Contacts of the helix formed by residues 340 - 356 (chain A) in PDB entry 2OIV
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 LEU 340 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A TRP* 3.5 38.6 - - + +
339A LEU* 1.3 76.7 - - - +
341A ASP* 1.3 67.2 + - - +
342A GLY* 3.2 6.5 - - - +
343A HIS* 3.0 35.2 + - + +
344A LEU* 3.3 11.3 + - - +
410A TRP* 4.1 3.1 - - - -
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Residues in contact with ASP 341 (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* 1.3 72.5 - - - +
342A GLY* 1.3 58.0 + - - +
344A LEU* 3.1 4.9 + - - +
345A ARG* 2.9 28.7 + - - +
368A ASP* 6.0 0.7 - - - +
369A SER* 2.5 37.6 + - - +
370A GLN* 3.6 36.3 + - + +
373A THR* 5.1 0.9 + - - -
404A ASN* 3.4 26.8 + - - +
410A TRP* 3.4 7.6 - - - -
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Residues in contact with GLY 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU* 3.2 5.9 - - - +
341A ASP* 1.3 79.5 - - - +
343A HIS* 1.3 56.5 + - - +
345A ARG* 3.8 7.1 - - - +
346A ALA* 2.8 29.1 + - - +
370A GLN* 5.4 2.6 - - - +
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Residues in contact with HIS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A TRP 4.7 3.8 - - - -
339A LEU* 3.7 28.7 - - + +
340A LEU* 3.0 49.6 + - + +
342A GLY* 1.3 73.3 - - - +
344A LEU* 1.3 65.8 + - - +
346A ALA* 3.3 1.9 + - + -
347A TYR* 3.0 20.1 + - - +
475A LEU* 5.1 1.1 - - - -
512A LEU* 3.3 36.5 - - + +
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 3.9 20.4 - - + -
340A LEU 3.3 15.7 + - - +
341A ASP* 3.1 8.7 + - - +
343A HIS* 1.3 77.4 - - - +
345A ARG* 1.3 59.3 + - - +
347A TYR* 3.2 1.7 + - - +
348A THR* 2.8 36.8 + - + +
369A SER* 5.0 4.7 - - - +
402A PRO* 3.7 33.4 - - + -
410A TRP* 3.6 37.9 - - + +
471A GLY* 4.9 1.3 - - - +
474A VAL* 3.9 19.7 - - + -
475A LEU* 3.8 24.0 - - + -
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Residues in contact with ARG 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ASP 2.9 17.3 + - - +
342A GLY* 3.9 8.1 - - - +
344A LEU* 1.3 77.1 - - - +
346A ALA* 1.3 56.0 + - - +
348A THR* 3.5 8.9 + - - -
349A ASP* 2.8 70.5 + - - +
366A PHE 5.7 2.4 + - - -
368A ASP* 2.8 56.6 + - - +
369A SER* 5.6 1.9 + - - +
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A GLY 2.8 22.2 + - - +
343A HIS* 3.5 6.5 - - + +
345A ARG* 1.3 72.0 - - - +
347A TYR* 1.3 64.1 + - - +
349A ASP* 3.6 6.0 - - - +
350A ASP* 3.0 25.0 + - - +
353A ARG* 5.2 0.9 + - - -
511A ARG 6.1 0.2 - - - -
512A LEU* 4.0 17.0 - - + +
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Residues in contact with TYR 347 (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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343A HIS 3.0 16.1 + - - +
344A LEU 3.6 3.8 - - - +
346A ALA* 1.3 78.4 - - - +
348A THR* 1.3 61.7 + - + +
350A ASP* 3.2 7.0 + - - +
351A LEU* 2.8 33.0 + - + -
354A ARG* 4.1 8.4 + - - -
475A LEU* 3.6 49.5 + - + -
476A THR* 5.5 0.7 - - - -
478A ILE* 6.0 0.9 - - + -
479A GLU* 2.5 35.3 + - - +
507A LEU* 6.1 0.2 - - - +
508A ILE* 4.1 33.1 - - + +
511A ARG* 3.3 43.3 + - + -
512A LEU* 4.1 9.1 - - + +
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Residues in contact with THR 348 (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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344A LEU* 2.8 28.5 + - + +
345A ARG* 3.5 15.4 + - - -
347A TYR* 1.3 72.2 - - + +
