Contacts of the helix formed by residues 375 - 386 (chain C) in PDB entry 1OJ7
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 THR 375 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365C MET 5.7 0.2 - - - -
366C THR* 3.3 21.3 - - - +
367C GLN* 3.5 22.2 - - - +
373C ASP* 3.2 9.4 + - - +
374C ILE* 1.3 72.2 - - - +
376C LEU* 1.3 67.2 + - - +
377C ASP* 3.9 14.1 + - - +
378C VAL* 3.0 15.1 + - - +
379C SER* 2.9 24.3 + - - -
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Residues in contact with LEU 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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357C LEU* 3.5 37.4 - - + +
360C LEU* 3.7 26.7 - - + -
361C GLU* 3.3 39.5 - - + +
365C MET 4.3 9.0 - - - +
366C THR* 4.4 12.5 + - + -
375C THR* 1.3 76.0 - - - +
377C ASP* 1.3 61.8 + - - +
379C SER* 3.4 3.3 + - - -
380C ARG* 2.9 27.8 + - - +
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Residues in contact with ASP 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C THR* 3.1 10.6 + - - +
376C LEU* 1.3 77.0 + - - +
378C VAL* 1.3 67.4 + - + +
380C ARG* 3.1 34.1 + - - +
381C ARG* 3.3 26.2 + - - +
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Residues in contact with VAL 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C GLU* 3.9 25.8 - - + +
296C LYS* 4.0 21.3 - - - +
373C ASP 3.5 21.8 - - - +
374C ILE* 3.9 15.5 - - + -
375C THR* 3.0 19.4 + - - +
377C ASP* 1.3 74.4 - - + +
379C SER* 1.3 66.0 + - - +
381C ARG* 3.1 10.3 + - - +
382C ILE* 3.0 25.6 + - + +
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Residues in contact with SER 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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269C LEU* 3.5 22.3 - - - +
357C LEU* 3.9 4.9 - - - -
360C LEU* 3.7 25.5 - - - +
365C MET 5.2 0.7 + - - -
368C LEU* 4.5 2.6 - - - +
374C ILE* 3.6 12.5 + - - +
375C THR 2.9 16.4 + - - -
376C LEU* 3.7 7.2 - - - +
378C VAL* 1.3 73.9 - - - +
380C ARG* 1.3 64.4 + - - +
382C ILE* 3.2 8.7 + - - +
383C TYR* 3.0 28.2 + - - -
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Residues in contact with ARG 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ILE* 4.4 8.0 - - + +
357C LEU* 3.6 26.6 - - + +
376C LEU 2.9 16.0 + - - +
377C ASP* 3.1 52.8 + - - +
378C VAL 3.2 0.2 - - - -
379C SER* 1.3 76.2 - - - +
381C ARG* 1.3 72.7 + - - +
383C TYR* 3.4 1.7 + - - +
384C GLU* 2.9 59.3 + - + +
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Residues in contact with ARG 381 (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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295C GLU* 2.9 43.5 + - - +
377C ASP* 3.3 14.3 + - - +
378C VAL* 3.1 11.2 + - - +
380C ARG* 1.3 92.6 - - - +
382C ILE* 1.3 58.0 + - - +
384C GLU* 3.9 8.7 - - - +
385C ALA* 3.0 30.7 + - - +
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Residues in contact with ILE 382 (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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269C LEU* 3.7 31.0 - - + -
288C VAL* 4.1 12.8 - - + -
291C ALA* 3.4 12.5 - - + +
292C LEU* 3.9 42.2 - - + +
295C GLU* 3.8 22.0 - - + -
296C LYS* 5.4 0.7 - - + -
374C ILE* 4.1 9.9 - - + -
378C VAL* 3.0 32.4 + - + +
379C SER 3.6 5.6 - - - +
381C ARG* 1.3 76.4 - - - +
383C TYR* 1.3 64.1 + - + +
385C ALA* 3.2 5.1 + - - -
386C ALA* 3.0 19.2 + - + +
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Residues in contact with TYR 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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269C LEU* 2.6 56.8 + - + +
272C GLU* 3.7 15.2 - - - +
273C LEU* 4.1 24.2 - - + -
288C VAL* 4.5 7.0 - - + -
343C LEU* 3.8 13.1 - - + +
353C ILE* 3.7 23.2 - - + +
356C LEU* 3.9 32.3 - - + -
357C LEU* 4.1 12.1 - - + -
360C LEU* 4.0 18.7 - - + +
379C SER 3.0 21.3 + - - +
380C ARG 3.9 2.0 - - - +
382C ILE* 1.3 77.1 - - + +
384C GLU* 1.3 62.7 + - - +
386C ALA* 3.1 20.6 + - + +
387C ARG 3.5 5.5 + - - -
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Residues in contact with GLU 384 (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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353C ILE* 3.9 21.2 - - + +
380C ARG* 2.9 47.4 + - + +
381C ARG* 3.9 9.4 - - - +
383C TYR* 1.3 75.0 - - - +
385C ALA* 1.3 61.6 + - - +
387C ARG* 3.3 32.3 + - - +
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Residues in contact with ALA 385 (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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291C ALA* 4.1 18.7 - - + +
294C ASN* 5.4 9.2 - - - +
295C GLU* 5.9 2.2 - - + +
331C ARG* 4.6 8.5 + - - -
342C HIS* 4.8 3.1 - - - -
381C ARG 3.0 19.8 + - - +
382C ILE* 3.2 6.0 + - - +
384C GLU* 1.3 77.0 - - - +
386C ALA* 1.3 59.0 + - - +
387C ARG 3.2 4.2 + - - +
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Residues in contact with ALA 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ILE* 3.6 28.5 - - + +
288C VAL* 5.1 2.0 - - + -
291C ALA* 4.0 14.1 - - + +
331C ARG* 5.4 1.3 - - - +
341C THR 5.1 1.3 - - - -
342C HIS* 3.4 10.5 - - - -
343C LEU* 2.9 27.1 + - + +
382C ILE* 3.0 13.0 + - + +
383C TYR* 3.1 17.8 + - + +
385C ALA* 1.3 76.9 - - - +
387C ARG* 1.3 60.3 + - - +
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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