Contacts of the strand formed by residues 182 - 188 (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 ALA 182 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140G LEU* 4.3 4.7 - - + -
151G TYR* 4.3 1.1 - - - -
152G VAL* 3.1 18.2 - - + +
155G VAL* 3.7 30.1 - - + -
176G VAL* 3.4 4.2 + - + -
177G ILE* 3.3 31.1 - - + +
180G GLY* 3.3 4.2 - - - -
181G MET* 1.3 83.0 + - - +
183G MET* 1.3 67.6 + - - +
184G TYR 4.0 6.3 - - - +
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Residues in contact with MET 183 (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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151G TYR* 3.5 39.0 - - + +
152G VAL 3.2 7.1 + - - +
153G ASP* 3.2 32.0 + - - +
177G ILE* 3.8 15.1 - - - +
180G GLY* 6.4 1.6 - - - -
182G ALA* 1.3 77.0 - - - +
184G TYR* 1.3 86.0 + - + +
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Residues in contact with TYR 184 (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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45G SER* 4.4 12.6 - - - -
46G GLY* 4.5 4.8 + - - -
47G LEU* 3.8 49.9 + - + +
153G ASP 2.8 17.7 + - - +
154G VAL* 3.3 5.2 - - + -
155G VAL* 3.0 25.8 + - - +
177G ILE* 3.8 10.5 - - - -
182G ALA* 3.6 2.1 - - - +
183G MET* 1.3 94.4 - - + +
185G TRP* 1.3 63.1 + - - +
208G ILE* 6.0 2.7 - - + -
211G ILE* 3.4 37.5 - - + -
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Residues in contact with TRP 185 (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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154G VAL* 3.9 5.4 - - - -
155G VAL* 3.1 23.6 - - + +
157G ALA* 4.9 0.4 - - + -
169G THR* 4.7 2.7 - - + -
170G VAL* 3.9 24.2 - - + -
173G MET* 3.4 44.3 - - + +
174G THR* 4.8 0.8 + - - -
177G ILE* 3.7 19.7 - - + +
184G TYR* 1.3 77.5 - - - +
186G GLY* 1.3 77.8 + - - +
187G THR* 3.9 18.6 - - + -
190G TRP* 4.2 13.9 - + - -
198G ALA* 4.0 17.5 - - + -
208G ILE* 2.7 28.9 + - + +
209G PRO 3.5 11.5 + - - -
210G PRO* 3.2 29.0 - - + +
211G ILE* 3.0 27.6 + - - +
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Residues in contact with GLY 186 (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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154G VAL* 3.9 3.5 - - - +
155G VAL 2.8 8.3 + - - -
156G PHE* 3.1 16.5 - - - -
157G ALA 3.0 23.6 + - - -
185G TRP* 1.3 86.6 - - - +
187G THR* 1.3 63.4 + - - -
210G PRO* 4.1 3.4 - - - -
212G CYS 3.2 15.0 - - - -
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Residues in contact with THR 187 (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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156G PHE* 3.3 6.4 - - - -
157G ALA 3.7 4.3 - - - +
185G TRP* 3.9 10.1 - - + -
186G GLY* 1.3 77.0 - - - -
188G SER* 1.3 62.5 + - - +
190G TRP* 3.4 51.1 - - + +
195G ILE* 3.6 15.2 - - + +
210G PRO* 4.2 13.6 - - + +
212G CYS 2.8 11.8 + - - -
213G GLU* 2.8 22.7 + - - +
214G GLN 2.8 22.5 + - - -
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Residues in contact with SER 188 (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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118G LYS* 4.8 0.7 - - - -
156G PHE* 4.6 7.0 - - - -
157G ALA 3.0 16.9 + - - -
158G ASN* 3.6 9.3 + - - -
159G ARG* 3.1 23.7 - - - -
187G THR* 1.3 78.5 - - - +
189G ARG* 1.3 68.7 + - - +
190G TRP* 3.1 7.1 - - - -
213G GLU* 3.6 0.4 - - - -
214G GLN* 3.1 16.6 + - - -
1001G NAP 2.7 36.8 + - - -
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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