Contacts of the strand formed by residues 436 - 442 (chain A) in PDB entry 4DKK
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 PHE 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A PHE 4.2 8.5 - - - +
429A PRO* 5.4 0.7 - - + -
430A LYS* 3.7 52.3 - - + +
434A ASN 4.2 1.3 - - - -
435A GLU* 1.3 77.2 - - - +
437A VAL* 1.3 66.3 + - - +
438A SER* 5.6 0.4 - - - +
453A ILE* 3.2 5.5 - - - +
454A GLY 2.8 33.1 + - - +
455A LYS 3.4 19.1 - - - -
456A ASP* 3.4 26.7 - - + +
457A VAL* 3.4 27.8 - - + +
460A CYS* 3.2 15.1 - - - -
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Residues in contact with VAL 437 (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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427A ASP* 3.7 0.5 - - - +
428A PHE* 3.0 55.4 + - + +
429A PRO 5.4 0.8 + - - -
431A ASN* 5.1 7.4 - - + +
435A GLU* 4.8 9.4 - - + +
436A PHE* 1.3 82.0 - - - +
438A SER* 1.3 73.1 + - - +
439A LEU* 5.8 2.0 - - + -
451A HIS* 5.1 7.0 - - + -
452A GLY 3.5 9.4 - - - +
453A ILE* 4.1 17.9 - - + -
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Residues in contact with SER 438 (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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425A TYR* 5.1 1.3 - - - -
426A LYS 3.2 5.6 - - - -
427A ASP* 2.7 28.3 + - - +
428A PHE* 5.0 0.7 - - - -
436A PHE* 5.6 0.5 - - - +
437A VAL* 1.3 79.0 + - - +
439A LEU* 1.3 67.0 + - - +
451A HIS* 3.1 7.6 - - - +
452A GLY 2.9 30.8 + - - -
457A VAL* 4.2 2.9 - - - +
460A CYS* 3.3 28.2 - - - +
461A HIS* 3.6 11.9 - - - -
464A ALA* 5.4 0.9 - - - -
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Residues in contact with LEU 439 (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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425A TYR* 3.2 8.7 - - - +
426A LYS* 2.7 47.6 + - + +
428A PHE* 4.4 27.1 - - + -
437A VAL* 5.8 2.0 - - + -
438A SER* 1.3 75.5 - - - +
440A ILE* 1.3 61.0 + - - +
449A ILE* 4.5 17.3 - - + -
450A SER 3.4 13.2 - - - +
451A HIS* 4.0 13.2 - - + -
464A ALA* 5.1 0.7 - - - -
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Residues in contact with ILE 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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412A LEU* 3.6 31.4 - - + -
423A VAL* 3.7 10.5 - - + -
424A GLU 3.5 11.0 - - - +
425A TYR* 3.4 31.2 - - + +
439A LEU* 1.3 75.5 - - - +
441A ASN* 1.3 63.5 + - - +
442A CYS* 4.6 1.1 - - - -
448A LEU 3.7 0.3 - - - +
449A ILE* 3.2 10.5 - - - +
450A SER* 2.9 51.4 + - - +
451A HIS 4.5 0.2 - - - +
464A ALA* 3.6 22.2 - - + -
465A ALA* 3.9 9.4 - - - -
468A ILE* 3.7 11.9 - - + -
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Residues in contact with ASN 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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422A GLN* 3.5 3.1 + - - +
423A VAL* 3.3 6.1 - - - +
424A GLU* 2.8 39.7 + - + +
440A ILE* 1.3 73.1 - - - +
442A CYS* 1.3 77.1 + - - +
443A SER* 4.0 8.3 - - - +
447A PRO* 3.3 25.2 - - - +
448A LEU 3.5 2.5 - - - -
449A ILE* 3.4 16.5 - - + +
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Residues in contact with CYS 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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412A LEU* 4.0 5.4 - - - -
421A PHE* 4.3 12.3 - - + -
422A GLN 3.4 4.3 - - - +
423A VAL* 3.7 25.1 - - - -
440A ILE* 4.6 1.3 - - - -
441A ASN* 1.3 79.1 + - - +
443A SER* 1.3 67.3 + - - +
444A SER* 3.4 0.7 + - - -
447A PRO* 3.5 3.3 - - - +
448A LEU* 2.8 46.2 + - + +
468A ILE* 3.4 38.8 - - + -
472A LEU* 5.9 0.4 - - + -
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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