Contacts of the helix formed by residues 372 - 382 (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 TRP 372 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C ALA* 5.6 2.7 - - - +
370C SER 3.6 2.5 + - - -
371C ARG* 1.3 70.6 - - - +
373C TYR* 1.3 66.4 + - - +
375C ALA* 3.0 11.1 + - - +
376C ARG* 3.0 21.5 + - - +
406C LEU* 5.8 2.2 - - + +
409C CYS* 4.8 20.0 - - + +
410C ALA* 4.9 15.5 - - + +
413C GLN* 5.7 5.6 - - + -
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Residues in contact with TYR 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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371C ARG* 3.4 5.1 - - + +
372C TRP* 1.3 77.4 - - - +
374C GLN* 1.3 63.0 + - - +
376C ARG* 3.2 8.9 + - - +
377C ASP* 2.9 25.4 + - - +
288E TYR* 6.0 6.3 - - + -
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Residues in contact with GLN 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C HIS* 5.5 5.2 - - + -
370C SER* 5.5 6.1 - - - -
371C ARG* 3.5 17.7 + - + +
372C TRP 3.2 0.4 - - - -
373C TYR* 1.3 78.0 - - - +
375C ALA* 1.3 56.3 + - - +
377C ASP* 3.2 8.6 + - - +
378C LEU* 2.9 28.8 + - - +
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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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363C ILE* 4.4 12.9 - - + +
366C HIS* 4.7 8.2 - - + +
367C ALA* 4.2 34.3 - - + +
371C ARG 3.8 2.2 + - - +
372C TRP* 3.0 12.6 + - - +
374C GLN* 1.3 79.7 - - - +
376C ARG* 1.3 63.1 + - - +
378C LEU* 3.2 8.5 + - - +
379C MET* 2.9 24.5 + - - +
406C LEU* 5.3 9.4 - - + -
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Residues in contact with ARG 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C TRP 3.0 12.3 + - - +
373C TYR* 3.5 11.2 - - - +
375C ALA* 1.3 76.7 - - - +
377C ASP* 1.3 62.4 + - - +
379C MET* 3.2 8.9 + - - +
380C LEU* 3.0 25.4 + - - +
406C LEU* 6.1 1.3 - - - +
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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
----------------------------------------------------------
373C TYR 2.9 13.4 + - - +
374C GLN* 3.4 11.4 - - - +
376C ARG* 1.3 75.9 - - - +
378C LEU* 1.3 63.7 + - - +
380C LEU* 3.4 4.2 + - - +
381C MET* 2.9 29.2 + - + +
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Residues in contact with LEU 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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362C HIS* 6.0 4.7 - - + -
363C ILE* 5.3 11.2 - - + +
374C GLN 2.9 13.5 + - - +
375C ALA* 3.2 12.5 + - - +
377C ASP* 1.3 76.1 - - - +
379C MET* 1.3 53.9 + - - +
381C MET* 3.8 3.5 - - - +
382C SER* 2.7 40.3 + - - -
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Residues in contact with MET 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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363C ILE* 5.7 6.9 - - + +
375C ALA 2.9 13.0 + - - +
376C ARG* 3.2 10.5 + - - +
378C LEU* 1.3 78.4 - - - +
380C LEU* 1.3 61.3 + - - +
381C MET 3.5 0.2 + - - -
382C SER* 3.6 10.5 + - - -
383C HIS* 3.7 8.7 + - - -
384C LEU 4.9 2.4 + - - -
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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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376C ARG 3.0 17.3 + - - +
377C ASP* 4.2 3.6 - - - +
379C MET* 1.3 76.0 - - - +
381C MET* 1.3 60.9 + - - +
383C HIS* 4.0 8.7 + - - +
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Residues in contact with MET 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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377C ASP 2.9 19.8 + - - +
378C LEU* 3.9 4.3 - - - +
380C LEU* 1.3 76.0 - - - +
382C SER* 1.3 63.9 + - - +
383C HIS* 3.1 8.9 + - - +
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Residues in contact with SER 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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359C ILE* 4.8 19.3 - - - -
378C LEU* 2.7 23.3 + - - -
379C MET* 3.8 8.1 - - - -
380C LEU 3.5 0.2 - - - -
381C MET* 1.3 73.2 - - - +
383C HIS* 1.3 69.3 + - - +
384C LEU* 4.8 6.6 - - - +
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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