Contacts of the strand formed by residues 476 - 480 (chain A) in PDB entry 1S2S
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 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406A LEU* 3.1 13.9 - - + +
408A ILE* 4.1 7.0 - - + -
440A ILE 4.1 0.4 - - - -
441A VAL* 3.3 8.9 - - - +
442A THR* 2.6 28.7 + - - -
443A GLU* 5.6 7.4 - - + +
444A ASN* 4.6 12.0 + - + -
462A ILE* 4.2 11.2 - - + +
465A LEU* 5.5 1.3 - - + -
466A LYS* 3.7 30.5 - - + +
469A SER* 3.5 35.7 - - - -
474A PHE* 4.0 13.9 - + + -
475A THR* 1.4 85.5 - - + +
477A ASP* 1.4 56.8 + - - +
478A LEU* 3.5 39.3 - - + -
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Residues in contact with ASP 477 (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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406A LEU 2.7 8.1 + - - -
407A SER* 2.9 26.5 - - - -
408A ILE* 2.6 39.9 + - - +
440A ILE* 3.3 34.3 - - - +
442A THR* 2.5 37.5 + - - +
444A ASN* 3.8 3.1 - - - +
476A TYR* 1.4 74.5 - - - +
478A LEU* 1.4 49.4 + - - +
479A TYR* 3.1 19.5 + - - +
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Residues in contact with LEU 478 (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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408A ILE* 3.3 25.1 - - + -
410A THR* 3.7 23.6 - - + +
444A ASN* 2.5 49.5 + - + +
447A ASP* 4.3 10.5 - - + -
461A CYS* 6.4 0.2 - - + -
462A ILE* 4.0 34.5 - - + +
465A LEU* 3.9 34.3 - - + -
474A PHE* 6.5 0.2 - - + -
476A TYR* 3.5 26.9 - - + -
477A ASP* 1.4 64.6 - - - +
479A TYR* 1.4 64.1 + - - +
480A LEU* 3.9 2.4 + - - +
510A VAL* 6.1 0.2 - - + -
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Residues in contact with TYR 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A SER* 4.8 6.7 - - - -
408A ILE 2.7 30.0 + - - -
409A VAL* 3.3 22.7 - - + -
410A THR 2.6 32.4 + - - -
477A ASP* 3.1 22.7 + - - +
478A LEU* 1.4 72.5 - - - +
480A LEU* 1.4 85.3 + - - +
481A VAL* 4.4 1.3 - - - -
482A THR* 4.7 5.4 - - - -
500A GLU* 2.5 28.7 + - - +
505A ARG* 4.2 12.9 + - - +
506A ALA* 3.5 24.8 - - + +
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Residues in contact with LEU 480 (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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410A THR* 3.6 6.3 - - + -
411A LEU* 3.9 12.1 - - - +
412A GLU* 3.8 40.6 - - + +
417A VAL* 4.3 9.9 - - + -
419A VAL* 4.2 19.3 - - + -
444A ASN* 4.9 2.9 - - - +
447A ASP* 4.4 7.9 - - - +
478A LEU 4.1 9.2 - - - +
479A TYR* 1.4 94.6 - - - +
481A VAL* 1.4 71.8 + - + +
482A THR* 4.9 0.5 + - - -
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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