Contacts of the strand formed by residues 483 - 489 (chain S) in PDB entry 1K4U
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 ILE 483 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461S GLN* 5.3 13.2 - - + +
462S VAL 5.4 1.1 - - - +
463S GLU* 4.0 22.4 - - + +
481S GLY 5.8 0.2 - - - -
482S ASP* 1.3 90.3 + - - +
484S ILE* 1.3 65.6 + - - +
485S LEU 4.0 0.2 + - - -
499S SER* 4.7 3.1 + - - -
514S SER* 6.1 0.7 - - - -
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Residues in contact with ILE 484 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461S GLN* 4.4 4.3 - - - +
462S VAL 4.2 23.3 + - - +
464S ALA* 3.7 28.3 - - + -
476S LEU* 3.6 27.6 - - + -
478S PHE* 3.8 26.9 - - + -
482S ASP* 3.0 28.2 + - + +
483S ILE* 1.3 81.0 - - - +
485S LEU* 1.3 75.9 + - - +
486S VAL* 3.5 5.1 + - - +
498S GLU 4.5 1.1 - - - +
499S SER* 3.9 21.1 - - - +
506S PHE* 4.0 21.1 - - + -
511S VAL* 4.7 3.1 - - + -
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Residues in contact with LEU 485 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458S LYS* 3.9 21.1 - - + -
459S GLY 4.6 1.1 - - - +
460S SER 3.4 9.6 - - - +
461S GLN* 5.3 2.7 - - + +
483S ILE 4.0 0.2 + - - -
484S ILE* 1.3 78.4 - - - +
486S VAL* 1.3 72.7 + - - +
487S LEU* 3.1 32.7 + - + -
498S GLU* 3.3 45.9 + - + +
499S SER* 4.6 1.6 + - - -
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Residues in contact with VAL 486 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459S GLY 3.3 0.2 - - - -
460S SER* 2.5 51.3 + - - +
461S GLN* 3.2 22.4 - - - +
462S VAL* 3.2 36.6 - - + +
484S ILE 3.7 1.5 - - - +
485S LEU* 1.3 73.0 - - - +
487S LEU* 1.3 55.0 + - - +
488S SER 3.5 19.7 - - - +
495S LEU* 3.1 32.3 - - + -
496S GLU 3.5 5.4 - - - +
506S PHE* 4.1 4.5 - - + -
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Residues in contact with LEU 487 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379P SER* 4.0 15.3 - - - +
457S LYS* 5.6 5.8 - - + +
458S LYS* 5.1 4.5 - - - -
459S GLY* 3.2 27.3 - - - +
485S LEU* 3.1 29.7 + - + -
486S VAL* 1.3 73.0 - - - +
488S SER* 1.3 63.9 + - - +
496S GLU* 2.7 51.4 + - + +
498S GLU* 3.7 27.1 - - + +
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Residues in contact with SER 488 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377P ARG* 4.3 11.5 - - - -
378P CYS* 5.8 0.7 - - - -
459S GLY* 4.8 1.1 - - - -
460S SER* 4.6 10.1 - - - -
486S VAL* 3.3 9.5 - - - +
487S LEU* 1.3 85.5 + - - +
489S LYS* 1.3 70.6 + - - +
495S LEU* 2.8 22.8 - - - +
496S GLU* 2.9 12.5 + - - +
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Residues in contact with LYS 489 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377P ARG* 3.2 22.0 - - - +
460S SER* 5.5 0.4 + - - -
488S SER* 1.3 80.8 + - - +
490S VAL* 1.3 62.1 + - - +
491S ASN* 4.4 3.1 - - - +
492S GLU* 3.7 42.9 - - - +
494S TRP 4.3 2.2 - - - +
495S LEU* 3.8 10.3 - - + -
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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