Contacts of the strand formed by residues 215 - 219 (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 215 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H HIS* 4.4 0.4 - - - -
207H LEU* 4.0 24.2 - - + -
208H SER 3.1 11.2 - - - +
209H VAL* 3.3 30.3 - - + -
214H ALA* 1.3 77.4 - - - +
216H ARG* 1.3 68.7 + - - +
228H ILE* 3.6 2.9 - - - +
229H PHE* 2.9 52.7 + - + +
235H HIS* 4.3 5.4 - - + -
239H VAL* 3.8 18.2 - - + -
242H ALA* 4.0 2.7 - - + -
251H ILE* 4.6 5.8 - - + -
253H SER* 4.0 25.6 - - - +
263H TRP* 4.4 6.1 - - + +
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Residues in contact with ARG 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188H GLY* 2.9 43.0 + - - -
189H HIS* 3.5 24.5 - - - +
190H GLY* 4.4 4.0 - - - +
206H LEU 3.4 0.3 - - - +
207H LEU* 3.7 4.2 - - - -
208H SER* 2.7 49.3 + - - +
212H ASP* 4.5 5.7 + - - -
214H ALA* 5.2 2.1 - - + +
215H LEU* 1.3 78.8 - - - +
217H LEU* 1.3 59.0 + - - +
218H TRP* 3.2 30.4 - - - +
225H LEU* 3.7 30.8 - - + +
227H ALA 3.4 4.0 - - - -
228H ILE* 4.3 22.9 - - + +
569I ASP 5.0 1.6 + - - -
570I THR* 3.9 3.8 - - - +
571I CYS* 3.7 23.0 - - - +
572I LEU* 4.6 0.2 - - - +
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Residues in contact with LEU 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205H LEU* 4.2 17.5 - - + -
206H LEU 3.6 8.5 - - - +
207H LEU* 4.3 7.0 - - + -
216H ARG* 1.3 70.8 - - - +
218H TRP* 1.3 53.4 + - - +
225H LEU* 3.4 2.1 - - - +
226H VAL* 2.8 41.9 + - + +
227H ALA 2.8 15.6 + - - +
229H PHE* 3.5 23.7 - - + -
244H TYR* 3.1 31.2 - - + +
251H ILE* 5.3 1.8 - - + -
265H ILE* 4.9 8.7 - - + -
270H MET* 3.8 28.3 - - + -
274H ILE* 4.2 20.6 - - + -
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Residues in contact with TRP 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H ILE* 3.5 24.8 - - + +
186H TYR* 4.0 33.7 - + + -
188H GLY* 4.1 25.1 - - - -
189H HIS* 4.2 10.8 - - + -
204H ASN 3.1 1.6 - - - +
205H LEU* 3.2 6.4 - - - +
206H LEU* 2.8 49.1 + - + +
208H SER* 2.6 23.1 + - - -
216H ARG* 3.2 44.3 + - + +
217H LEU* 1.3 73.0 - - - +
219H ASN* 1.3 62.5 + - - +
220H ILE* 3.8 6.7 - - + -
223H ASP 5.9 0.9 - - - -
224H THR 3.6 7.2 - - - +
225H LEU* 4.1 26.5 - - + -
226H VAL* 4.2 3.6 - - - -
572I LEU* 4.1 18.6 - - + -
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Residues in contact with ASN 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H ASN* 3.5 6.9 - - - +
205H LEU* 3.8 9.9 - - + -
218H TRP* 1.3 70.7 - - - +
220H ILE* 1.3 57.3 + - - +
221H GLN* 3.1 22.5 + - - +
222H THR* 3.2 15.7 + - - -
223H ASP* 3.0 24.0 + - - -
224H THR* 3.0 26.4 + - - +
226H VAL* 3.9 3.5 - - + +
277H SER* 2.8 26.4 + - - +
278H TYR* 3.3 36.5 - - - +
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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
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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