Contacts of the strand formed by residues 215 - 219 (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 215 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207K LEU* 4.0 17.3 - - + -
208K SER 3.2 9.2 - - - +
209K VAL* 3.4 29.6 - - + -
214K ALA* 1.3 74.2 - - - +
216K ARG* 1.3 61.4 + - - +
228K ILE* 3.4 6.9 - - - +
229K PHE* 2.7 61.0 + - + +
235K HIS* 4.0 10.1 - - + -
239K VAL* 3.8 12.6 - - + -
242K ALA* 4.0 5.4 - - + -
251K ILE* 4.3 8.1 - - + -
253K SER* 3.5 33.7 - - - +
263K TRP* 4.3 6.3 - - + +
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Residues in contact with ARG 216 (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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188K GLY* 3.5 38.2 + - - -
189K HIS* 3.5 20.6 + - + +
190K GLY 5.0 0.8 - - - +
207K LEU* 3.3 6.8 - - - +
208K SER* 2.8 38.3 + - - +
212K ASP* 4.5 10.9 + - - -
214K ALA* 5.1 1.8 - - + +
215K LEU* 1.3 78.0 - - - +
217K LEU* 1.3 59.7 + - - +
218K TRP* 3.4 31.2 - - - +
225K LEU* 3.4 34.1 - - + +
227K ALA 3.5 3.1 - - - -
228K ILE* 3.8 29.1 - - + +
569L ASP 4.5 3.6 + - - -
570L THR* 3.9 3.6 - - - +
571L CYS* 3.8 21.4 - - - +
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Residues in contact with LEU 217 (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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199K HIS* 5.7 0.2 - - + -
205K LEU* 4.2 17.0 - - + -
206K LEU 3.4 11.9 - - - +
207K LEU* 4.2 5.2 - - + +
216K ARG* 1.3 72.6 - - - +
218K TRP* 1.3 58.0 + - - +
225K LEU* 3.3 3.5 - - - +
226K VAL* 2.8 39.8 + - + +
227K ALA 3.0 12.6 + - - +
229K PHE* 3.9 19.8 - - + -
244K TYR* 3.1 32.1 - - + +
251K ILE* 5.2 2.0 - - + -
265K ILE* 4.9 9.2 - - + -
270K MET* 3.9 26.2 - - + -
274K ILE* 4.1 22.7 - - + -
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Residues in contact with TRP 218 (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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172K ILE* 3.6 21.3 - - + +
186K TYR* 4.0 36.6 - + + -
188K GLY* 4.0 28.5 - - - -
189K HIS* 4.2 9.9 - - - -
204K ASN 3.4 0.3 - - - +
205K LEU* 3.3 10.0 - - - +
206K LEU* 2.8 47.0 + - + +
208K SER* 3.0 21.0 + - - -
216K ARG* 3.4 36.3 - - + +
217K LEU* 1.3 76.3 - - - +
219K ASN* 1.3 64.1 + - - +
220K ILE* 3.7 11.7 - - + -
223K ASP 5.9 0.4 - - - -
224K THR 3.4 8.1 - - - +
225K LEU* 4.1 20.4 - - + -
226K VAL* 3.9 4.7 - - - +
572L LEU* 4.1 25.6 - - + -
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Residues in contact with ASN 219 (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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186K TYR* 5.0 0.4 - - - -
204K ASN* 3.5 7.2 - - - +
205K LEU* 4.0 4.9 - - + +
218K TRP* 1.3 71.0 - - - +
220K ILE* 1.3 59.2 + - - +
221K GLN* 3.2 13.7 + - - +
222K THR* 3.2 15.0 + - - -
223K ASP* 3.0 23.6 + - - -
224K THR* 2.8 28.1 + - - +
226K VAL* 3.6 5.5 - - + +
277K SER* 2.8 25.0 + - - +
278K TYR* 3.1 46.8 - - - +
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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