Contacts of the strand formed by residues 470 - 474 (chain A) in PDB entry 1ASZ
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 TYR 470 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A TYR* 4.0 17.9 - + - -
354A VAL* 4.1 7.4 - - - +
355A LEU* 3.8 24.2 - - + -
358A LEU* 3.9 21.8 - - + +
444A ILE* 4.8 1.1 - - + -
445A LEU 3.3 15.9 - - - +
446A ASP* 3.8 11.4 - - - +
448A PHE* 3.8 4.0 - - - -
453A ARG* 3.4 2.3 + - - +
468A ASN 3.4 8.7 - - - -
469A SER* 1.3 86.5 - - - +
471A ASP* 1.3 72.5 + - - +
472A PHE* 4.0 14.4 - + - -
480A LEU* 4.2 3.6 - - + -
482A GLY* 2.9 34.3 + - - -
483A ALA* 3.0 32.5 + - - -
523A ALA* 4.4 0.5 - - - +
524A GLY* 2.9 24.9 + - - -
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Residues in contact with ASP 471 (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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443A TYR 3.9 0.3 - - - +
444A ILE* 4.0 0.5 - - - +
445A LEU 2.9 30.4 + - - -
448A PHE* 3.7 19.8 - - + -
453A ARG* 3.2 11.0 + - - -
470A TYR* 1.3 86.1 - - - +
472A PHE* 1.3 74.2 + - - +
473A PHE* 3.4 26.6 - - + -
478A GLU* 3.9 16.3 - - + +
480A LEU 3.3 13.5 - - - +
481A SER* 3.0 19.6 + - - -
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Residues in contact with PHE 472 (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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355A LEU* 4.7 2.7 - - + -
358A LEU* 3.7 31.9 - - + -
359A SER* 4.2 2.0 - - - -
362A PHE* 3.2 41.3 - + - -
442A PHE* 3.7 18.6 - + + -
443A TYR 3.7 4.3 - - - -
444A ILE* 3.8 34.8 - - + -
470A TYR* 4.0 17.0 - + - -
471A ASP* 1.3 82.0 - - - +
473A PHE* 1.3 68.4 + - - +
478A GLU* 3.6 3.3 - - - -
479A ILE* 3.1 28.7 + - + -
480A LEU* 3.2 37.0 + - + +
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Residues in contact with PHE 473 (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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422A LEU* 5.2 5.2 - - + -
427A GLU* 3.6 31.0 - - + -
441A ASP 3.6 1.6 - - - +
442A PHE* 3.2 24.2 - - - -
443A TYR* 3.1 59.2 + + + -
445A LEU* 3.6 30.7 - - + -
448A PHE* 4.7 2.0 - + - -
471A ASP* 3.4 34.3 - - + -
472A PHE* 1.3 76.8 - - - +
474A MET* 1.3 62.6 + - - +
476A GLY* 4.1 10.8 - - - -
477A GLU 3.2 23.8 - - - +
478A GLU* 3.7 6.1 - - + -
479A ILE* 4.3 0.9 - - - +
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Residues in contact with MET 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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366A PHE* 3.1 41.3 - - + -
389A PHE* 3.6 18.2 - - + -
441A ASP 3.6 2.9 - - - -
442A PHE* 4.6 1.3 - - + -
473A PHE* 1.3 78.1 - - - +
475A ARG* 1.3 61.1 + - - +
476A GLY 3.0 1.8 - - - -
477A GLU* 2.6 40.7 + - - +
479A ILE* 3.5 46.1 - - + +
532A VAL* 4.0 17.0 - - + +
535A PHE* 3.8 13.0 - - + -
536A TYR* 3.8 28.3 - - + +
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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