Contacts of the helix formed by residues 501 - 506 (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 501 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A TRP* 3.7 27.1 - - + -
493A MET* 5.2 0.2 - - + -
497A GLN 4.7 1.6 - - - +
498A TRP* 2.9 27.9 + - + +
499A ASN 3.9 2.0 - - - +
500A THR* 1.3 85.0 - - - +
502A ASP* 1.3 60.0 + - - +
503A TYR 4.3 4.0 - - - +
504A PHE* 2.8 25.3 + - + +
505A GLU 3.2 8.7 + - - -
510A HIS* 4.9 5.2 - - + +
515A VAL* 4.4 13.0 - - + -
518A GLN* 4.4 15.7 - - - +
519A LEU* 4.3 18.4 - - + -
522A ARG* 4.1 13.2 - - - +
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Residues in contact with ASP 502 (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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499A ASN 4.2 5.4 - - - +
500A THR* 3.8 2.1 + - - +
501A VAL* 1.3 74.3 - - - +
503A TYR* 1.3 62.0 + - + +
505A GLU* 3.1 25.0 + - - +
506A THR* 2.9 35.8 + - + +
518A GLN* 5.7 1.0 - - - +
684A PRO* 5.2 8.1 - - - +
686A LYS* 3.2 41.6 + - - +
695A ASP* 5.5 8.8 + - - +
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Residues in contact with TYR 503 (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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476A VAL* 4.1 0.5 - - - +
478A TRP* 3.7 8.3 - - + -
501A VAL* 3.4 2.4 - - - +
502A ASP* 1.3 80.0 - - + +
504A PHE* 1.3 57.4 + - - +
506A THR* 3.9 5.8 - - - -
507A ASP* 3.1 5.4 + - - -
508A LYS* 2.8 70.4 + - + +
509A ALA 3.1 27.8 - - - -
510A HIS* 3.5 28.3 - + + -
664A ASP* 4.7 9.1 - - + +
695A ASP 5.6 1.1 - - - -
698A ILE* 3.6 22.9 - - + +
699A LYS* 3.2 40.5 - - - +
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Residues in contact with PHE 504 (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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469A VAL* 3.6 23.8 - - + -
470A PHE* 3.7 24.9 - + - -
473A LYS* 2.9 40.7 + - + +
476A VAL* 3.9 22.2 - - + -
478A TRP* 3.8 14.0 - - + -
479A ALA* 4.2 7.9 - - + -
495A THR* 4.1 10.8 - - + -
498A TRP* 3.2 54.1 - + + +
499A ASN* 3.4 23.8 - - - -
501A VAL* 2.8 6.5 + - + +
503A TYR* 1.3 77.2 - - - +
505A GLU* 1.3 65.9 + - - +
507A ASP* 3.1 7.6 + - - -
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Residues in contact with GLU 505 (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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473A LYS* 3.2 16.2 + - - +
499A ASN* 3.8 33.5 - - - +
501A VAL 3.2 2.3 + - - +
502A ASP* 3.1 27.3 + - - +
504A PHE* 1.3 81.9 - - - +
506A THR* 1.3 66.2 + - + +
507A ASP* 4.8 0.2 - - - +
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Residues in contact with THR 506 (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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502A ASP* 2.9 23.5 + - + +
503A TYR* 3.9 4.9 - - - -
505A GLU* 1.3 86.0 - - + +
507A ASP* 1.3 71.9 + - - +
508A LYS* 3.5 36.8 + - - +
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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