Contacts of the helix formed by residues 369 - 379 (chain B) in PDB entry 2JDQ
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 ASN 369 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328B ASP* 3.6 27.2 + - - +
332B GLN* 5.6 0.4 + - - -
368B GLY* 1.3 75.8 - - - +
370B ARG* 1.3 59.0 + - - +
371B ALA* 3.1 12.2 + - - +
372B GLN* 3.0 43.7 + - - +
373B ILE* 2.9 26.5 + - - +
692D ARG* 3.5 11.7 - - - +
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Residues in contact with ARG 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B ASN* 1.3 73.5 - - - +
371B ALA* 1.3 61.3 + - - +
373B ILE* 3.5 6.8 + - - +
374B GLN* 3.0 23.2 + - - +
410B GLY 3.1 23.2 + - - +
411B GLY 3.9 11.1 + - - -
412B SER* 3.4 26.1 - - - +
415B GLN* 3.2 27.1 + - - +
453B LEU* 6.3 0.4 - - - +
692D ARG* 3.5 11.6 - - - +
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B ASN* 3.1 10.8 + - - +
370B ARG* 1.3 78.7 - - - +
372B GLN* 1.3 59.6 + - + +
374B GLN* 3.4 8.9 + - - +
375B THR* 3.0 28.9 + - - -
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Residues in contact with GLN 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ASP* 2.8 35.4 + - - +
331B THR* 3.3 19.8 + - - -
332B GLN* 3.0 31.1 + - - +
335B LEU* 3.7 12.3 - - + +
365B ILE* 4.3 13.3 - - + +
368B GLY* 3.5 8.7 - - - -
369B ASN* 3.0 45.9 + - - +
371B ALA* 1.3 77.0 - - + +
373B ILE* 1.3 65.0 + - - +
375B THR* 3.3 16.4 + - - +
376B VAL* 3.4 17.8 + - - +
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Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B THR* 3.7 29.2 - - - +
368B GLY 4.2 2.2 - - - +
369B ASN 2.9 19.5 + - - +
370B ARG* 3.8 7.0 - - - +
372B GLN* 1.3 74.8 - - - +
374B GLN* 1.3 62.4 + - - +
376B VAL* 3.2 11.3 + - - +
377B ILE* 3.1 29.0 + - + +
382B PHE* 4.8 3.4 - - + -
407B ALA* 3.7 27.1 - - + +
410B GLY* 3.3 40.8 - - - +
411B GLY* 3.5 5.4 - - - +
415B GLN* 4.0 18.2 - - + +
419B LEU* 5.9 1.3 - - + -
692D ARG* 4.1 1.8 - - - +
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Residues in contact with GLN 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B ARG 3.0 18.9 + - - +
371B ALA* 3.5 9.2 - - - +
372B GLN 3.2 0.2 - - - -
373B ILE* 1.3 74.3 - - - +
375B THR* 1.3 58.7 + - - +
377B ILE* 3.4 24.6 - - - +
378B ASP* 2.8 65.3 + - - +
415B GLN* 2.9 33.3 + - - +
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Residues in contact with THR 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B GLN* 5.8 1.2 + - - -
335B LEU* 4.6 17.0 - - + +
340B LEU* 3.1 29.5 - - + +
371B ALA 3.0 16.1 + - - -
372B GLN* 3.3 12.3 + - - -
374B GLN* 1.3 75.7 - - - +
376B VAL* 1.3 56.2 + - - +
378B ASP* 3.8 7.8 - - + +
379B ALA* 3.1 28.1 + - + +
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Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B LEU* 3.9 17.0 - - + -
362B ILE* 4.1 10.8 - - + -
365B ILE* 3.8 23.3 - - + -
366B THR* 4.1 12.6 - - + -
372B GLN 3.4 14.8 - - - +
373B ILE* 3.2 7.8 + - - +
375B THR* 1.3 74.3 - - - +
377B ILE* 1.3 66.9 + - - +
379B ALA* 3.3 8.7 + - - +
381B ILE* 3.4 44.2 + - + +
382B PHE* 3.5 23.6 - - + -
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Residues in contact with ILE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B ILE* 3.1 22.1 + - + +
374B GLN* 3.4 29.2 - - - +
376B VAL* 1.3 75.0 - - - +
378B ASP* 1.3 60.1 + - - +
380B ASN* 3.0 25.1 + - - +
382B PHE* 3.6 24.6 + - + -
415B GLN* 3.7 42.4 - - + +
418B TYR* 3.9 39.5 + - + -
419B LEU* 5.7 2.2 - - + -
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Residues in contact with ASP 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B GLN* 2.8 52.0 + - - +
375B THR* 4.0 8.5 - - + +
377B ILE* 1.3 73.8 - - - +
379B ALA* 1.3 58.0 + - - +
380B ASN* 3.2 13.4 + - - +
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B LEU* 3.9 28.0 - - + -
341B GLN* 5.1 4.9 - - + +
344B LEU* 3.6 16.6 - - - +
375B THR* 3.1 18.6 + - + +
376B VAL 3.7 5.8 - - - +
377B ILE 3.1 1.0 + - - -
378B ASP* 1.3 76.0 - - - +
380B ASN* 1.3 72.6 + - - +
381B ILE* 3.3 11.0 + - + +
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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