Contacts of the strand formed by residues 562 - 566 (chain A) in PDB entry 1SQ0
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 562 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A VAL* 4.0 11.7 - - - -
557A GLU 3.6 3.1 - - - -
558A TYR* 4.5 0.9 - - - -
561A GLY* 1.3 73.6 + - - -
563A HIS* 1.3 65.4 + - - +
564A ALA 4.0 0.7 - - - -
596A GLU* 4.1 3.8 + - - +
597A VAL* 3.6 18.8 + - - +
600A TYR* 3.4 45.7 - - - +
237B LYS 4.0 1.2 - - - +
238B ALA* 3.0 24.3 - - - +
239B MET 2.9 14.7 + - - -
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Residues in contact with HIS 563 (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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556A VAL* 3.2 4.4 - - - +
557A GLU* 2.6 53.7 + - - +
559A HIS* 3.1 38.1 + + - -
561A GLY* 4.0 2.5 - - - -
562A SER* 1.3 84.1 - - - +
564A ALA* 1.3 61.4 + - - +
565A TYR* 3.6 14.9 + - + +
231B LYS* 6.0 2.2 - - + -
236B VAL* 3.8 19.8 - - + +
238B ALA* 3.3 25.6 - - + +
240B THR* 4.3 11.1 + - - -
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Residues in contact with ALA 564 (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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555A VAL 3.4 6.1 - - - +
556A VAL* 4.1 15.7 - - + -
562A SER 4.0 0.8 - - - -
563A HIS* 1.3 71.3 - - - +
565A TYR* 1.3 63.5 + - - +
566A ILE 4.8 7.2 - - - +
567A GLY* 6.1 1.1 - - - -
600A TYR* 3.7 24.2 - - + +
605A ILE* 6.2 0.2 - - + -
235B ASP 3.5 2.6 - - - +
236B VAL* 3.5 0.2 - - - -
237B LYS* 3.0 39.2 + - + +
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Residues in contact with TYR 565 (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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555A VAL* 2.9 11.6 + - + +
557A GLU* 4.1 10.4 + - + -
563A HIS* 3.6 23.0 + - + +
564A ALA* 1.3 75.5 - - - +
566A ILE* 1.3 66.6 + - + +
570A ASP* 4.6 3.0 - - - +
572A LYS* 5.2 1.0 + - - -
580A ILE* 3.3 29.9 - - + +
583A GLN* 4.6 4.3 - - + -
584A VAL* 3.4 43.2 - - + +
585A LYS* 2.9 36.1 + - + +
234B VAL 4.8 3.8 - - - -
235B ASP* 3.1 28.8 - - + +
236B VAL* 3.5 34.7 - - + +
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Residues in contact with ILE 566 (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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541A MET* 4.0 20.0 - - + -
553A VAL* 3.9 16.4 - - + +
554A ALA* 3.2 6.3 - - - +
555A VAL* 3.0 44.1 + - + +
556A VAL* 5.2 1.0 - - - +
564A ALA* 3.6 7.0 - - - +
565A TYR* 1.3 87.0 + - - +
567A GLY* 1.3 71.8 + - - +
570A ASP* 3.8 7.2 - - + +
577A LEU* 3.6 52.3 - - + +
580A ILE* 3.5 17.9 - - + -
581A ALA 4.2 3.8 - - - +
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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