Contacts of the strand formed by residues 206 - 213 (chain A) in PDB entry 2BGY
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 GLU 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A LYS* 3.6 1.6 - - - -
202A THR* 3.0 35.1 + - - +
203A LYS* 3.2 38.1 + - + +
204A ASP 3.0 8.6 + - - +
205A ASN* 1.3 84.7 - - + +
207A TRP* 1.3 69.0 + - - +
228A THR* 4.1 10.1 - - + +
229A LEU 3.2 4.0 - - - +
230A LYS* 3.6 44.0 + - + +
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Residues in contact with TRP 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 3.7 41.7 - - + +
158A ASN 3.5 25.6 - - - -
161A ASP* 3.8 15.5 - - + -
178A ASN* 3.7 25.1 - - + -
199A PHE* 4.3 11.4 - - + -
200A VAL 3.5 7.4 - - - +
201A LYS* 3.6 36.0 - - + +
206A GLU* 1.3 83.1 + - - +
208A ALA* 1.3 66.0 + - - +
209A VAL* 3.8 1.9 + - - +
228A THR* 3.4 3.5 - - - +
229A LEU* 2.8 44.3 + - + +
231A PHE* 3.7 24.7 - + - -
267A GLN* 2.9 25.1 + - - -
273A ASN* 4.0 10.3 - - - -
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A TYR 3.5 0.9 - - - +
199A PHE* 3.4 4.2 - - - -
200A VAL* 2.8 37.6 + - + +
202A THR* 3.7 22.9 - - + +
207A TRP* 1.3 73.4 - - - +
209A VAL* 1.3 60.9 + - - +
210A TYR* 4.1 22.9 - - + +
225A ALA* 4.1 11.2 - - + -
227A THR 3.7 4.9 - - - -
228A THR* 4.0 8.5 - - - +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A VAL* 3.6 29.4 - - + -
198A TYR 3.2 4.3 - - - +
199A PHE* 4.0 15.5 - - + -
207A TRP 3.9 3.6 - - - +
208A ALA* 1.3 78.2 - - - +
210A TYR* 1.3 60.7 - - - +
211A THR* 4.6 5.6 - - + -
225A ALA* 3.4 1.9 - - - +
226A SER* 2.8 33.8 + - - -
227A THR* 2.9 29.6 + - + +
229A LEU* 3.8 29.8 - - + -
260A LEU* 5.7 0.2 - - + -
262A PHE* 3.8 14.4 - - + -
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Residues in contact with TYR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A PHE* 3.4 55.2 - + + +
196A ASN 3.8 0.3 - - - +
197A VAL* 3.4 4.9 - - - +
198A TYR* 2.8 36.3 + - + +
200A VAL* 3.9 28.1 - - + +
208A ALA* 4.1 18.9 - - + +
209A VAL* 1.3 76.8 - - - +
211A THR* 1.3 63.5 + - - +
222A PRO* 4.1 13.2 - - + -
223A THR* 3.9 15.2 + - - -
224A THR 3.6 17.7 - - - -
225A ALA* 3.5 23.9 + - + +
226A SER 4.5 2.2 - - - +
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Residues in contact with THR 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A MET* 4.6 11.7 - - + -
196A ASN 3.2 10.5 - - - +
197A VAL* 4.4 11.9 - - + -
198A TYR* 5.4 0.4 - - - -
209A VAL* 4.6 3.4 - - + -
210A TYR* 1.3 78.6 - - - +
212A HIS* 1.3 64.8 + - - +
222A PRO* 3.5 18.0 - - - +
224A THR 5.7 0.2 + - - -
226A SER* 2.7 30.0 + - - +
245A ILE* 3.6 27.3 - - + +
260A LEU* 4.4 16.4 - - + -
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Residues in contact with HIS 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 4.5 20.5 - - + +
195A MET* 3.5 7.6 - - - +
196A ASN* 2.9 37.2 + - + +
198A TYR* 4.7 4.5 - - + -
211A THR* 1.3 78.8 + - - +
213A ASP* 1.3 74.3 + - - +
214A SER* 3.3 13.1 + - - -
216A ASP 5.0 1.8 + - - -
219A ALA* 3.6 29.6 + - + +
220A THR 3.4 28.1 + - - -
221A ALA* 4.3 2.2 - - - -
222A PRO* 3.7 22.0 - - + +
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Residues in contact with ASP 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A HIS* 2.5 41.0 + - - +
194A ASP 4.1 1.3 + - - -
195A MET* 3.7 17.4 - - + +
212A HIS* 1.3 84.3 + - - +
214A SER* 1.3 58.8 + - - +
215A SER* 3.1 27.7 + - - -
216A ASP* 3.3 23.9 + - + +
219A ALA* 4.2 4.9 - - + +
247A THR* 3.4 1.1 - - - -
248A GLY* 2.9 30.3 + - - +
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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