Contacts of the strand formed by residues 471 - 476 (chain A) in PDB entry 1SLL
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 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A ASP* 2.8 13.3 + - + -
349A TYR* 3.5 46.0 - + + +
350A ILE* 3.0 28.2 + - - +
469A LYS 4.1 8.7 - - - -
470A GLN* 1.3 77.1 - - - +
472A ASP* 1.3 59.8 + - - +
482A GLU* 3.8 14.1 - - + -
483A SER 3.5 23.6 - - - -
484A LYS* 3.7 30.3 - - + -
485A THR* 4.3 1.3 - - - -
496A LYS* 3.0 29.4 + - - +
497A ASN* 3.0 28.3 + - + -
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Residues in contact with ASP 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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349A TYR* 4.7 0.2 - - - -
350A ILE* 3.6 14.5 - - + +
352A LYS* 3.0 26.0 + - - +
471A TYR* 1.3 76.8 - - - +
473A TYR* 1.3 75.6 + - - +
474A ASN* 3.1 21.8 + - - +
481A ILE 4.3 0.2 - - - -
482A GLU* 3.4 4.9 - - - +
483A SER* 2.8 35.4 + - - +
485A THR* 3.6 21.8 - - + +
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Residues in contact with TYR 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TYR* 3.6 22.3 - - - +
322A LYS* 4.3 1.1 - - + +
349A TYR* 3.7 24.0 - + + -
350A ILE* 2.8 37.5 + - + -
352A LYS* 2.8 54.8 + - + +
354A ILE* 3.9 18.5 - - + +
356A TRP* 4.0 15.3 - + - -
367A ILE* 4.0 26.9 - - + -
472A ASP* 1.3 84.3 + - - +
474A ASN* 1.3 60.7 + - - +
480A LEU* 4.0 18.4 - - + -
481A ILE 3.2 8.1 - - - +
482A GLU* 4.2 6.5 - - + -
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Residues in contact with ASN 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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352A LYS* 3.0 19.8 + - - -
354A ILE* 4.7 6.5 - - - +
472A ASP* 3.1 26.0 + - - +
473A TYR* 1.3 76.0 - - - +
475A PHE* 1.3 63.1 + - - +
480A LEU* 3.6 6.9 - - - +
481A ILE* 2.7 42.6 + - + +
483A SER* 5.0 4.9 + - - -
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Residues in contact with PHE 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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354A ILE* 5.0 7.5 - - + +
355A ASP 5.3 1.3 - - - -
356A TRP* 3.6 35.4 - + - -
357A PRO* 3.4 43.3 - - + -
362A GLY* 4.3 2.7 - - - -
365A VAL* 3.9 27.1 - - + -
474A ASN* 1.3 76.7 - - - +
476A SER* 1.3 59.9 + - - +
477A GLY 3.5 22.4 + - - +
478A ASN* 3.7 16.4 - - - -
479A ASN 3.2 13.0 - - - -
480A LEU* 3.6 16.4 - - + -
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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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474A ASN 3.8 0.4 + - - -
475A PHE* 1.3 72.1 - - - +
477A GLY* 1.3 63.0 + - - +
478A ASN 3.3 0.3 + - - -
479A ASN* 2.7 30.2 + - - +
481A ILE* 3.7 27.1 - - - -
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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