Contacts of the helix formed by residues 426 - 434 (chain A) in PDB entry 3OJW
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 HIS 426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A LEU* 4.5 16.8 - - + +
377A ILE 3.5 16.3 + - - +
378A THR* 3.5 28.2 + - - +
379A ASN 3.9 5.6 - - - -
381A PRO* 3.9 2.0 - - - -
424A ARG 4.5 2.9 + - - -
425A ARG* 1.3 73.2 - - - +
427A ILE* 1.3 67.7 + - - +
428A LEU* 3.5 20.7 - - + +
429A ALA* 3.1 44.5 + - + +
430A ILE* 3.0 20.0 + - - +
484A ARG* 4.3 15.7 - - + -
485A VAL 5.4 2.0 - - - -
486A ASN* 3.8 27.8 + - - -
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Residues in contact with ILE 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ILE* 3.9 12.3 - - + -
377A ILE* 3.7 39.4 + - + +
379A ASN 4.6 1.2 + - - -
381A PRO* 3.7 19.2 - - + +
385A VAL* 5.2 1.8 - - + -
389A LEU* 4.2 18.8 - - + -
426A HIS* 1.3 76.0 - - - +
428A LEU* 1.3 65.6 + - - +
430A ILE* 3.4 5.9 + - + +
431A LEU* 3.1 40.4 + - + +
444A LEU* 4.0 32.5 - - + -
448A LEU* 4.4 16.6 - - + -
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Residues in contact with LEU 428 (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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330A LEU* 3.3 30.3 - - + +
333A GLN* 3.7 34.5 - - + +
334A ILE* 4.0 20.4 - - + -
337A ILE* 4.3 21.5 - - + -
377A ILE 5.8 0.2 - - - +
426A HIS* 3.3 14.1 - - + +
427A ILE* 1.3 80.6 - - + +
429A ALA* 1.3 64.0 + - - +
431A LEU* 3.0 8.5 + - - +
432A GLN* 2.9 48.8 + - + +
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Residues in contact with ALA 429 (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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425A ARG* 4.1 14.1 - - + -
426A HIS* 3.1 31.4 + - + +
428A LEU* 1.3 78.6 - - - +
430A ILE* 1.3 58.0 + - - +
432A GLN* 3.2 3.7 + - - -
433A ASP* 2.8 37.0 + - - +
484A ARG* 3.6 37.1 + - - +
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Residues in contact with ILE 430 (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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381A PRO* 4.2 13.0 - - + -
386A LEU* 4.2 28.0 - - + -
389A LEU* 4.7 7.4 - - + -
402A LEU* 4.5 2.0 - - + -
405A MET* 6.0 0.2 - - + -
419A TRP* 4.8 12.1 - - + -
420A VAL* 5.0 6.1 - - + -
425A ARG* 3.7 28.3 - - + -
426A HIS 3.0 32.0 + - - +
427A ILE* 3.7 12.1 - - + +
428A LEU 3.2 0.2 - - - -
429A ALA* 1.3 75.6 - - - +
431A LEU* 1.3 58.9 + - - +
433A ASP* 4.4 5.2 - - - -
434A TYR* 3.0 41.2 + - + +
437A LEU* 3.8 21.8 - - + -
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Residues in contact with LEU 431 (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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334A ILE* 4.5 10.3 - - + -
337A ILE* 3.9 38.6 - - + +
338A LEU* 4.4 15.5 - - + -
389A LEU* 5.2 1.6 - - + -
427A ILE* 3.1 38.0 + - + +
428A LEU* 3.0 12.8 + - - +
430A ILE* 1.3 76.6 - - - +
432A GLN* 1.3 58.8 + - - +
434A TYR 3.3 19.6 - - - +
435A PRO* 3.9 4.3 - - - +
437A LEU* 4.2 34.0 - - + +
439A PRO* 4.3 16.8 - - + -
444A LEU* 4.7 3.4 - - + -
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Residues in contact with GLN 432 (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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333A GLN* 4.2 12.5 - - - +
337A ILE* 3.6 20.8 - - + +
428A LEU* 2.9 39.1 + - + +
429A ALA* 3.8 5.7 - - - +
431A LEU* 1.3 75.0 - - - +
433A ASP* 1.3 65.6 + - - +
434A TYR 3.4 0.7 + - - -
435A PRO* 3.6 13.7 - - - +
484A ARG* 3.1 34.2 + - - +
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Residues in contact with ASP 433 (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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398A GLU* 4.4 1.7 - - - +
419A TRP* 3.5 21.6 - - + -
425A ARG* 2.7 38.9 + - - -
429A ALA 2.8 20.0 + - - +
430A ILE 3.9 3.1 - - - +
432A GLN* 1.3 78.8 - - - +
434A TYR* 1.3 66.1 + - + +
435A PRO* 3.4 7.8 - - - +
484A ARG* 2.8 25.4 + - - -
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Residues in contact with TYR 434 (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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398A GLU* 3.5 38.1 - - + +
401A HIS* 2.5 48.0 + + + -
402A LEU* 3.8 21.1 - - + -
405A MET* 3.2 14.3 - - + +
419A TRP* 3.5 32.6 - + - -
430A ILE* 3.0 36.2 + - + +
431A LEU 3.3 10.4 - - - +
433A ASP* 1.3 83.9 - - + +
435A PRO* 1.3 60.6 - - - +
436A SER 3.2 2.7 - - - -
437A LEU* 3.0 35.0 + - + +
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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