Contacts of the strand formed by residues 212 - 216 (chain G) in PDB entry 2R9R
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 CYS 212 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G LEU* 3.5 32.8 - - + -
154G VAL* 5.4 0.4 - - + -
156G PHE* 3.9 16.3 - - + -
185G TRP 4.2 0.8 + - - -
186G GLY* 3.2 3.3 - - - -
187G THR* 2.8 29.0 + - - +
210G PRO* 3.7 2.9 - - - +
211G ILE* 1.3 93.0 - - + +
213G GLU* 1.3 67.5 + - - +
238G VAL* 3.9 7.6 - - - +
239G GLY 3.4 10.1 - - - +
241G MET* 3.6 27.6 - - - -
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Residues in contact with GLU 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G THR* 2.8 35.7 + - - +
189G ARG 3.0 13.5 + - - -
190G TRP 3.3 15.9 + - - -
195G ILE* 3.5 23.8 - - + +
212G CYS* 1.3 76.5 - - - +
214G GLN* 1.3 72.5 + - - +
215G ALA* 3.5 3.5 + - + +
224G LYS* 2.9 27.5 + - - +
229G LEU* 3.9 26.7 - - + -
238G VAL* 3.8 8.3 - - + +
239G GLY 3.0 7.9 + - - +
240G ALA* 3.5 4.9 - - - +
241G MET 2.9 23.2 + - - +
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Residues in contact with GLN 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G ASP* 3.0 28.4 + - - +
118G LYS* 3.3 12.1 - - - +
156G PHE* 3.3 30.6 - - + -
187G THR 2.8 10.6 + - - +
188G SER* 3.1 22.0 + - - +
189G ARG 3.5 2.9 + - - -
213G GLU* 1.3 78.1 - - - +
215G ALA* 1.3 56.9 + - - +
241G MET* 3.0 33.5 - - + +
243G TRP* 3.0 14.7 + - + -
321G LEU* 3.7 9.9 - - + +
1001G NAP 2.8 36.1 + - - +
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Residues in contact with ALA 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G ARG* 5.8 0.4 - - - +
213G GLU* 3.5 14.5 + - - +
214G GLN* 1.3 74.0 - - - +
216G GLU* 1.3 66.3 + - - +
224G LYS* 3.9 24.2 - - + +
225G VAL* 4.0 19.3 - - + -
229G LEU* 4.1 9.9 - - + -
240G ALA* 5.7 0.2 - - + -
241G MET 3.1 5.9 + - - -
242G THR* 3.0 10.9 - - + +
243G TRP* 2.9 25.1 + - - -
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Residues in contact with GLU 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G ALA* 1.3 74.5 - - - +
217G TYR* 1.3 63.8 + - - +
218G HIS* 3.3 26.3 + - + -
221G GLN* 3.7 41.9 + - + +
224G LYS* 5.6 3.0 - - - +
225G VAL* 4.0 7.3 + - - +
243G TRP* 3.3 53.1 - - + +
244G SER* 4.6 3.1 - - - -
247G ALA* 5.7 0.2 - - - -
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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