Contacts of the helix formed by residues 473 - 481 (chain A) in PDB entry 4UHX
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 ALA 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A ILE* 2.9 21.4 + - + +
463A TYR* 5.2 1.1 - - + -
471A ILE 4.1 1.0 + - - -
472A CYS* 1.3 67.4 - - - +
474A LYS* 1.3 62.0 + - - +
475A ASN 3.4 2.9 - - - -
477A CYS* 3.2 27.2 + - - -
497A ILE* 3.3 33.2 - - + -
500A GLU* 3.4 22.9 - - + +
501A VAL* 4.8 11.5 - - + +
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Residues in contact with LYS 474 (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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394A GLU* 3.1 42.3 + - + +
472A CYS* 2.9 17.0 + - + +
473A ALA* 1.3 72.7 - - - +
475A ASN* 1.3 86.2 + - - +
477A CYS* 3.9 4.9 - - - +
478A GLN* 3.1 28.8 + - - +
500A GLU* 3.4 11.1 + - - +
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Residues in contact with ASN 475 (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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474A LYS* 1.3 103.1 + - - +
476A SER* 1.3 65.2 + - - +
478A GLN* 3.5 6.3 + - - +
479A LYS* 3.2 31.2 + - + +
500A GLU* 3.1 20.5 + - - +
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Residues in contact with SER 476 (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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473A ALA 4.0 1.3 - - - -
475A ASN* 1.3 75.1 - - - +
477A CYS* 1.3 63.1 + - - +
479A LYS* 3.1 6.5 + - - +
480A LEU* 3.1 29.2 + - - +
496A LEU* 2.9 49.2 + - - +
497A ILE* 3.4 24.5 + - - -
500A GLU* 2.8 24.4 + - - -
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Residues in contact with CYS 477 (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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459A LEU* 3.2 48.6 - - + +
460A CYS* 4.1 0.4 - - - -
461A ILE* 3.7 41.5 - - - -
473A ALA* 3.2 23.2 + - - +
474A LYS* 3.9 5.4 - - - +
476A SER* 1.3 79.9 - - - +
478A GLN* 1.3 61.2 + - - +
480A LEU* 3.2 11.0 + - - +
481A ILE* 3.2 21.8 + - - +
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Residues in contact with GLN 478 (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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474A LYS 3.1 19.6 + - - +
475A ASN* 3.7 9.4 - - - +
476A SER 3.3 0.2 - - - -
477A CYS* 1.3 74.5 - - - +
479A LYS* 1.3 62.0 + - + +
481A ILE* 3.4 31.8 + - - +
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Residues in contact with LYS 479 (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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475A ASN* 3.2 14.7 + - + +
476A SER 3.1 9.0 + - - +
478A GLN* 1.3 78.6 - - + +
480A LEU* 1.3 59.8 + - - +
481A ILE 3.4 4.6 + - - +
483A ARG* 3.5 25.2 + - - +
496A LEU* 3.6 31.4 - - + -
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Residues in contact with LEU 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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456A ILE* 3.2 19.2 - - + +
459A LEU* 3.7 28.0 - - + -
461A ILE* 5.2 6.3 - - + -
476A SER* 3.1 21.4 + - - +
477A CYS* 3.2 7.6 + - - +
479A LYS* 1.3 75.3 - - - +
481A ILE* 1.3 63.1 + - - +
483A ARG* 3.3 35.9 + - - +
489A MET* 4.0 15.0 - - + -
492A ILE* 4.5 4.9 - - + -
493A ALA* 3.8 41.7 - - + +
496A LEU* 4.5 9.9 - - + -
497A ILE* 5.6 1.6 - - + -
523A LEU* 6.4 0.4 - - + -
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Residues in contact with ILE 481 (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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456A ILE* 3.5 22.9 - - + +
457A ARG* 3.7 17.7 - - - +
458A GLU* 3.9 7.2 - - - -
459A LEU* 3.9 23.1 - - + +
477A CYS 3.2 20.8 + - - +
478A GLN* 3.4 28.8 + - - +
479A LYS 4.2 4.9 - - - +
480A LEU* 1.3 76.8 - - - +
482A GLY* 1.3 62.9 + - - +
483A ARG* 3.4 2.0 + - - +
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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