Contacts of the helix formed by residues 476 - 488 (chain A) in PDB entry 2HWK
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 VAL 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A PHE* 3.9 19.3 - - + -
473A LYS* 3.2 33.0 - - + -
474A ALA 3.6 1.2 - - - -
475A ASN* 1.3 80.6 - - - +
477A CYS* 1.3 52.7 + - - +
478A TRP* 2.9 16.6 - - + +
479A ALA* 2.6 34.7 + - + -
480A LYS* 3.1 17.6 + - - +
503A TYR 4.1 16.8 - - - +
504A PHE* 3.9 21.1 - - + +
507A ASP* 3.8 14.1 - - - +
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Residues in contact with CYS 477 (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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474A ALA 5.2 2.8 + - - +
475A ASN* 3.4 11.0 - - - -
476A VAL* 1.3 76.3 - - - +
478A TRP* 1.3 61.6 + - - +
480A LYS* 3.2 22.0 + - + +
481A ALA* 2.9 24.3 + - - +
509A ALA* 6.6 0.7 - - - -
545A ASN 5.3 0.2 - - - -
546A HIS* 3.2 38.4 - - + +
547A TRP* 3.5 27.7 - - - +
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Residues in contact with TRP 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ASN 3.0 19.7 + - - -
476A VAL* 3.5 11.3 - - + +
477A CYS* 1.3 82.8 - - - +
479A ALA* 1.3 88.9 + - + +
481A ALA* 3.7 0.3 + - - +
482A LEU* 3.3 27.7 + - - +
498A TRP* 4.1 5.4 - + - -
501A VAL* 3.7 22.9 - - + -
503A TYR* 3.7 30.5 - - + -
504A PHE* 3.8 15.9 - - + -
508A LYS 2.9 18.4 + - - -
509A ALA* 4.2 0.4 - - - -
510A HIS* 3.4 39.4 - - + +
512A ALA* 3.8 12.3 - - - +
515A VAL* 3.6 40.6 - - + -
547A TRP* 3.9 20.4 - - + -
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Residues in contact with ALA 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A PHE* 3.8 17.5 - - + -
476A VAL* 2.6 23.5 + - + +
478A TRP* 1.3 90.0 - - + +
480A LYS* 1.3 61.1 + - - +
482A LEU 3.4 1.0 + - - -
483A VAL* 3.3 17.8 + - - +
498A TRP* 3.4 43.8 - - + -
504A PHE* 4.2 2.7 - - + -
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Residues in contact with LYS 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A PHE* 3.9 49.3 + - + -
473A LYS 5.0 8.1 + - - -
474A ALA 6.3 0.2 - - - -
476A VAL* 3.1 18.1 + - - +
477A CYS* 3.2 21.2 + - + +
479A ALA* 1.3 76.9 - - - +
481A ALA* 1.3 65.0 + - - +
482A LEU 3.2 0.3 + - - -
483A VAL* 3.3 13.8 + - - +
484A PRO* 3.6 8.5 - - - +
549A ASN* 4.5 1.7 - - - +
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Residues in contact with ALA 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A CYS 2.9 16.1 + - - +
478A TRP 3.9 5.8 - - - +
479A ALA 3.3 0.2 - - - -
480A LYS* 1.3 77.2 - - - +
482A LEU* 1.3 57.9 + - - +
484A PRO* 3.2 12.3 - - - +
485A VAL* 4.1 1.0 - - - +
512A ALA* 4.9 0.4 - - + -
540A LEU* 3.6 22.8 - - + +
547A TRP* 4.0 17.7 - - + -
548A ASP* 4.1 13.5 - - - +
549A ASN* 2.9 32.4 + - - +
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Residues in contact with LEU 482 (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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478A TRP 3.3 16.8 + - - +
479A ALA 3.4 6.7 + - - +
480A LYS 3.1 0.8 - - - -
481A ALA* 1.3 80.4 - - - +
483A VAL* 1.3 66.5 + - - +
485A VAL* 2.8 17.6 + - + +
486A LEU* 2.9 19.0 + - + +
498A TRP* 4.1 15.7 - - + -
512A ALA* 3.5 25.4 - - + +
515A VAL* 3.5 33.2 - - + -
516A LEU* 3.9 22.4 - - + +
519A LEU* 4.5 5.2 - - + -
540A LEU* 3.9 24.7 - - + -
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Residues in contact with VAL 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A PHE* 3.7 26.5 - - + -
479A ALA 3.3 14.6 + - - +
480A LYS 3.3 7.2 + - - +
482A LEU* 1.3 75.9 - - - +
484A PRO* 1.4 65.0 - - + +
486A LEU* 3.4 9.2 + - - +
487A LYS* 3.1 49.8 + - - +
491A ILE 4.4 1.4 - - - +
492A ASP* 5.4 4.0 - - - +
493A MET* 6.2 0.4 - - + -
498A TRP* 4.4 10.1 - - + +
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Residues in contact with PRO 484 (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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480A LYS 3.6 6.7 - - - +
481A ALA 3.2 14.1 - - - +
483A VAL* 1.4 93.9 - - + +
485A VAL* 1.3 65.3 + - - +
487A LYS* 3.6 15.3 + - + +
488A THR* 3.5 17.5 + - - +
538A VAL* 3.8 25.1 - - + +
549A ASN* 3.3 23.3 - - - +
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Residues in contact with VAL 485 (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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481A ALA 4.1 1.1 - - - +
482A LEU* 2.8 18.1 + - + +
484A PRO* 1.3 70.3 - - - +
486A LEU* 1.3 61.9 + - - +
488A THR* 2.6 29.7 + - - -
516A LEU* 4.0 18.4 - - + -
533A PHE* 3.8 23.5 - - + -
538A VAL* 4.0 25.4 - - + -
540A LEU* 3.9 34.3 - - + -
556A TYR* 4.1 19.1 - - + -
557A GLY 4.6 2.9 - - - +
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Residues in contact with LEU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 2.9 21.6 + - + +
483A VAL* 3.8 7.4 - - - +
485A VAL* 1.3 73.7 - - + +
487A LYS* 1.3 65.5 + - - +
489A ALA* 3.0 9.9 + - - +
491A ILE* 2.9 53.4 + - + +
493A MET* 3.8 27.6 - - + -
498A TRP* 3.9 23.6 - - + -
516A LEU* 4.1 23.1 - - + -
519A LEU* 4.0 23.3 - - + -
523A PHE* 5.8 0.7 - - + -
533A PHE* 4.7 9.2 - - + -
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Residues in contact with LYS 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A VAL* 3.1 35.9 + - - +
484A PRO* 3.7 13.5 - - + +
485A VAL 3.1 0.6 - - - -
486A LEU* 1.3 78.4 - - - +
488A THR* 1.3 55.6 + - - +
490A GLY* 2.9 19.7 + - - -
491A ILE 3.4 14.1 - - - +
492A ASP* 3.7 24.8 + - - +
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Residues in contact with THR 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A PRO 3.5 16.4 - - - +
485A VAL 2.6 16.6 + - - +
487A LYS* 1.3 77.2 - - - +
489A ALA* 1.3 56.0 + - - +
490A GLY 3.2 1.9 + - - -
533A PHE* 4.0 1.4 - - - -
537A THR* 4.0 24.5 - - + +
538A VAL* 4.5 5.4 - - + -
557A GLY* 3.7 1.5 - - - -
558A LEU* 2.9 47.3 + - - +
577A VAL 4.4 0.9 - - - +
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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