Contacts of the helix formed by residues 482 - 488 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B ALA 3.0 14.3 + - - +
478B HIS* 3.7 32.5 - - + +
481B ILE* 1.3 69.9 - - - +
483B PRO* 1.3 72.7 - - + +
485B VAL* 3.1 10.3 + - + +
486B LEU* 2.9 43.1 + - + +
507B LEU* 4.4 15.9 - - + -
511B CYS* 4.6 6.7 - - - -
515B ILE* 3.8 26.7 - - + -
519B HIS* 4.3 18.2 - - + +
520B MET* 4.5 15.3 - - + -
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Residues in contact with PRO 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B HIS 3.3 18.2 - - - +
479B ALA* 3.8 17.5 - - - +
480B THR 4.3 1.3 - - - +
481B ILE 3.3 10.1 - - - +
482B ILE* 1.3 91.9 - - + +
484B LYS* 1.3 59.4 + - + +
486B LEU* 3.4 6.5 + - + +
487B ALA* 2.9 30.6 + - - +
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Residues in contact with LYS 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B GLU* 3.6 36.8 + - - +
443B ASN* 6.2 1.6 - - + -
444B SER* 6.1 4.5 - - - -
447B MET* 3.9 26.2 - - + -
480B THR 4.7 11.4 - - - +
481B ILE 3.2 8.8 + - - +
483B PRO* 1.3 80.5 - - + +
485B VAL* 1.3 68.5 + - - +
487B ALA* 3.5 8.6 + - + +
488B MET* 3.4 31.0 + - + +
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Residues in contact with VAL 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B MET* 4.3 7.6 - - - -
481B ILE* 3.2 32.1 - - + +
482B ILE* 3.1 8.7 + - + +
484B LYS* 1.3 76.9 - - - +
486B LEU* 1.3 64.7 + - + +
488B MET* 3.2 13.3 - - - +
500B THR* 3.0 62.8 + - + +
503B CYS* 3.9 20.9 - - + -
504B ILE* 4.0 11.0 - - + -
507B LEU* 4.0 8.7 - - + -
520B MET* 6.2 0.7 - - - -
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Residues in contact with LEU 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ILE* 2.9 29.8 + - + +
483B PRO* 3.8 5.6 - - + +
485B VAL* 1.3 79.8 - - + +
487B ALA* 1.3 55.9 + - - +
489B SER* 2.5 38.1 + - - +
500B THR* 5.3 0.4 - - + -
504B ILE* 5.3 6.5 - - + -
519B HIS* 3.6 28.7 - - + +
520B MET* 5.0 2.9 - - + -
523B THR* 3.2 35.9 - - + +
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Residues in contact with ALA 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483B PRO 2.9 19.7 + - - +
484B LYS* 3.7 12.1 - - + +
485B VAL 3.4 0.4 - - - -
486B LEU* 1.3 75.8 - - - +
488B MET* 1.3 57.1 + - + +
489B SER 3.7 0.2 + - - -
490B GLY* 4.4 2.9 + - - -
491B ASP* 3.3 9.4 - - - +
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Residues in contact with MET 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B MET* 4.6 20.6 - - + -
484B LYS* 3.4 23.5 + - + +
485B VAL* 3.2 18.2 - - - +
487B ALA* 1.3 75.9 - - - +
489B SER* 1.3 63.9 + - - +
490B GLY 3.1 3.1 - - - -
491B ASP* 3.0 33.7 + - - +
496B HIS* 3.6 30.3 - - + +
497B ARG* 4.0 7.1 + - - +
499B THR* 3.9 22.4 - - + -
500B THR* 3.2 9.0 - - - +
503B CYS* 6.2 0.7 - - - -
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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
------------------------------------------------------------
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