Contacts of the strand formed by residues 493 - 499 (chain A) in PDB entry 3KN5
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 HIS 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A TYR* 5.9 1.6 - - - -
456A ILE* 3.7 27.9 - - + +
457A ILE 3.1 16.6 + - - +
458A SER* 3.5 16.0 - - - -
459A LYS* 2.7 22.0 + - - +
489A HIS* 3.7 0.3 - - - -
490A ASP* 2.7 32.8 + - - -
492A LEU* 1.3 103.7 + - + +
494A THR* 1.3 58.2 + - - +
495A PHE* 3.8 20.5 - + + -
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Residues in contact with THR 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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455A LYS 3.5 1.7 - - - +
456A ILE* 3.5 3.8 - - - -
457A ILE* 2.8 39.5 + - - +
458A SER 5.6 0.4 + - - -
459A LYS* 2.8 21.4 + - - +
462A GLU* 3.0 20.0 + - - +
465A THR* 4.1 12.1 - - - +
469A ILE* 4.3 2.7 - - + -
487A VAL* 4.0 6.3 - - + -
488A PHE 3.4 10.5 - - - +
489A HIS* 3.7 16.4 - - - +
493A HIS* 1.3 74.3 - - - +
495A PHE* 1.3 63.4 + - - +
496A LEU* 3.6 23.1 - - + -
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Residues in contact with PHE 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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417A SER* 4.4 2.7 - - - -
419A PHE* 3.8 42.6 - + + -
420A TYR* 4.0 24.0 - + - -
454A VAL* 4.2 3.4 - - + -
455A LYS 3.6 3.8 - - - -
456A ILE* 3.5 35.4 - - + -
486A GLU 3.7 0.9 - - - +
487A VAL* 3.3 7.1 - - - -
488A PHE* 2.8 63.0 + - + -
489A HIS 4.9 0.2 - - - -
490A ASP* 3.5 29.2 - - + -
493A HIS* 3.8 28.0 - + + -
494A THR* 1.3 73.6 - - - +
496A LEU* 1.3 65.6 + - - +
497A VAL* 4.0 0.7 - - - -
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Residues in contact with LEU 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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454A VAL* 3.3 2.6 - - - -
455A LYS* 2.9 47.1 + - + +
457A ILE* 4.3 17.5 - - + -
465A THR* 5.1 0.4 - - - +
468A GLU* 4.1 30.3 - - + +
469A ILE* 4.1 25.1 - - + -
472A LEU* 4.7 11.4 - - + -
484A LEU* 3.9 16.6 - - + -
486A GLU 3.7 3.8 - - - -
487A VAL* 4.3 3.6 - - + -
494A THR* 3.6 22.4 - - + -
495A PHE* 1.3 79.0 - - - +
497A VAL* 1.3 63.4 + - - +
498A MET* 3.6 11.9 + - - +
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Residues in contact with VAL 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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419A PHE* 3.8 33.0 - - + -
423A TYR* 4.0 27.8 - - + +
443A CYS* 4.8 0.7 - - - -
452A PHE* 3.7 35.9 - - + -
453A ALA 3.4 3.1 - - - +
454A VAL* 3.9 7.6 - - + -
484A LEU* 3.8 1.1 - - - +
485A HIS* 2.8 37.8 + - + +
486A GLU* 2.9 21.5 + - + +
488A PHE* 4.5 6.5 - - + -
496A LEU* 1.3 72.6 - - - +
498A MET* 1.3 56.5 + - - +
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Residues in contact with MET 498 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A ANP 3.9 16.2 - - - +
452A PHE* 3.4 9.4 - - - +
453A ALA* 2.8 31.2 + - + +
454A VAL 5.6 0.2 - - - -
455A LYS* 5.2 7.9 - - + +
472A LEU* 4.2 14.1 - - + -
482A VAL* 3.8 24.7 - - + -
483A LYS 3.5 25.6 - - - +
484A LEU* 3.6 32.8 - - + +
485A HIS* 3.9 3.6 - - - -
496A LEU* 4.0 19.1 - - - +
497A VAL* 1.3 74.9 - - - +
499A GLU* 1.3 73.0 + - - +
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Residues in contact with GLU 499 (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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400A ANP 2.8 24.6 + - - -
452A PHE* 4.3 3.8 - - - -
453A ALA 4.4 0.2 - - - -
482A VAL* 3.6 8.1 - - + -
483A LYS* 3.1 35.8 + - - +
485A HIS* 3.6 23.5 + - + -
498A MET* 1.3 73.9 - - - +
500A LEU* 1.3 61.2 + - - +
501A LEU* 3.4 21.2 + - + +
553A THR* 4.8 2.4 - - - +
562A LYS* 3.2 33.9 + - - +
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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