Contacts of the helix formed by residues 474 - 480 (chain A) in PDB entry 1B3U
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 LYS 474 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A VAL* 4.1 6.6 + - + +
473A GLY* 1.3 71.4 - - - -
475A GLU* 1.3 63.9 + - + +
477A ALA* 3.2 10.0 + - - +
478A HIS* 2.9 28.8 + - - +
510A VAL 3.5 21.2 + - - +
511A CYS* 3.7 28.5 + - - +
512A GLY* 4.2 7.3 - - - +
515A ILE* 4.0 19.1 - - + +
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Residues in contact with GLU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PHE 6.1 0.2 - - - +
473A GLY* 3.2 1.4 - - - -
474A LYS* 1.3 85.0 - - + +
476A TRP* 1.3 56.5 + - - +
478A HIS* 3.2 25.9 + - - +
479A ALA* 2.9 34.0 + - - +
515A ILE* 4.4 10.7 - - - +
83B GLU* 3.8 42.5 - - + +
119B SER* 6.5 0.9 - - - -
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Residues in contact with TRP 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A VAL* 3.6 27.2 + - + +
438A PHE* 4.2 12.9 + - + -
443A ASN* 4.0 19.5 - - - -
468A LEU* 4.0 37.9 - - + -
469A VAL* 4.2 7.0 - - + -
472A PHE* 3.6 47.0 + + + +
473A GLY 3.1 12.0 + - - +
475A GLU* 1.3 78.4 - - - +
477A ALA* 1.3 66.5 + - - +
479A ALA* 4.8 3.1 - - - -
480A THR* 2.7 67.6 + - + +
481A ILE* 3.4 30.7 - - + -
121B SER* 4.7 7.6 - - - +
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Residues in contact with ALA 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A VAL* 4.1 19.1 - - + -
473A GLY 3.2 5.8 + - - +
474A LYS* 3.2 12.7 + - - +
476A TRP* 1.3 87.4 - - + +
478A HIS* 1.3 58.9 + - - +
481A ILE* 2.9 35.4 + - + -
482A ILE* 3.1 13.9 + - + -
507A LEU* 5.1 1.8 - - + -
511A CYS* 3.9 24.0 - - - -
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Residues in contact with HIS 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A LYS 2.9 16.4 + - - +
475A GLU* 3.5 28.3 - - - +
477A ALA* 1.3 76.9 - - - +
479A ALA* 1.3 59.9 + - + +
482A ILE* 3.8 19.5 - - + +
483A PRO* 3.2 22.5 - - - +
515A ILE* 4.2 17.9 - - + +
519A HIS* 3.3 45.2 + + - -
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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
----------------------------------------------------------
475A GLU* 2.9 18.5 + - - +
476A TRP* 4.2 2.9 - - - +
478A HIS* 1.3 82.3 - - + +
480A THR* 1.3 62.7 + - - +
483A PRO* 3.6 16.1 - - - +
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Residues in contact with THR 480 (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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438A PHE 4.2 5.6 - - - +
439A ASP* 5.5 1.3 - - - -
440A GLU 5.7 0.2 - - - +
443A ASN* 3.4 25.1 + - - +
476A TRP* 2.7 51.1 + - + +
479A ALA* 1.3 80.4 - - - +
481A ILE* 1.3 57.6 - - - +
483A PRO* 4.1 2.8 - - - +
484A LYS* 3.4 27.4 - - - +
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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