Contacts of the helix formed by residues 458 - 461 (chain B) in PDB entry 5C16
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 SER 458 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B LEU 4.1 1.0 + - - -
457B ASP* 1.3 69.8 + - - +
459B TYR* 1.3 67.9 + - - +
461B ARG* 2.8 43.1 + - - +
462B THR* 3.6 7.5 + - - +
579B ASN 5.5 1.8 - - - -
581B GLU 4.4 1.6 - - - -
582B ASN* 3.3 45.2 + - - +
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Residues in contact with TYR 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B VAL 5.4 1.0 + - - -
235B GLU* 3.6 10.3 + - - -
238B ARG* 3.3 60.5 - - - +
457B ASP* 3.0 7.5 + - - +
458B SER* 1.3 80.1 + - - +
460B TYR* 1.3 69.3 + + - +
461B ARG 2.9 4.2 + - - -
462B THR* 2.7 39.1 + - + -
464B LYS* 4.3 6.3 + - + +
465B GLY* 3.2 30.5 + - - -
468B THR* 3.6 19.8 + - + +
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Residues in contact with TYR 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLU* 2.5 30.4 + - - -
238B ARG* 3.2 8.7 + - - -
239B GLN* 3.4 11.6 + - - -
293B TRP* 3.8 5.5 - + - -
453B MET* 3.5 54.4 - - + +
454B LEU* 3.2 27.5 - - + +
457B ASP* 3.1 29.5 + - + +
459B TYR* 1.3 89.3 - + - +
461B ARG* 1.3 56.4 + - - +
462B THR 3.4 0.4 - - - -
465B GLY 3.3 20.9 - - - -
466B PHE* 3.3 23.8 - - - +
468B THR* 4.7 1.6 - - + -
469B LEU* 3.7 25.8 - - + -
472B LYS* 4.1 2.6 - - - -
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Residues in contact with ARG 461 (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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454B LEU* 3.0 21.8 + - + -
455B MET 2.9 29.5 + - - -
456B LEU 4.3 0.6 - - - -
457B ASP 4.0 0.8 + - - +
458B SER* 2.8 40.6 + - - +
460B TYR* 1.3 77.8 - - - +
462B THR* 1.3 62.9 + - - +
518B ALA 3.3 21.1 - - - +
519B PHE* 3.4 37.7 - - + +
520B GLU 3.0 24.0 + - - -
521B PHE* 4.3 4.2 - - - -
577B PHE* 5.3 2.0 - - + -
581B GLU 3.2 25.3 + - - -
583B HIS 3.3 20.0 + - - -
585B LEU* 3.4 29.1 - - - +
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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