Contacts of the helix formed by residues 482 - 489 (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 ILE 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477A ALA* 3.1 6.4 + - + +
478A HIS* 3.8 24.9 - - - +
481A ILE* 1.3 73.7 - - - +
483A PRO* 1.3 73.9 - - + +
485A VAL* 3.0 10.3 + - + +
486A LEU* 2.8 45.5 + - + +
507A LEU* 4.3 17.0 - - + -
511A CYS* 4.9 5.6 - - - -
515A ILE* 3.5 33.0 - - + -
519A HIS* 4.0 17.9 - - + +
520A MET* 4.5 17.3 - - + -
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Residues in contact with PRO 483 (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 HIS 3.2 20.6 - - - +
479A ALA* 3.6 17.9 - - - +
480A THR 4.1 0.9 - - - +
481A ILE 3.4 9.6 - - - +
482A ILE* 1.3 92.4 - - + +
484A LYS* 1.3 65.2 + - + +
486A LEU* 3.4 8.6 + - + +
487A ALA* 3.1 21.4 + - - +
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Residues in contact with LYS 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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440A GLU* 2.9 51.3 - - - +
443A ASN* 4.1 12.6 - - + +
444A SER* 5.8 0.7 - - - -
447A MET* 4.2 26.2 - - + -
480A THR* 3.4 28.9 - - - +
481A ILE* 3.1 5.7 + - - +
483A PRO* 1.3 75.2 - - + +
485A VAL* 1.3 66.8 + - - +
487A ALA* 3.0 17.9 + - - +
488A MET* 3.2 19.6 + - + +
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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
----------------------------------------------------------
447A MET* 4.0 13.5 - - - -
481A ILE* 3.1 32.2 + - + +
482A ILE* 3.0 12.5 + - + +
484A LYS* 1.3 77.2 - - - +
486A LEU* 1.3 66.0 + - + +
488A MET* 3.4 11.6 + - - +
500A THR* 3.1 58.3 + - + +
503A CYS* 4.0 15.5 - - + -
504A ILE* 4.1 15.3 - - + -
507A LEU* 4.4 5.2 - - + -
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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
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482A ILE* 2.8 32.0 + - + +
483A PRO* 3.7 7.6 - - + +
485A VAL* 1.3 85.2 - - + +
487A ALA* 1.3 59.4 + - - +
489A SER* 2.5 30.2 + - - +
500A THR* 4.9 1.1 - - - -
504A ILE* 5.0 4.3 - - + -
519A HIS* 3.6 29.6 - - + +
520A MET* 5.0 0.7 - - + -
523A THR* 3.0 35.4 - - + +
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Residues in contact with ALA 487 (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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483A PRO 3.1 13.1 + - - +
484A LYS* 3.0 13.8 + - - +
486A LEU* 1.3 77.1 - - - +
488A MET* 1.3 61.7 + - + +
490A GLY* 3.3 12.8 + - - -
491A ASP* 3.4 9.5 - - - +
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Residues in contact with MET 488 (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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447A MET* 4.6 18.6 - - + -
484A LYS* 3.2 8.7 + - + +
485A VAL* 3.8 19.1 - - - +
486A LEU 3.2 1.0 - - - -
487A ALA* 1.3 72.3 - - + +
489A SER* 1.3 62.4 + - - +
490A GLY 2.9 6.4 + - - -
491A ASP* 3.3 34.2 + - - +
496A HIS* 3.9 27.8 - - + +
497A ARG* 3.4 11.6 - - - +
499A THR* 3.6 32.3 - - + -
500A THR* 3.5 15.5 - - - +
503A CYS* 5.3 0.9 - - - -
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Residues in contact with SER 489 (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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486A LEU* 2.5 23.2 + - - +
488A MET* 1.3 77.8 - - - +
490A GLY* 1.3 58.2 + - - +
497A ARG* 2.8 30.3 - - - +
500A THR* 3.5 9.5 + - - -
523A THR* 4.0 18.3 - - - +
526A ARG* 3.2 32.8 + - - -
527A MET* 4.2 14.3 - - - +
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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