + - - +
374C ASN* 3.8 2.2 - - + +
375C ALA* 3.0 27.5 + - - +
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Residues in contact with LEU 372 (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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259C PRO 4.6 2.0 - - - +
260C THR* 3.8 36.3 - - + +
296C TYR* 3.5 43.5 - - + -
329C ASP 3.6 13.9 - - - +
330C ASP* 3.5 36.1 - - - +
331C GLN* 3.6 9.6 - - + +
334C VAL* 3.9 9.9 - - + +
357C ASP* 3.2 10.0 + - - +
371C PRO* 1.3 78.4 - - - +
373C THR* 1.3 59.9 + - - +
375C ALA* 3.0 6.1 + - - +
376C ILE* 2.9 33.7 + - + +
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Residues in contact with THR 373 (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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24C LEU* 4.2 7.7 - - + +
26C CYS* 4.0 23.3 - - - -
50C LEU* 3.6 35.7 - - + -
51C CYS* 4.1 0.9 - - - -
260C THR* 4.4 0.3 - - - +
351C VAL* 3.9 21.5 - - + +
354C LEU* 4.0 9.2 - - + +
357C ASP* 2.7 21.2 + - - +
370C PHE* 4.2 0.2 - - - -
372C LEU* 1.3 75.7 - - - +
374C ASN* 1.3 57.2 - - - +
376C ILE* 3.2 10.5 + - - +
377C LYS* 2.9 26.7 + - - +
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Residues in contact with ASN 374 (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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47C ASP* 5.1 5.5 + - - +
50C LEU* 3.2 21.0 - - - +
368C LEU* 5.6 6.5 - - + +
369C ARG* 2.8 28.5 + - - +
370C PHE* 2.9 21.3 + - - +
371C PRO* 3.9 4.0 - - + +
373C THR* 1.3 73.8 - - - +
375C ALA* 1.3 61.2 + - - +
377C LYS* 3.7 11.3 + - - +
378C ASP* 2.9 43.6 + - - +
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Residues in contact with ALA 375 (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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331C GLN* 3.9 18.2 - - + -
334C VAL* 3.6 19.5 - - + -
335C LYS* 2.9 38.6 + - - +
371C PRO 3.0 15.6 + - - +
372C LEU 3.0 8.9 + - - +
374C ASN* 1.3 78.3 - - - +
376C ILE* 1.3 56.4 + - - +
378C ASP* 3.4 2.4 + - - -
379C ALA* 3.0 16.8 + - - +
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Residues in contact with ILE 376 (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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24C LEU* 3.8 22.9 - - + -
258C ILE* 4.0 28.9 - - + -
260C THR* 5.6 1.1 - - + -
334C VAL* 3.8 19.7 - - + -
338C VAL* 3.7 21.8 - - + -
349C ALA* 3.9 7.6 - - + -
351C VAL* 3.7 28.3 - - + -
372C LEU* 2.9 21.2 + - + +
373C THR* 3.5 9.9 - - - +
375C ALA* 1.3 75.1 - - - +
377C LYS* 1.3 61.1 + - - +
379C ALA* 3.1 2.6 + - - +
380C LEU* 2.9 36.3 + - + +
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Residues in contact with LYS 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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24C LEU* 3.7 17.0 - - + +
47C ASP* 5.5 1.0 + - - -
49C PHE* 2.6 35.7 + - - +
50C LEU* 3.5 26.3 - - + +
373C THR 2.9 16.5 + - - +
374C ASN* 3.7 13.1 + - - +
376C ILE* 1.3 76.5 - - - +
378C ASP* 1.3 68.5 + - - +
380C LEU* 3.3 6.2 + - - +
381C ALA* 3.1 24.8 + - + +
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Residues in contact with ASP 378 (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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335C LYS* 3.7 16.2 + - - +
374C ASN* 2.9 29.3 + - - +
375C ALA* 4.6 1.7 - - - -
377C LYS* 1.3 85.0 - - - +
379C ALA* 1.3 58.5 + - - +
381C ALA* 3.5 5.0 + - - +
382C ALA* 3.0 30.1 + - - +
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Residues in contact with ALA 379 (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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335C LYS* 3.8 22.8 - - + +
338C VAL* 3.4 30.7 - - + -
342C LYS* 3.1 19.8 + - - +
375C ALA 3.0 17.2 + - - +
376C ILE 3.1 2.0 + - - +
378C ASP* 1.3 77.6 - - - +
380C LEU* 1.3 62.6 + - - +
382C ALA* 3.3 12.8 + - - +
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Residues in contact with LEU 380 (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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22C TYR* 3.4 49.4 - - + +
23C LYS 4.0 18.6 - - - +
24C LEU* 4.2 18.8 - - + -
338C VAL* 3.6 21.3 - - + -
341C LEU* 4.0 19.1 - - + -
342C LYS* 3.3 14.0 + - + +
348C GLY* 4.8 1.3 - - - -
349C ALA* 4.4 3.1 - - + -
376C ILE* 2.9 36.7 + - + +
377C LYS* 3.7 5.4 - - - +
379C ALA* 1.3 76.4 - - - +
381C ALA* 1.3 59.1 + - - +
383C THR 3.9 0.9 + - - -
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Residues in contact with ALA 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LYS* 3.1 17.6 + - + +
378C ASP* 4.0 4.9 - - - +
380C LEU* 1.3 74.5 - - - +
382C ALA* 1.3 59.8 + - - +
383C THR 3.1 6.6 + - - -
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Residues in contact with ALA 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LYS* 3.7 0.9 - - - +
378C ASP 3.0 18.6 + - - +
379C ALA* 3.3 11.3 + - - +
381C ALA* 1.3 76.0 - - - +
383C THR 1.2 47.0 + - - +
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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
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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