Contacts of the strand formed by residues 386 - 390 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378H ALA* 4.8 2.5 - - + -
379H LEU 3.6 17.0 - - - +
380H GLY* 3.9 2.2 - - - +
384H GLY 4.1 1.2 + - - -
385H LYS* 1.3 89.2 - - - +
387H TYR* 1.3 64.1 + - - +
388H VAL* 5.0 0.7 - - + -
403H THR* 3.5 13.5 - - - -
404H LEU* 3.1 35.8 + - + +
413H ILE* 4.0 11.9 - - + -
416H THR* 3.5 32.1 - - + -
425H LEU* 4.2 17.0 - - + -
427H ALA* 3.9 13.9 - - + -
437H TRP* 3.5 34.5 - - + +
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Residues in contact with TYR 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357H ASP 4.4 2.5 - - - -
358H TYR* 3.7 26.9 - + + -
359H SER* 3.0 35.9 + - - -
378H ALA* 3.4 0.7 - - - -
379H LEU* 2.9 38.7 + - + +
381H ASN* 3.6 29.9 + - + -
385H LYS* 3.7 28.0 + - + +
386H LEU* 1.3 77.6 - - - +
388H VAL* 1.3 61.4 + - - +
389H TRP* 3.3 30.1 - + + -
401H CYS* 3.7 21.8 - - + -
402H THR 4.0 2.0 - - - -
403H THR* 3.8 17.9 - - + -
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Residues in contact with VAL 388 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H LYS 3.9 4.9 - - - +
80H TYR* 5.1 4.0 - - + +
82H PHE* 3.8 31.9 - - + -
376H MET* 4.2 8.7 - - + -
377H LEU 3.2 13.5 - - - +
378H ALA* 4.2 5.4 - - + -
386H LEU* 5.0 1.3 - - + -
387H TYR* 1.3 77.6 - - - +
389H TRP* 1.3 66.0 + - - +
401H CYS* 3.7 1.4 - - - -
402H THR* 3.1 41.9 + - - +
404H LEU* 4.6 10.3 - - + -
418H PHE* 4.2 9.9 - - + -
425H LEU* 3.7 28.5 - - + -
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Residues in contact with TRP 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H LYS 4.7 2.7 - - - -
80H TYR* 4.8 0.9 - - - -
328H ILE* 4.0 20.9 - - + -
356H PHE* 3.5 48.7 - + + +
357H ASP 3.3 27.0 + - - +
358H TYR* 4.4 7.9 - + - -
376H MET* 3.3 9.2 - - - +
377H LEU* 2.8 53.7 + - + +
379H LEU* 3.9 18.8 - - + -
387H TYR* 3.3 41.3 - + + -
388H VAL* 1.3 74.7 - - - +
390H ASP* 1.3 61.8 + - - +
397H HIS* 5.5 4.5 - - + -
400H LYS 4.9 3.8 - - - -
401H CYS* 3.5 32.5 - - + +
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Residues in contact with ASP 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H LYS* 4.1 34.2 + - + +
80H TYR* 3.6 24.3 + - + -
356H PHE* 4.5 9.0 - - - -
375H LYS 3.6 7.3 - - - +
389H TRP* 1.3 78.2 - - - +
391H LEU* 1.3 70.0 + - - +
392H GLU* 3.1 18.2 + - - +
393H VAL* 3.2 41.6 + - + +
400H LYS 5.1 5.5 + - - +
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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
------------------------------------------------------------
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