Contacts of the strand formed by residues 469 - 474 (chain B) 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 SER 469 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351B TYR* 4.5 0.2 - - - -
446B ASP* 2.8 6.9 + - - +
447B LYS* 2.6 32.5 + - - +
448B PHE* 4.3 4.5 - - - -
453B ARG* 2.9 42.0 - - - +
457B THR* 2.9 25.1 + - - -
467B SER* 3.1 11.2 + - - -
468B ASN* 1.3 71.1 + - - +
470B TYR* 1.3 60.9 + - - +
482B GLY 3.6 7.0 - - - -
483B ALA* 3.4 7.0 - - - +
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Residues in contact with TYR 470 (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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351B TYR* 3.8 26.7 - + - -
354B VAL* 4.3 4.7 - - + +
355B LEU* 3.2 37.9 - - + -
358B LEU* 4.2 7.4 - - + -
444B ILE* 4.2 13.0 - - + -
445B LEU 3.3 12.3 - - - +
446B ASP* 4.4 4.3 - - + +
453B ARG* 3.2 9.2 + - - +
469B SER* 1.3 79.6 - - - +
471B ASP* 1.3 76.3 + - - +
472B PHE* 4.1 4.0 - + - -
480B LEU* 3.9 12.8 - - + -
482B GLY* 2.8 47.8 + - - +
483B ALA* 2.9 21.4 + - - -
523B ALA* 3.8 6.3 - - + +
524B GLY 2.5 26.9 + - - -
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Residues in contact with ASP 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ILE* 3.6 3.6 - - - +
445B LEU 3.1 25.7 + - - -
448B PHE* 3.2 26.4 - - + -
453B ARG* 3.0 25.9 + - - -
470B TYR* 1.3 89.7 - - - +
472B PHE* 1.3 69.6 + - - +
473B PHE* 3.9 19.5 - - + -
478B GLU* 4.2 14.8 - - - +
480B LEU 3.1 8.3 - - - +
481B SER* 3.0 18.0 - - - -
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Residues in contact with PHE 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LEU* 4.4 7.9 - - + -
358B LEU* 4.4 8.7 - - + -
359B SER* 4.4 11.4 - - - -
362B PHE* 4.2 15.9 - + - -
442B PHE* 3.1 36.8 - + - -
443B TYR 4.0 1.1 - - - -
444B ILE* 3.5 42.4 - - + -
470B TYR* 4.1 13.7 - + - -
471B ASP* 1.3 78.0 - - - +
473B PHE* 1.3 62.4 + - - +
478B GLU* 3.3 7.1 - - - -
479B ILE* 2.8 35.3 + - + -
480B LEU* 2.8 56.6 + - + -
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Residues in contact with PHE 473 (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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422B LEU* 5.0 4.9 - - + -
427B GLU* 3.9 25.1 - - + -
441B ASP 3.6 0.6 - - - +
442B PHE* 3.4 32.7 - - - -
443B TYR* 3.0 63.0 + + + -
445B LEU* 3.4 36.8 - - + -
448B PHE* 4.7 2.0 - + - -
471B ASP* 3.9 24.5 - - + -
472B PHE* 1.3 78.6 - - - +
474B MET* 1.3 60.6 + - - +
476B GLY* 4.0 12.8 - - - -
477B GLU 2.9 21.8 - - - +
478B GLU* 3.6 11.9 - - + -
479B ILE* 4.5 0.9 - - - -
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Residues in contact with MET 474 (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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362B PHE* 4.5 0.2 - - - -
366B PHE* 3.2 31.2 - - + -
389B PHE* 3.4 26.5 - - + -
441B ASP 3.5 2.0 - - - -
442B PHE* 4.4 1.3 - - - -
473B PHE* 1.3 72.0 - - - +
475B ARG* 1.3 73.5 + - - +
476B GLY 3.1 0.7 - - - -
477B GLU* 2.7 22.5 + - - +
479B ILE* 3.2 44.4 - - + +
531B ARG 4.5 1.1 - - - +
532B VAL* 3.3 47.1 - - + +
535B PHE* 3.7 19.2 - - + -
536B TYR* 4.8 1.3 - - + +
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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