Contacts of the helix formed by residues 457 - 461 (chain A) in PDB entry 6PAU
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 GLU 457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A TYR* 2.5 32.5 + - - +
359A GLN* 4.1 12.6 + - - +
360A PHE* 4.5 9.0 - - + -
426A HIS* 2.7 28.7 + - - -
431A LEU* 3.8 15.3 - - + +
456A MET* 1.3 80.3 - - - +
458A ASN* 1.3 62.5 + - - +
459A LYS* 3.2 3.1 - - - -
460A THR* 2.8 43.5 + - + +
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Residues in contact with ASN 458 (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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421A SER* 4.4 10.5 + - - -
424A ASN* 5.1 5.2 + - - +
431A LEU* 5.2 2.1 - - - +
452A ALA* 4.2 12.9 - - - +
453A LEU 2.8 31.7 + - - +
454A ASP* 4.3 1.3 - - - -
455A LEU* 2.9 30.1 + - - +
456A MET* 3.3 8.2 - - - +
457A GLU* 1.3 80.5 + - - +
459A LYS* 1.3 63.1 + - - +
460A THR 2.9 2.1 + - - -
461A PHE* 3.0 41.9 + - + -
462A LEU* 3.1 19.3 + - + +
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Residues in contact with LYS 459 (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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297A TRP* 6.1 1.1 - - + +
454A ASP* 3.6 35.9 + - + +
456A MET 5.1 1.3 + - - +
457A GLU 3.2 1.4 - - - -
458A ASN* 1.3 76.3 - - - +
460A THR* 1.3 62.3 + - + +
461A PHE 3.3 0.7 + - - -
462A LEU* 4.0 15.6 + - + +
463A GLU* 5.0 3.1 + - - +
488A SER* 3.3 19.8 + - - -
489A GLU* 3.2 34.1 + - + +
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Residues in contact with THR 460 (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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431A LEU* 3.7 16.3 - - - +
432A LEU* 4.8 1.4 - - - +
457A GLU* 2.8 34.5 + - + +
458A ASN 2.9 1.4 + - - -
459A LYS* 1.3 80.6 - - + +
461A PHE* 1.3 57.6 + - - +
464A LYS* 4.1 21.5 - - - +
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Residues in contact with PHE 461 (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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421A SER* 5.3 0.2 - - - -
431A LEU* 3.8 22.7 - - + -
432A LEU* 3.5 31.0 - - + +
435A MET* 3.5 42.4 - - + -
452A ALA* 4.9 2.7 - - + -
458A ASN* 3.0 49.9 + - + -
460A THR* 1.3 80.7 + - - +
462A LEU* 1.3 85.8 + - + +
463A GLU 3.4 2.2 - - - -
464A LYS* 3.2 3.3 + - - -
465A LEU* 2.9 36.6 + - + +
467A PHE* 3.9 15.9 - + - -
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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