Contacts of the strand formed by residues 472 - 478 (chain A) in PDB entry 2JI8
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 VAL 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A CYS* 3.6 39.3 - - + +
439A ALA* 4.1 11.4 - - + -
446A VAL* 3.4 20.2 - - + +
465A ILE* 3.9 17.9 - - + -
470A LEU* 2.7 31.4 + - + -
471A PRO* 1.3 75.9 - - - +
473A THR* 1.3 67.0 + - - +
474A VAL* 4.3 14.6 - - + -
509A MET* 4.8 1.0 - - - +
537A LYS 3.7 1.6 + - - +
538A PRO* 3.5 2.1 - - - +
539A CYS 2.8 27.7 + - - +
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Residues in contact with THR 473 (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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446A VAL 2.8 12.8 + - - -
447A ILE* 3.4 5.9 - - - +
448A ALA 2.9 25.6 + - - +
471A PRO 5.2 1.2 + - - -
472A VAL* 1.3 74.2 + - - +
474A VAL* 1.3 62.0 + - - +
475A ILE* 3.7 1.9 + - + -
529A LEU* 4.2 11.4 - - + -
532A ALA* 3.5 42.6 + - + +
533A VAL* 3.9 14.9 - - - +
537A LYS 4.9 0.5 + - - -
539A CYS* 3.4 8.4 - - + +
541A ILE* 3.8 26.7 - - + -
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Residues in contact with VAL 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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432A MET* 3.8 29.8 - - + -
448A ALA* 3.9 5.2 - - + -
450A GLU* 4.0 16.8 - - + -
455A PHE* 4.2 2.2 - - + -
462A LEU* 3.9 13.0 - - + -
465A ILE* 4.6 1.6 - - + -
472A VAL* 4.3 15.5 - - + -
473A THR* 1.3 72.0 - - - +
475A ILE* 1.3 57.5 + - - +
476A ILE* 3.7 27.6 - - + -
509A MET* 5.1 1.1 - - + -
539A CYS 3.0 9.9 + - - +
540A LEU* 3.2 18.0 - - + +
541A ILE* 2.6 34.3 + - - +
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Residues in contact with ILE 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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384A VAL* 4.0 24.7 - - + -
447A ILE* 3.8 27.1 - - + -
448A ALA 2.7 16.1 + - - +
449A VAL* 3.7 7.1 - - + -
450A GLU* 2.8 30.1 + - - +
473A THR* 4.4 3.1 - - + +
474A VAL* 1.3 74.3 - - - +
476A ILE* 1.3 62.8 + - - +
477A MET* 3.7 15.3 + - - +
525A LEU* 4.3 13.2 - - + -
529A LEU* 4.1 15.5 - - + -
541A ILE* 3.4 20.4 - - + +
543A ALA* 4.1 22.2 - - + -
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Residues in contact with ILE 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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450A GLU* 3.6 5.8 - - + -
452A ASP* 3.8 29.2 - - + -
455A PHE* 3.4 46.2 - - + -
474A VAL* 3.7 13.2 - - + -
475A ILE* 1.3 70.5 - - - +
477A MET* 1.3 61.3 + - - +
478A ASN* 2.8 16.0 + - + +
505A TYR* 3.9 24.5 - - + -
540A LEU* 4.0 24.2 - - + -
541A ILE 2.9 10.5 + - - +
542A ASN* 4.1 7.6 - - - +
543A ALA* 2.9 24.0 + - - +
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Residues in contact with MET 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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377A TYR* 3.7 30.9 + - + +
380A SER* 3.4 26.9 - - - +
381A LEU* 3.8 24.0 - - + -
403A ALA* 4.0 16.2 - - + -
449A VAL* 3.9 19.3 - - + -
450A GLU 2.8 20.0 + - - +
451A GLY* 4.5 0.8 - - - -
452A ASP* 3.5 15.9 + - - +
475A ILE* 4.2 17.5 - - - +
476A ILE* 1.3 68.0 - - - +
478A ASN* 1.3 57.5 + - - +
479A ASN* 3.1 13.4 + - - +
525A LEU* 6.2 1.1 - - - -
543A ALA* 3.9 4.3 - - - -
545A ILE* 3.7 23.6 - - + -
1566A TPP 5.2 0.7 + - - +
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Residues in contact with ASN 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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452A ASP* 3.8 7.8 - - - +
476A ILE* 2.8 13.1 + - + +
477A MET* 1.3 67.9 - - - +
479A ASN* 1.3 58.6 + - - +
480A GLY 3.6 5.9 + - - -
501A THR 4.7 0.2 - - - +
502A ARG* 3.2 39.4 + - - +
503A GLY 3.0 22.0 + - - -
505A TYR* 3.5 15.5 - - - -
542A ASN* 2.8 31.5 + - - +
543A ALA 2.9 13.0 + - - +
544A MET* 3.9 8.3 - - - -
545A ILE 3.1 19.6 + - - -
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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