Contacts of the strand formed by residues 216 - 219 (chain B) 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 ARG 216 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B GLY* 3.3 41.3 + - - -
189B HIS* 3.5 27.1 - - + +
190B GLY 5.3 0.4 - - - +
207B LEU* 3.3 3.9 - - - -
208B SER* 2.7 43.9 + - - +
212B ASP* 4.8 6.3 + - - -
214B ALA* 4.9 2.4 - - + +
215B LEU* 1.3 78.0 - - - +
217B LEU* 1.3 58.6 + - - +
218B TRP* 3.1 34.9 - - + +
225B LEU* 3.2 27.1 - - + +
227B ALA 3.3 4.3 - - - -
228B ILE* 3.9 29.9 - - + +
569C ASP 4.8 1.4 + - - -
570C THR* 3.9 9.7 - - - +
571C CYS* 3.7 16.2 - - - +
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B HIS* 5.4 0.2 - - + -
205B LEU* 4.4 20.2 - - + -
206B LEU 3.3 11.2 - - - +
207B LEU* 4.2 9.8 - - + +
216B ARG* 1.3 70.6 - - - +
218B TRP* 1.3 59.8 + - - +
225B LEU* 3.2 4.4 - - - +
226B VAL* 2.8 37.0 + - + +
227B ALA 2.8 18.3 + - - +
229B PHE* 4.1 15.3 - - + -
244B TYR* 3.1 32.1 - - + +
251B ILE* 5.0 1.1 - - + -
265B ILE* 4.5 13.7 - - + -
270B MET* 3.7 28.9 - - + -
274B ILE* 4.9 9.6 - - + -
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Residues in contact with TRP 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 4.0 12.9 - - + +
186B TYR* 3.7 50.9 - + + -
188B GLY* 4.2 12.1 - - - -
189B HIS* 4.4 7.6 - - - -
204B ASN 3.0 13.3 - - - +
205B LEU* 3.4 9.4 - - - +
206B LEU* 2.6 39.5 + - + +
208B SER* 2.5 27.7 + - - -
216B ARG* 3.1 49.3 + - + +
217B LEU* 1.3 74.3 - - - +
219B ASN* 1.3 62.9 + - - +
220B ILE* 3.8 0.7 - - + -
223B ASP 6.0 0.2 - - - -
224B THR 3.4 19.1 - - - +
225B LEU* 3.8 26.7 - - + -
226B VAL* 4.3 0.9 - - - -
572C LEU* 4.3 13.5 - - + -
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Residues in contact with ASN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B TYR* 5.5 0.2 - - - -
204B ASN* 3.3 24.7 - - - +
205B LEU* 4.2 5.8 - - + +
218B TRP* 1.3 70.8 - - - +
220B ILE* 1.3 58.7 + - - +
221B GLN* 3.7 2.9 + - - +
222B THR* 2.8 25.2 + - - +
223B ASP* 3.2 22.2 + - - -
224B THR* 3.0 26.4 + - - +
226B VAL* 4.1 6.3 - - + +
277B SER* 3.7 20.4 + - - +
278B TYR* 3.5 40.9 + - - +
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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