Contacts of the strand formed by residues 439 - 446 (chain A) in PDB entry 3KK2
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 THR 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A ALA 3.2 8.4 + - - -
438A GLU* 1.3 72.3 - - - +
440A PHE* 1.3 61.9 + - - +
441A TYR* 3.5 24.7 + - + +
459A THR* 3.1 5.7 - - - -
460A ASN* 2.7 44.5 + - - -
494A ASN* 3.5 16.9 + - + +
496A VAL* 4.4 4.9 - - + -
287B LYS 3.9 0.4 - - - +
288B ALA* 3.4 5.5 - - - +
289B LEU* 3.0 49.7 + - + -
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Residues in contact with PHE 440 (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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438A GLU* 3.3 34.8 - - + -
439A THR* 1.3 74.1 - - - +
441A TYR* 1.3 59.5 + - - +
442A VAL* 3.8 4.4 + - + -
457A TYR* 3.8 24.7 - + + -
458A VAL 3.8 1.8 - - - -
459A THR* 3.4 21.8 - - + +
463A ARG* 4.0 1.6 - - - -
485A ALA* 3.4 40.2 - - + -
488A ASP 3.6 11.9 - - - -
489A SER* 3.5 28.5 - - - -
493A VAL* 3.4 19.3 - - + -
494A ASN 2.6 14.4 + - - +
495A ILE* 3.4 3.3 - - + +
496A VAL* 2.6 34.3 + - - +
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Residues in contact with TYR 441 (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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439A THR* 3.5 20.0 - - + -
440A PHE* 1.3 72.4 - - - +
442A VAL* 1.3 61.0 + - - +
457A TYR* 3.0 3.5 - - - -
458A VAL* 2.7 48.2 + - + +
460A ASN* 5.0 1.3 - - + -
496A VAL* 3.6 27.8 - - + +
542A ILE 5.2 0.9 - - - -
543A GLY 4.5 0.7 + - - -
544A GLY* 3.5 48.0 + - - +
545A ASN* 3.9 4.5 - - - -
548A VAL* 3.4 7.2 - - + +
254B VAL* 4.0 3.1 - - - +
258B GLN* 3.2 31.1 + - - -
286B THR* 4.1 18.4 - - - -
287B LYS 2.7 32.2 + - - -
289B LEU* 3.8 5.4 - - - +
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Residues in contact with VAL 442 (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 PHE* 4.2 2.7 - - + -
441A TYR* 1.3 78.5 - - - +
443A ASP* 1.3 67.3 + - - +
456A GLY 3.4 3.6 - - - +
457A TYR* 3.7 12.3 - - + -
478A GLU* 4.3 2.5 - - + +
481A ALA* 3.8 19.3 - - + +
482A ILE* 4.1 12.6 - - + -
485A ALA* 3.7 29.8 - - + -
495A ILE* 3.8 16.8 - - + -
496A VAL 2.8 24.7 + - - +
497A THR* 3.8 26.1 - - - +
498A ASP 4.5 0.9 + - - -
545A ASN* 4.5 6.1 + - - -
548A VAL* 3.8 3.8 - - - +
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Residues in contact with ASP 443 (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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442A VAL* 1.3 78.6 - - - +
444A GLY* 1.3 72.4 + - - +
456A GLY 3.0 30.9 + - - +
478A GLU* 2.4 13.0 - - - +
481A ALA* 3.3 10.6 - - - +
498A ASP* 3.1 11.6 - - - +
545A ASN* 4.0 1.9 + - - +
548A VAL* 3.6 19.0 - - + +
549A ASP* 3.0 36.7 - - - +
552A VAL* 3.5 14.6 - - + +
601A MG 2.2 29.1 - - - -
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Residues in contact with GLY 444 (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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443A ASP* 1.3 91.9 + - - +
445A ALA* 1.3 62.4 + - - +
454A LYS 3.4 10.1 - - - -
474A ASN* 4.5 2.8 + - - -
477A THR* 3.2 27.1 - - - -
478A GLU* 3.4 16.9 + - - +
552A VAL* 3.8 4.4 - - - +
601A MG 3.7 1.9 - - - -
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Residues in contact with ALA 445 (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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444A GLY* 1.3 73.5 - - - +
446A ALA* 1.3 61.1 + - - +
452A LEU 4.2 0.2 - - - +
453A GLY* 3.2 3.3 - - - -
454A LYS 3.1 32.0 + - - +
474A ASN* 3.6 9.0 - - - +
477A THR* 3.2 5.2 + - - +
552A VAL* 3.5 28.1 - - + +
553A SER* 4.4 10.1 - - - +
555A GLY* 5.8 6.3 - - - +
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Residues in contact with ALA 446 (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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445A ALA* 1.3 76.8 - - - +
447A ASN* 1.3 66.8 + - - +
448A ARG* 3.3 10.5 + - - +
452A LEU 3.5 5.2 - - - +
472A THR* 4.0 12.1 - - + +
473A THR* 3.5 10.5 - - - -
474A ASN* 2.9 41.9 + - - +
477A THR* 3.8 7.6 - - + -
555A GLY* 5.2 3.9 - - - +
723T C 5.5 1.2 - - - +
724T T 5.0 5.0 + - - -
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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