349A ASP* 1.3 60.7 + - - +
351A LEU* 4.2 6.3 - - + -
352A ALA* 2.9 29.8 + - - +
366A PHE* 3.4 35.4 + - + +
367A ALA 4.9 6.9 + - - +
402A PRO* 5.7 2.5 - - + -
475A LEU* 4.0 17.5 - - + -
478A ILE* 4.1 24.7 - - + -
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Residues in contact with ASP 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ARG* 2.8 65.1 + - - +
346A ALA* 3.6 6.0 - - - +
348A THR* 1.3 71.0 + - - +
350A ASP* 1.3 64.9 + - - +
352A ALA* 3.3 6.4 + - - +
353A ARG* 3.1 47.7 + - - +
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Residues in contact with ASP 350 (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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346A ALA 3.0 18.6 + - - +
347A TYR* 3.6 6.1 - - - +
349A ASP* 1.3 75.9 - - - +
351A LEU* 1.3 62.9 + - - +
353A ARG* 3.2 22.9 + - - +
354A ARG* 2.9 52.4 + - - +
511A ARG* 4.0 26.8 - - - +
514A GLN* 5.1 11.9 - - - +
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A TYR* 2.8 23.7 + - + +
348A THR* 3.7 6.7 - - - +
350A ASP* 1.3 78.3 + - - +
352A ALA* 1.3 64.1 + - - +
354A ARG* 3.0 24.9 + - - +
355A LEU* 2.9 45.4 + - + +
366A PHE* 3.4 29.2 - - + -
478A ILE* 3.8 20.4 - - + -
479A GLU* 3.4 41.7 - - - +
482A ALA* 4.3 3.4 - - + -
483A HIS* 4.2 3.8 - - + +
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Residues in contact with ALA 352 (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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348A THR 2.9 18.0 + - - +
349A ASP* 3.7 7.0 - - - +
350A ASP 3.3 0.2 - - - -
351A LEU* 1.3 75.7 - - - +
353A ARG* 1.3 62.5 + - - +
355A LEU* 3.2 5.8 + - - +
356A ARG* 3.1 25.5 + - - +
366A PHE* 3.9 20.6 - - + -
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Residues in contact with ARG 353 (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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346A ALA 5.2 0.8 + - - -
349A ASP* 3.1 46.3 + - - +
350A ASP* 3.2 23.5 + - - +
352A ALA* 1.3 75.7 - - - +
354A ARG* 1.3 62.9 + - + +
355A LEU 3.3 0.7 + - - -
356A ARG* 3.4 53.0 + - - +
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Residues in contact with ARG 354 (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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347A TYR* 3.9 5.1 + - - -
350A ASP* 2.9 38.7 + - - +
351A LEU* 3.0 33.1 + - - +
353A ARG* 1.3 76.2 - - + +
355A LEU* 1.3 64.4 + - + +
356A ARG 3.7 1.4 + - - +
358A GLU* 4.8 5.2 - - - +
479A GLU* 2.9 41.2 + - - -
483A HIS* 4.6 5.3 + - - -
511A ARG* 3.5 38.2 - - - +
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 2.9 25.8 + - + +
352A ALA* 3.2 4.2 + - - +
354A ARG* 1.3 81.9 - - + +
356A ARG* 1.3 65.2 + - - +
357A GLY 3.3 0.3 + - - -
358A GLU* 3.0 25.2 + - + +
361A ALA* 3.3 12.6 - - + +
364A LEU* 3.9 27.6 - - + -
366A PHE* 4.0 14.1 - - + -
482A ALA* 3.9 16.4 - - + -
483A HIS* 3.8 29.4 - - + +
486A LEU* 3.6 26.7 - - + -
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Residues in contact with ARG 356 (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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352A ALA 3.1 17.9 + - - +
353A ARG* 3.4 43.6 + - - +
354A ARG 3.4 1.6 - - - +
355A LEU* 1.3 77.6 - - - +
357A GLY* 1.3 61.5 + - - +
358A GLU* 3.3 5.7 + - - +
361A ALA* 5.0 1.8 - - - -
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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