Contacts of the helix formed by residues 369 - 379 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A ASP* 3.4 25.2 + - - +
332A GLN* 5.5 0.4 + - - -
368A GLY* 1.3 76.4 - - - +
370A ARG* 1.3 60.0 + - - +
371A ALA* 3.1 15.5 - - - +
372A GLN* 2.8 39.6 + - - +
373A ILE* 2.9 24.7 + - - +
692E ARG* 3.5 11.7 - - - +
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Residues in contact with ARG 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A ASN* 1.3 76.1 - - - +
371A ALA* 1.3 53.2 + - - +
373A ILE* 3.4 7.5 + - - -
374A GLN* 2.8 30.1 + - - +
410A GLY 3.3 22.6 + - - +
411A GLY 3.8 12.9 + - - -
412A SER* 3.9 32.9 - - - +
415A GLN* 3.1 18.5 + - - +
453A LEU* 5.6 4.2 - - - +
456A GLN* 5.8 3.2 - - - +
692E ARG* 3.6 12.6 - - - +
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A GLN* 5.8 1.8 - - - +
369A ASN* 3.1 17.9 - - - +
370A ARG* 1.3 76.9 - - - +
372A GLN* 1.3 60.6 + - + +
374A GLN* 3.1 9.7 + - - +
375A THR* 3.0 31.3 + - - +
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Residues in contact with GLN 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ASP* 2.8 35.4 + - - +
331A THR* 3.8 11.9 + - - -
332A GLN* 3.0 34.9 + - - +
335A LEU* 3.5 15.7 - - + -
365A ILE* 4.3 11.2 - - + +
368A GLY* 3.4 9.4 - - - -
369A ASN* 2.8 44.5 + - - +
371A ALA* 1.3 72.5 - - + +
373A ILE* 1.3 65.4 + - - +
375A THR* 2.8 25.5 + - + -
376A VAL* 3.3 11.9 + - - +
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A THR* 3.6 32.3 - - + +
368A GLY 4.0 5.2 - - - +
369A ASN 2.9 18.2 + - - +
370A ARG* 3.7 6.5 - - - +
372A GLN* 1.3 75.2 - - - +
374A GLN* 1.3 62.1 + - - +
376A VAL* 3.2 9.9 + - - +
377A ILE* 3.1 28.2 + - + +
382A PHE* 4.9 4.5 - - + -
407A ALA* 3.6 26.5 - - + +
410A GLY* 3.5 34.8 - - - -
411A GLY* 3.6 6.3 - - - +
415A GLN* 4.0 18.6 - - + +
419A LEU* 6.1 1.3 - - + -
692E ARG* 4.3 0.2 - - - +
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A ARG 2.8 17.3 + - - +
371A ALA* 3.1 12.1 + - - +
373A ILE* 1.3 73.8 - - - +
375A THR* 1.3 57.1 + - + +
377A ILE* 3.1 19.9 + - - +
378A ASP* 2.8 57.4 + - - +
415A GLN* 2.7 38.6 + - - +
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Residues in contact with THR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A GLN* 5.6 5.4 - - - +
335A LEU* 3.7 17.1 - - + +
340A LEU* 3.4 19.9 - - - +
371A ALA 3.0 17.8 + - - +
372A GLN* 2.8 20.6 + - + +
374A GLN* 1.3 75.5 - - + +
376A VAL* 1.3 63.3 + - - +
378A ASP* 3.2 7.8 + - - +
379A ALA* 3.0 24.3 + - - +
465B ILE* 6.4 1.6 - - + -
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Residues in contact with VAL 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A LEU* 4.0 15.3 - - + -
362A ILE* 4.2 11.2 - - + -
365A ILE* 3.8 23.8 - - + -
366A THR* 4.1 13.0 - - + -
372A GLN 3.4 14.6 - - - +
373A ILE 3.2 6.3 + - - +
375A THR* 1.3 78.0 + - - +
377A ILE* 1.3 63.1 + - - +
379A ALA 3.4 7.3 + - - -
381A ILE* 3.4 48.2 + - + +
382A PHE* 3.6 21.5 - - + -
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Residues in contact with ILE 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A ILE* 3.1 15.7 + - + +
374A GLN* 3.1 26.9 + - - +
376A VAL* 1.3 76.3 - - - +
378A ASP* 1.3 62.3 + - - +
380A ASN* 3.1 20.6 + - - -
382A PHE* 3.7 27.8 - - + -
415A GLN* 3.6 43.3 - - + +
418A TYR* 3.6 43.4 + - + -
419A LEU* 5.0 1.8 - - + -
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Residues in contact with ASP 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A GLN* 2.8 48.1 + - - +
375A THR* 3.8 6.5 - - - +
377A ILE* 1.3 73.2 - - - +
379A ALA* 1.3 58.0 + - - +
380A ASN* 3.1 7.9 + - - +
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A LEU* 3.9 23.6 - - + +
341A GLN* 5.2 2.7 - - + +
344A LEU* 3.4 18.1 - - + +
375A THR 3.0 15.3 + - - +
377A ILE 3.3 0.4 - - - -
378A ASP* 1.3 74.3 - - - +
380A ASN* 1.3 68.4 + - - +
381A ILE* 3.7 23.1 - - + -
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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