Contacts of the strand formed by residues 493 - 499 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420B TYR* 5.6 3.1 - - - -
456B ILE* 3.6 27.8 - - + +
457B ILE 3.3 6.4 + - - +
458B SER* 3.7 22.0 - - - -
459B LYS* 2.8 19.5 + - - +
489B HIS* 3.6 0.5 - - - -
490B ASP* 2.6 30.6 + - - +
492B LEU* 1.3 104.4 + - + +
494B THR* 1.3 59.3 + - - +
495B PHE* 3.8 24.7 - + + -
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Residues in contact with THR 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B LYS 3.3 4.9 - - - +
456B ILE* 3.4 1.7 - - - -
457B ILE* 2.8 40.3 + - - +
459B LYS* 2.9 19.6 + - - +
462B GLU* 3.0 23.6 + - - -
465B THR* 4.0 12.6 - - - +
469B ILE* 4.4 2.5 - - + -
487B VAL* 4.2 7.6 - - + -
488B PHE 3.4 11.0 - - - +
489B HIS* 3.7 12.2 - - - +
493B HIS* 1.3 74.0 - - - +
495B PHE* 1.3 63.9 + - - +
496B LEU* 3.5 24.7 - - + -
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Residues in contact with PHE 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B SER* 4.8 2.2 - - - -
419B PHE* 3.6 42.0 - + + -
420B TYR* 4.1 24.0 - + - -
454B VAL* 3.8 9.2 - - + -
455B LYS 3.5 4.3 - - - -
456B ILE* 3.8 31.4 - - + -
486B GLU 3.8 0.7 - - - +
487B VAL* 3.3 7.6 - - - +
488B PHE* 2.8 60.9 + - + +
489B HIS 4.8 0.7 - - - -
490B ASP* 3.7 31.0 - - + -
493B HIS* 3.8 25.4 - + + -
494B THR* 1.3 73.0 - - - +
496B LEU* 1.3 64.6 + - - +
497B VAL* 3.9 0.4 - - + -
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B VAL* 3.3 3.9 - - - -
455B LYS* 2.9 42.3 + - + +
457B ILE* 3.9 18.6 - - + -
465B THR* 5.0 1.8 - - - +
468B GLU* 3.7 34.5 - - + +
469B ILE* 4.1 21.1 - - + -
472B LEU* 4.5 10.8 - - + -
484B LEU* 3.9 15.7 - - + -
486B GLU 3.8 4.3 - - - -
487B VAL* 4.7 2.7 - - + -
494B THR* 3.5 29.4 - - + -
495B PHE* 1.3 73.5 - - - +
497B VAL* 1.3 61.4 + - - +
498B MET* 3.4 11.9 + - - +
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Residues in contact with VAL 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B PHE* 4.1 17.9 - - + -
423B TYR* 3.8 22.9 - - + +
443B CYS* 4.6 3.8 - - - -
452B PHE* 3.6 33.4 - - + -
453B ALA 3.5 4.7 - - - +
454B VAL* 4.4 2.9 - - + -
484B LEU* 3.6 1.7 - - - +
485B HIS* 2.8 36.5 + - - +
486B GLU* 2.9 24.1 + - + +
488B PHE* 3.8 29.8 - - + -
495B PHE 4.8 0.9 - - - +
496B LEU* 1.3 72.3 - - - +
498B MET* 1.3 52.6 + - - +
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Residues in contact with MET 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B ANP 3.8 22.9 - - - +
452B PHE* 3.3 11.1 - - - +
453B ALA* 2.7 39.6 + - + +
454B VAL 5.4 0.2 - - - -
455B LYS* 5.0 9.2 - - + +
472B LEU* 4.3 12.3 - - + -
482B VAL* 3.8 25.1 - - + -
483B LYS 3.2 28.7 - - - +
484B LEU* 3.6 28.5 - - + +
485B HIS* 5.1 0.4 - - - -
496B LEU* 3.8 21.1 - - + +
497B VAL* 1.3 73.9 - - - +
499B GLU* 1.3 60.3 + - - +
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Residues in contact with GLU 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B ANP 2.5 31.0 + - - -
452B PHE* 4.4 11.2 - - + -
482B VAL* 3.6 10.3 - - + -
483B LYS* 2.9 42.2 + - + +
485B HIS* 5.1 2.4 - - - +
498B MET* 1.3 70.7 - - - +
500B LEU* 1.3 55.2 + - - +
501B LEU* 3.5 22.0 + - + +
553B THR* 5.2 1.6 - - - +
562B LYS* 3.0 27.5 + - - +
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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