Contacts of the strand formed by residues 386 - 390 (chain K) in PDB entry 5LS6
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 LEU 386 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378K ALA* 4.6 0.7 - - + -
379K LEU 3.9 3.1 - - - +
380K GLY* 4.2 4.7 - - - +
384K GLY 3.7 3.0 + - - +
385K LYS* 1.3 78.8 - - - +
387K TYR* 1.3 70.8 + - - +
403K THR* 3.6 4.0 - - - -
404K LEU* 3.1 49.2 + - + +
413K ILE* 4.0 14.6 - - + -
416K THR* 3.7 29.8 - - + -
425K LEU* 4.0 19.5 - - + -
427K ALA* 3.7 19.1 - - + -
437K TRP* 3.4 38.6 - - + +
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Residues in contact with TYR 387 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357K ASP 4.6 3.1 - - - -
358K TYR* 3.6 28.0 - + + -
359K SER* 2.9 37.3 + - - -
378K ALA* 3.4 2.1 - - - +
379K LEU* 3.1 39.3 + - + +
381K ASN* 3.8 25.6 - - + -
385K LYS* 3.5 29.4 + - + +
386K LEU* 1.3 72.7 - - - +
388K VAL* 1.3 69.9 + - - +
389K TRP* 3.5 26.0 - + + -
401K CYS* 3.6 20.0 - - + -
402K THR 4.1 0.7 - - - -
403K THR* 4.0 20.4 - - + +
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Residues in contact with VAL 388 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K LYS 4.1 2.8 - - - +
80K TYR* 5.2 4.9 - - + +
82K PHE* 4.2 25.1 - - + -
376K MET* 4.4 15.7 - - + -
377K LEU 3.2 12.1 - - - +
378K ALA* 4.5 4.5 - - + -
386K LEU* 4.8 0.7 - - + -
387K TYR* 1.3 79.6 - - - +
389K TRP* 1.3 68.2 + - - +
401K CYS* 3.0 12.6 - - - -
402K THR* 2.8 46.3 + - - +
404K LEU* 4.4 11.2 - - + -
418K PHE* 4.7 2.9 - - + -
425K LEU* 4.2 24.9 - - + -
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Residues in contact with TRP 389 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K LYS 5.1 2.2 - - - -
80K TYR* 5.0 1.0 - - - -
328K ILE* 4.2 9.2 - - + -
356K PHE* 3.3 54.3 - + + +
357K ASP 3.6 24.9 + - - +
358K TYR* 4.1 17.9 - + + -
376K MET* 3.3 8.5 - - - +
377K LEU* 2.9 58.1 + - + +
379K LEU* 3.9 21.3 - - + -
387K TYR* 3.5 34.5 - + + -
388K VAL* 1.3 77.9 - - - +
390K ASP* 1.3 61.0 + - - +
397K HIS* 5.4 4.7 - - + -
400K LYS* 4.8 4.3 - - - -
401K CYS* 3.4 29.4 - - + +
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Residues in contact with ASP 390 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K LYS* 4.7 21.7 + - + +
80K TYR* 3.1 35.4 + - + -
356K PHE* 4.7 6.6 - - - -
375K LYS 3.3 9.0 - - - +
389K TRP* 1.3 76.2 - - - +
391K LEU* 1.3 62.2 + - - +
392K GLU* 3.4 15.7 + - - +
393K VAL* 3.2 47.7 + - + +
397K HIS* 5.5 0.7 + - - +
400K LYS 5.1 6.1 + - - +
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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