Contacts of the strand formed by residues 489 - 497 (chain A) in PDB entry 3S3J
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 PHE 489 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A VAL* 4.9 1.3 - - + -
481A GLN* 4.5 20.9 - - - +
482A SER 5.3 2.2 - - - +
483A MET* 4.0 29.4 - - + -
487A SER* 4.0 15.9 - - - +
488A ASP* 1.3 79.3 - - - +
490A ASP* 1.3 72.1 + - - +
491A VAL* 3.9 13.2 - - + -
545A CYS* 4.5 2.8 - - - -
546A ILE* 2.6 74.0 + - + +
551A TYR* 4.2 9.2 - + - -
561A ILE* 4.6 8.1 - - + -
582A LEU* 4.6 3.4 - - + -
584A LEU* 3.5 31.0 - - + -
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Residues in contact with ASP 490 (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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479A VAL* 4.2 12.1 - - - +
481A GLN* 5.2 6.4 + - - +
489A PHE* 1.3 81.2 - - - +
491A VAL* 1.3 67.9 + - - +
492A PHE* 3.7 33.5 - - + -
543A PRO* 4.7 9.4 - - + +
544A LEU 3.3 6.3 - - - +
545A CYS* 3.3 30.5 + - - +
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Residues in contact with VAL 491 (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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477A ILE* 4.7 3.4 - - + -
478A ARG 3.8 7.9 - - - +
479A VAL* 4.2 7.0 - - + -
489A PHE* 3.9 15.2 + - + -
490A ASP* 1.3 77.0 - - - +
492A PHE* 1.3 65.4 + - - +
509A LEU* 4.6 3.1 - - + +
542A VAL 3.7 0.3 - - - +
543A PRO* 3.3 3.6 - - - +
544A LEU* 2.9 55.8 + - + +
546A ILE* 4.2 12.3 - - + -
563A VAL* 4.2 24.9 - - + -
582A LEU* 3.6 31.2 - - + -
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Residues in contact with PHE 492 (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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477A ILE* 3.3 11.5 - - - +
478A ARG* 2.9 59.7 + - + +
479A VAL 4.4 10.8 - - - -
490A ASP* 3.7 33.9 - - + -
491A VAL* 1.3 74.9 - - - +
493A ALA* 1.3 60.8 + - - +
494A HIS* 3.4 0.6 + - + +
509A LEU* 4.9 1.8 - - - -
541A SER* 3.9 31.4 - - - -
542A VAL 3.2 3.8 - - - +
543A PRO* 3.7 33.0 - - + -
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Residues in contact with ALA 493 (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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475A MET* 4.4 11.4 - - - -
476A ARG 4.1 2.5 - - - -
477A ILE* 4.8 3.8 - - - -
492A PHE* 1.3 68.5 - - - +
494A HIS* 1.3 59.9 + - - +
495A ILE* 3.6 6.3 + - + +
507A LEU* 4.3 20.2 - - + -
509A LEU* 4.0 26.4 - - + +
540A LYS 3.4 3.6 - - - +
542A VAL* 2.7 48.8 + - + +
565A ALA* 4.4 2.0 - - + -
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Residues in contact with HIS 494 (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 ALA 3.8 0.7 - - - +
475A MET* 3.4 3.6 - - - -
476A ARG* 2.9 60.7 + - + +
478A ARG* 3.4 46.9 + - + -
492A PHE* 3.4 1.1 + - + +
493A ALA* 1.3 70.3 - - - +
495A ILE* 1.3 60.2 + - - +
496A THR* 3.8 13.4 + - - -
539A GLU* 3.1 40.7 + - + -
540A LYS 3.4 6.4 + - - -
541A SER* 3.2 22.4 + - - +
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Residues in contact with ILE 495 (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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473A MET* 4.4 7.4 - - + -
474A ALA 3.4 8.7 - - - +
475A MET* 3.8 25.1 - - + -
493A ALA* 4.0 10.5 - - + +
494A HIS* 1.3 75.8 - - - +
496A THR* 1.3 63.4 + - - +
507A LEU* 4.2 9.0 - - + -
532A LEU* 3.9 28.9 - - + -
534A LEU* 3.7 29.4 - - + +
539A GLU* 3.1 6.7 - - - +
540A LYS* 2.8 42.4 + - + +
542A VAL* 4.5 4.3 - - + -
567A LEU* 4.0 26.5 - - + -
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Residues in contact with THR 496 (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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472A GLY 5.1 1.1 - - - +
473A MET* 3.0 9.9 - - - +
474A ALA* 2.9 46.6 + - + +
494A HIS* 3.8 21.2 + - - -
495A ILE* 1.3 74.3 + - - +
497A ASN* 1.3 63.0 + - - +
498A ASN* 3.7 29.8 - - + +
538A SER 4.0 5.8 - - - +
539A GLU* 4.1 8.6 + - + +
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Residues in contact with ASN 497 (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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472A GLY 4.1 0.7 - - - -
473A MET* 4.0 8.1 - - - +
495A ILE 4.2 1.0 + - - -
496A THR* 1.3 72.5 - - - +
498A ASN* 1.3 58.4 + - - +
499A THR* 3.1 14.1 + - - +
501A GLU 2.9 24.7 + - - -
503A TYR* 2.9 28.3 - - - -
534A LEU* 3.4 24.9 + - + -
535A GLU 3.0 22.2 + - - +
536A PRO* 3.9 2.8 - - - +
537A PHE* 2.9 26.9 + - - -
538A SER 2.9 16.2 + - - +
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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