Contacts of the strand formed by residues 239 - 244 (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 239 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194K ASN* 3.2 15.8 + - - -
209K VAL* 3.6 26.5 - - + +
210K SER 3.0 22.7 + - - +
213K HIS 3.5 28.9 - - - +
214K ALA 3.9 4.9 - - - +
215K LEU* 3.8 15.9 - - + -
235K HIS* 3.5 27.1 - - + -
237K ASP 3.3 0.4 + - - -
238K GLU* 1.3 70.1 - - - +
240K LEU* 1.3 60.3 + - - +
241K SER 3.8 8.5 - - - +
253K SER* 4.0 5.4 - - - -
254K CYS 3.4 16.4 - - - +
255K GLY* 4.1 0.9 - - - -
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Residues in contact with LEU 240 (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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194K ASN* 3.5 28.4 - - + +
195K GLU* 3.7 2.4 - - - +
209K VAL* 4.0 2.2 - - - -
238K GLU* 3.4 18.4 + - + +
239K VAL* 1.3 74.3 - - - +
241K SER* 1.3 61.0 + - - +
254K CYS 3.0 4.9 + - - -
255K GLY* 4.0 0.2 - - - -
256K MET* 3.7 23.6 - - + +
308K TYR* 4.0 8.7 - - + -
309K VAL 3.5 25.1 - - - +
310K ASP* 3.8 22.8 - - + +
364K TRP* 3.5 34.1 - - + -
365K TYR* 4.9 3.6 - - + -
367K ARG* 3.1 27.8 + - - +
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Residues in contact with SER 241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195K GLU* 2.5 23.0 + - - -
209K VAL* 4.1 7.0 - - - -
239K VAL* 3.7 3.2 - - - +
240K LEU* 1.3 79.3 - - - +
242K ALA* 1.3 69.2 + - - +
253K SER* 3.2 3.5 - - - -
254K CYS* 2.9 36.1 + - - +
310K ASP 3.5 16.4 - - - -
311K CYS* 3.5 11.6 - - - -
312K VAL* 3.4 15.4 + - - -
313K ARG* 3.6 7.8 + - - -
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Residues in contact with ALA 242 (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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195K GLU* 3.8 5.6 + - + +
197K LYS* 3.2 26.2 + - + +
207K LEU* 4.1 6.7 - - + -
209K VAL* 3.6 23.6 - - + +
215K LEU* 4.0 6.1 - - + -
241K SER* 1.3 82.2 + - - +
243K ASP* 1.3 61.2 + - - +
251K ILE* 4.1 6.7 - - + -
252K MET 3.1 13.9 - - - +
253K SER* 3.7 9.0 - - - -
312K VAL* 3.6 6.9 - - - +
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Residues in contact with ASP 243 (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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197K LYS* 3.6 25.0 + - - +
207K LEU* 5.2 0.7 - - - -
242K ALA* 1.3 74.8 - - - +
244K TYR* 1.3 87.9 + - - +
251K ILE* 3.4 6.1 - - - -
252K MET 2.8 30.6 + - - +
312K VAL* 3.4 16.3 - - + +
313K ARG* 3.3 32.1 - - - +
314K TRP* 3.3 16.2 + - + +
374K GLN* 5.9 0.5 + - - -
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Residues in contact with TYR 244 (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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197K LYS* 3.9 13.5 - - + -
198K PHE 3.4 27.4 - - - +
199K HIS* 3.5 34.3 - + - -
200K PRO* 3.9 13.0 - - + -
205K LEU 3.3 9.9 + - - -
207K LEU* 3.1 30.6 - - + +
217K LEU* 3.1 28.1 - - + +
243K ASP* 1.3 99.3 + - - +
245K ASP* 1.3 73.6 + - - +
248K GLY* 4.6 3.1 - - - -
250K LYS 3.4 8.3 - - - +
251K ILE* 3.9 14.4 - - + +
265K ILE* 3.8 17.5 - - + -
314K TRP* 3.3 4.8 - - - +
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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