Contacts of the strand formed by residues 486 - 492 (chain A) in PDB entry 4PO2
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 LEU 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A LEU* 4.3 22.2 - - + -
442A VAL* 4.3 6.7 - - + -
456A LEU* 4.6 2.2 - - + -
478A PHE* 4.0 24.0 - - + -
479A ASP 3.3 27.4 - - - +
480A ILE* 3.8 19.7 - - + +
484A GLY 3.6 4.5 + - - +
485A ILE* 1.3 71.9 - - - +
487A ASN* 1.3 65.6 + - - +
488A VAL* 3.7 19.5 - - + -
501A ILE 3.8 0.7 - - - +
502A THR* 3.4 4.5 - - - +
503A ILE* 2.8 65.9 + - + +
504A THR 5.4 0.4 - - - +
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Residues in contact with ASN 487 (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 THR 3.5 3.1 - - - +
478A PHE* 3.8 0.3 - - - -
479A ASP* 2.8 50.1 + - + +
481A ASP* 5.3 3.6 + - - +
485A ILE* 4.1 18.8 + - - +
486A LEU* 1.3 75.7 + - - +
488A VAL* 1.3 63.1 + - - +
489A THR* 4.1 4.0 + - - +
500A LYS* 3.4 28.6 + - - +
501A ILE 3.4 2.2 - - - +
502A THR* 2.6 29.4 + - - +
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Residues in contact with VAL 488 (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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440A ILE* 4.2 11.2 - - + -
442A VAL* 4.1 10.8 - - + -
459A PHE* 3.6 16.8 - - + -
476A VAL* 4.4 5.2 - - + -
477A THR 3.3 4.0 - - - +
478A PHE* 3.6 50.9 - - + -
486A LEU* 3.7 20.0 - - + -
487A ASN* 1.3 75.7 - - - +
489A THR* 1.3 61.4 + - - +
500A LYS* 3.1 4.7 - - - +
501A ILE* 2.9 46.3 + - + -
503A ILE* 4.9 0.2 - - + -
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Residues in contact with THR 489 (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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459A PHE* 4.3 1.8 - - - -
475A GLU 3.6 1.3 - - - +
476A VAL* 3.3 5.5 - - - +
477A THR* 2.9 44.5 + - - +
487A ASN* 4.7 4.2 + - - +
488A VAL* 1.3 79.1 + - - +
490A ALA* 1.3 64.2 + - - +
491A THR* 3.8 18.2 - - - +
498A ALA* 4.3 8.5 - - + -
499A ASN 3.4 11.2 - - - +
500A LYS* 3.7 21.9 + - + +
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Residues in contact with ALA 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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440A ILE* 3.9 23.1 - - + -
459A PHE* 3.8 20.8 - - + -
461A LEU* 3.8 17.8 - - + +
474A ILE* 4.3 6.1 - - + -
475A GLU 3.4 4.3 - - - +
476A VAL* 4.4 3.1 - - + -
489A THR* 1.3 73.4 - - - +
491A THR* 1.3 62.2 + - - +
498A ALA* 3.1 4.7 - - - +
499A ASN 2.9 32.4 + - - -
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Residues in contact with THR 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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461A LEU* 3.9 4.0 - - - +
474A ILE* 3.5 2.9 - - - +
475A GLU* 2.9 55.2 + - + +
489A THR* 3.8 10.2 - - - +
490A ALA* 1.3 76.2 + - - +
492A ASP* 1.3 73.4 + - - +
493A LYS* 3.4 6.0 + - + -
496A GLY* 3.7 19.5 - - - +
497A LYS 3.3 10.1 - - - +
498A ALA* 3.6 10.2 - - + +
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Residues in contact with ASP 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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461A LEU* 3.7 9.3 - - + +
462A SER 5.1 0.5 - - - +
463A GLY 4.3 4.0 - - - +
464A ILE* 3.8 30.8 + - - +
465A PRO* 3.9 4.5 - - - +
472A PRO* 5.8 1.7 - - - +
473A GLN 4.3 4.0 + - - +
474A ILE* 4.0 16.9 - - + +
491A THR* 1.3 71.6 - - - +
493A LYS* 1.3 55.5 + - - +
494A SER* 2.6 33.7 + - - -
495A THR* 3.8 12.5 + - - +
496A GLY* 2.6 36.0 + - - -
497A LYS* 2.7 20.9 + - + +
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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