Contacts of the strand formed by residues 477 - 483 (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 GLU 477 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332B HIS* 2.7 44.6 + - - -
333B ARG* 2.8 28.4 + - - +
427B GLU* 3.2 3.1 - - - +
428B LYS* 4.5 20.1 - - + +
473B PHE* 2.9 8.8 - - - -
474B MET* 2.7 42.0 + - - +
475B ARG 4.0 7.2 - - - +
476B GLY* 1.3 80.0 - - - +
478B GLU* 1.3 64.6 + - - +
479B ILE* 3.5 0.9 + - - +
535B PHE* 3.4 30.2 - - + -
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Residues in contact with GLU 478 (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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333B ARG* 3.6 2.0 + - - +
427B GLU* 3.0 16.8 + - - +
471B ASP* 4.2 17.0 - - - +
472B PHE 3.3 6.5 - - - +
473B PHE* 3.6 8.7 - - + -
477B GLU* 1.3 72.3 - - - +
479B ILE* 1.3 61.4 - - - +
480B LEU 3.7 15.3 - - - +
481B SER* 3.1 24.6 - - - -
531B ARG* 2.8 38.0 + - - +
535B PHE* 3.8 2.1 - - - -
701B ATP 2.7 58.8 + - - +
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Residues in contact with ILE 479 (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* 3.5 30.1 - - + -
442B PHE* 4.0 8.3 - - + -
472B PHE* 2.8 28.0 + - + +
474B MET* 3.2 63.3 - - + +
478B GLU* 1.3 75.5 - - - +
480B LEU* 1.3 59.0 + - + +
527B ILE* 3.4 18.9 - - - +
528B GLY 3.6 4.5 + - - -
531B ARG* 4.6 6.1 - - - -
532B VAL* 4.1 10.5 - - + +
535B PHE* 3.9 11.9 - - + -
701B ATP 2.5 16.7 + - - -
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Residues in contact with LEU 480 (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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358B LEU* 3.7 28.3 - - + -
362B PHE* 4.1 8.7 - - + -
470B TYR* 3.9 7.4 - - + -
471B ASP* 3.1 9.4 - - - +
472B PHE* 2.8 66.5 + - + -
478B GLU* 3.7 4.6 - - - +
479B ILE* 1.3 83.8 - - + +
481B SER* 1.3 65.4 + - - +
482B GLY* 3.3 23.8 - - - +
525B GLY* 4.5 1.1 - - - -
526B GLY 3.1 19.7 - - - +
527B ILE* 4.0 15.9 - - + -
701B ATP 3.0 4.6 + - - -
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Residues in contact with SER 481 (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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453B ARG* 3.5 12.0 + - - -
471B ASP* 3.0 11.7 + - - -
478B GLU* 3.1 19.2 + - - -
480B LEU* 1.3 74.9 - - - +
482B GLY* 1.3 56.6 + - - +
525B GLY* 3.8 0.2 - - - -
526B GLY* 3.0 24.7 + - - -
701B ATP 3.2 41.4 + - - -
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Residues in contact with GLY 482 (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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453B ARG* 5.2 1.3 - - - +
469B SER* 3.6 0.9 - - - -
470B TYR* 2.8 56.4 + - - +
480B LEU* 3.3 8.0 - - - +
481B SER* 1.3 75.1 + - - +
483B ALA* 1.3 60.8 + - - +
485B ARG* 5.4 1.3 - - - -
524B GLY 3.5 7.9 - - - -
525B GLY* 3.8 2.5 - - - -
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Residues in contact with ALA 483 (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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453B ARG* 5.3 1.1 - - + -
454B PRO* 6.2 0.9 - - + -
456B TYR* 6.0 3.4 - - + -
457B THR* 3.9 16.2 - - - +
468B ASN 3.1 17.3 - - - +
469B SER* 3.4 14.8 - - - +
470B TYR* 2.9 14.6 + - - -
482B GLY* 1.3 73.9 - - - -
484B GLN* 1.3 56.2 + - - +
485B ARG* 2.5 33.1 + - - +
523B ALA* 3.3 0.2 - - - -
524B GLY 2.8 20.7 + - - -
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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