Contacts of the strand formed by residues 350 - 357 (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 VAL 350 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165J PHE* 4.7 5.2 - - + -
167J ASN* 2.8 44.0 + - + +
169J GLU* 3.6 6.4 - - - +
299K PHE* 4.0 16.8 - - + -
301K THR* 3.8 22.9 - - + +
303K ASP* 4.4 14.8 - - + +
304K ILE* 3.9 28.3 - - + -
331K TRP* 4.3 2.2 - - + -
332K LYS 3.5 9.2 - - - +
334K GLY 3.0 6.0 - - - +
348K SER 5.0 2.2 - - - +
349K ASN* 1.3 77.2 - - - +
351K THR* 1.3 69.7 + - - +
352K ILE* 5.1 0.4 - - + -
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Residues in contact with THR 351 (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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34J ARG* 4.5 12.3 - - - +
165J PHE* 6.3 0.2 - - - -
167J ASN* 4.9 1.1 - - - +
169J GLU* 4.0 9.3 + - - +
331K TRP* 3.4 0.3 - - - -
332K LYS* 2.9 44.7 + - - +
334K GLY 2.7 15.1 + - - -
335K LYS* 3.2 1.6 - - - -
336K MET* 3.2 47.5 + - + +
350K VAL* 1.3 82.3 + - - +
352K ILE* 1.3 67.3 + - - +
353K LEU* 3.4 12.5 - - + +
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Residues in contact with ILE 352 (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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27J ARG* 5.7 2.5 - - - +
34J ARG* 5.6 3.1 - - - +
38J VAL* 5.2 2.4 - - - +
165J PHE* 3.7 36.5 - - + -
304K ILE* 3.5 23.6 - - + +
329K VAL* 3.5 27.4 - - + -
330K CYS 3.9 2.0 - - - -
331K TRP* 3.4 21.5 - - + -
350K VAL* 5.1 0.4 - - + -
351K THR* 1.3 76.7 - - - +
353K LEU* 1.3 63.8 + - - +
354K GLY* 3.7 10.5 - - - +
355K ARG* 3.5 24.0 - - - +
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Residues in contact with LEU 353 (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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38J VAL* 4.3 20.2 - - + +
41J MET* 5.1 6.7 - - + -
42J PHE* 3.9 28.4 - - + -
318K LEU* 3.3 48.9 - - + -
330K CYS* 3.0 14.6 + - - +
331K TRP* 4.4 2.5 - - - -
332K LYS* 4.5 1.3 - - + -
336K MET* 3.5 34.1 - - + -
351K THR* 3.4 25.1 - - + +
352K ILE* 1.3 77.4 - - - +
354K GLY* 1.3 59.2 + - - +
396K PRO* 4.2 12.0 - - - +
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Residues in contact with GLY 354 (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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329K VAL* 3.6 5.2 - - - +
330K CYS* 3.3 30.4 + - - +
352K ILE* 3.7 4.8 - - - +
353K LEU* 1.3 79.3 - - - +
355K ARG* 1.3 67.8 + - - +
356K PHE* 5.5 0.2 - - - -
396K PRO* 4.8 7.9 - - - -
397K HIS* 4.1 18.6 - - - -
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Residues in contact with ARG 355 (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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27J ARG* 3.7 22.9 - - - +
165J PHE* 4.5 23.6 - - - +
304K ILE 5.2 5.3 + - - -
327K ALA* 4.5 9.3 - - + +
328K ILE 3.5 5.8 - - - +
329K VAL* 4.1 24.2 - - + +
352K ILE* 3.5 24.6 - - - +
354K GLY* 1.3 75.9 - - - +
356K PHE* 1.3 63.5 + - - +
357K ASP* 3.9 20.5 + - - +
397K HIS* 2.7 37.5 + - - +
398K LYS 4.0 1.4 + - - +
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Residues in contact with PHE 356 (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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42J PHE* 6.0 1.8 - + - -
315K LEU* 5.8 2.5 - - + -
320K LEU* 3.8 23.8 - - + -
327K ALA* 3.2 6.6 - - - -
328K ILE* 2.8 56.9 + - + +
330K CYS* 4.6 8.3 - - + -
355K ARG* 1.3 71.9 - - - +
357K ASP* 1.3 62.0 + - - +
358K TYR* 3.7 4.7 - - - -
377K LEU* 4.1 8.7 - - + -
389K TRP* 3.3 54.7 - + + +
390K ASP 4.7 6.5 - - - -
391K LEU* 4.1 19.5 - - + -
397K HIS* 3.5 42.4 - + + -
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Residues in contact with ASP 357 (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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326K ASN 3.9 5.6 - - - +
327K ALA* 4.4 6.5 - - - +
355K ARG* 4.0 23.6 - - - +
356K PHE* 1.3 71.5 - - - +
358K TYR* 1.3 60.4 + - - +
387K TYR* 4.6 5.0 - - - -
389K TRP* 3.6 15.9 + - - +
398K LYS* 3.9 28.1 + - - +
401K CYS* 5.3 2.1 - - - +
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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