Contacts of the strand formed by residues 211 - 217 (chain B) in PDB entry 2R5N
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 HIS 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B TRP* 1.3 72.0 - - - +
212B VAL* 1.3 64.9 + - - +
213B ILE* 3.4 31.8 - - + +
230B GLU* 2.8 30.3 + - + +
231B ALA* 4.0 3.6 - - - -
234B VAL* 3.7 40.5 - - + +
237B LYS* 3.9 12.0 - - + +
238B PRO 2.9 8.8 + - - +
239B SER* 2.9 28.6 + - - +
240B LEU 2.8 26.0 + - - +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ALA* 3.7 30.1 - - + +
205B PHE* 3.7 29.4 - - + -
206B GLU* 3.7 34.8 + - + +
210B TRP* 3.7 4.7 + - + +
211B HIS* 1.3 84.9 + - - +
213B ILE* 1.3 66.7 - - - +
214B ARG* 4.0 13.0 + - + +
230B GLU* 5.1 0.7 - - - +
240B LEU* 3.4 11.4 - - + +
242B MET* 3.8 19.7 - - + -
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B HIS* 3.4 33.7 - - + +
212B VAL* 1.3 71.8 - - - +
214B ARG* 1.3 67.0 + - - +
216B ILE* 3.6 23.3 - - + +
226B ARG* 3.5 24.2 - - - +
227B ALA* 3.2 31.0 - - + +
230B GLU* 3.6 18.2 - - + +
231B ALA 4.0 0.7 - - - +
240B LEU 2.9 11.6 + - - +
241B LEU* 4.0 13.5 - - + -
242B MET* 2.8 32.9 + - - +
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Residues in contact with ARG 214 (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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200B ASP* 4.9 3.2 + - - -
202B ALA* 3.5 39.3 - - + +
203B MET* 3.9 7.3 - - - +
206B GLU* 2.8 43.9 + - - -
212B VAL* 3.9 12.2 + - + +
213B ILE* 1.3 81.2 - - - +
215B ASP* 1.3 83.8 + - - +
216B ILE* 3.3 5.6 + - - +
242B MET* 4.0 6.5 - - + -
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Residues in contact with ASP 215 (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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214B ARG* 1.3 86.6 - - - +
216B ILE* 1.3 64.4 + - - +
217B ASP 3.6 2.1 + - - -
223B SER* 4.8 1.2 + - - -
242B MET* 3.8 9.4 + - - +
244B LYS* 5.7 4.5 - - - -
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Residues in contact with ILE 216 (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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213B ILE* 3.6 30.3 - - + +
214B ARG 4.1 0.7 - - - +
215B ASP* 1.3 77.9 - - - +
217B ASP* 1.3 70.0 + - - +
218B GLY 3.1 1.3 + - - +
223B SER* 3.5 25.6 - - - +
224B ILE* 4.1 15.0 - - + -
226B ARG* 5.4 1.1 - - - +
227B ALA* 3.5 19.3 - - + -
241B LEU* 3.5 34.3 - - + -
242B MET 3.0 14.6 + - - +
243B CYS* 4.2 9.4 - - - -
244B LYS* 2.8 34.1 + - - +
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Residues in contact with ASP 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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215B ASP 3.6 3.4 + - - -
216B ILE* 1.3 68.9 - - - +
218B GLY* 1.3 58.8 + - - +
219B HIS* 2.9 28.7 + - - +
220B ASP* 3.1 42.6 + - + +
223B SER* 3.2 15.1 + - - +
224B ILE* 3.7 5.2 - - - +
244B LYS* 4.3 5.9 - - - +
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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