Contacts of the strand formed by residues 226 - 230 (chain B) in PDB entry 2RHG
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 ALA 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B PRO* 3.2 3.2 - - - +
225B ASP* 1.3 84.7 - - + +
227B VAL* 1.3 66.6 + - - +
228B ILE* 4.6 1.6 - - + +
250B VAL* 4.6 0.4 - - - -
251B GLY* 3.2 16.4 - - - +
253B ILE* 4.1 24.0 - - + -
361B MET* 4.5 2.7 - - + -
371B LEU 3.5 2.0 + - - +
372B LEU* 3.5 21.7 - - + +
373B VAL 3.1 22.3 + - - +
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B THR* 5.1 0.2 - - + -
224B PRO* 4.2 12.1 - - + -
226B ALA* 1.3 76.2 - - - +
228B ILE* 1.3 64.1 + - - +
240B MET* 3.9 18.8 - - + -
241B PHE* 3.9 15.5 - - + -
244B PHE* 4.0 28.3 - - + -
250B VAL* 4.3 4.5 - - + -
251B GLY 2.8 14.9 + - - +
252B LEU* 3.6 22.4 - - + -
253B ILE* 2.9 26.0 + - - +
373B VAL* 3.3 21.3 - - + +
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ALA 4.6 0.9 - - - +
227B VAL* 1.3 83.2 - - - +
229B ALA* 1.3 64.4 + - - +
240B MET* 5.7 0.9 - - - -
253B ILE* 3.3 24.0 - - + +
255B VAL* 3.7 26.2 - - + -
354B ALA* 3.8 16.4 - - - +
357B HIS* 4.4 3.4 - - + -
358B ALA* 3.7 23.3 - - + -
361B MET* 3.5 31.4 - - + -
372B LEU* 4.5 11.4 - - + -
373B VAL 2.9 12.6 + - - +
374B VAL* 3.4 11.0 - - + -
375B ASN* 2.9 25.9 + - - -
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Residues in contact with ALA 229 (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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228B ILE* 1.3 77.9 - - - +
230B CYS* 1.3 62.3 + - - +
231B VAL* 4.0 0.9 - - - +
236B ASN* 3.5 22.0 - - - +
237B ALA* 3.7 21.1 - - + +
240B MET* 4.8 3.4 - - + -
241B PHE* 4.7 6.5 - - + -
253B ILE 3.1 6.1 + - - -
254B GLY* 3.4 6.4 - - - -
255B VAL* 2.9 22.2 + - - -
354B ALA* 3.8 9.0 - - - -
375B ASN* 3.8 12.1 - - + +
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Residues in contact with CYS 230 (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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229B ALA* 1.3 75.3 - - - +
231B VAL* 1.3 57.9 + - - +
232B GLY 4.1 0.2 + - - -
236B ASN* 3.1 35.1 - - - +
237B ALA* 3.6 8.8 - - - +
255B VAL* 3.3 14.1 - - - +
304B LEU* 3.9 12.1 - - + -
350B GLU 3.3 36.1 - - - +
351B SER* 4.1 2.0 - - - -
353B HIS* 4.3 9.2 - - + -
354B ALA* 3.6 8.7 - - + +
375B ASN 5.3 0.8 + - - -
377B SER* 3.9 7.4 - - - -
399B PLP 3.9 18.6 + - - -
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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
------------------------------------------------------------
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