Contacts of the strand formed by residues 205 - 212 (chain E) in PDB entry 2BNR
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 205 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158E TRP 3.7 1.3 + - - +
159E VAL* 3.4 6.6 - - - +
160E ASN* 2.9 48.9 + - - +
161E GLY 4.9 6.1 + - - -
203E ARG 3.7 0.4 + - - +
204E ASN* 1.3 73.6 - - - +
206E PHE* 1.3 65.4 + - - +
207E ARG* 4.0 31.1 + - + +
236E GLU* 2.5 31.6 + - + +
237E ALA 3.9 3.4 - - - -
238E TRP* 3.4 49.3 - + + -
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Residues in contact with PHE 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E VAL* 5.5 1.4 - - + +
141E LEU* 3.5 31.0 - - + -
157E TRP* 5.0 5.2 - - + -
158E TRP 3.6 3.4 - - - -
159E VAL* 4.1 9.0 - - + -
192E LEU* 3.9 15.0 - - + -
194E VAL* 4.3 16.4 - - + -
198E PHE* 3.7 42.6 - + - -
199E TRP* 3.7 33.0 - + - -
204E ASN* 3.6 24.5 - - + -
205E HIS* 1.3 75.8 - - - +
207E ARG* 1.3 61.7 + - - +
236E GLU* 3.1 6.3 - - - +
237E ALA* 2.7 49.6 + - + +
239E GLY* 3.8 5.2 - - - -
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Residues in contact with ARG 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E TRP* 3.5 9.3 - - - -
158E TRP* 2.8 76.8 + - + +
161E GLY* 6.1 1.2 - - - -
205E HIS* 4.0 21.4 - - + -
206E PHE* 1.3 75.3 - - - +
208E CYS* 1.3 61.3 + - - +
209E GLN* 3.0 37.3 + - - +
232E ILE* 5.1 0.8 - - - +
234E SER* 3.0 34.2 + - - -
235E ALA 3.4 13.9 - - - +
236E GLU* 4.2 7.4 - - + -
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Residues in contact with CYS 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E VAL* 4.1 5.2 - - + +
125E VAL* 3.6 17.1 - - + +
143E CYS* 2.0 50.5 - - + -
155E LEU* 3.8 24.9 - - - -
156E SER 3.6 3.8 - - - -
157E TRP* 4.0 10.5 - - + -
207E ARG* 1.3 72.6 - - - +
209E GLN* 1.3 61.9 + - - +
210E VAL* 4.4 2.0 - - - -
233E VAL 4.0 0.3 - - - +
234E SER* 3.2 5.5 - - - -
235E ALA 2.8 27.6 + - - -
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Residues in contact with GLN 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E GLU 3.6 1.8 + - - +
155E LEU* 3.3 4.2 - - - +
156E SER* 2.8 57.2 + - - +
158E TRP* 3.7 19.7 + - + +
207E ARG* 3.0 39.4 + - - +
208E CYS* 1.3 72.1 - - - +
210E VAL* 1.3 66.5 + - - +
211E GLN* 5.0 8.1 - - - +
232E ILE* 3.5 40.4 - - + +
234E SER* 3.6 3.6 - - - -
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Residues in contact with VAL 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E PRO* 3.8 22.9 - - + -
123E VAL* 3.5 30.1 - - + -
145E ALA* 4.1 16.8 - - + -
153E VAL* 3.9 26.0 - - + -
154E GLU 3.5 5.4 - - - +
155E LEU* 4.2 17.9 - - + -
188E LEU* 6.1 0.2 - - + -
208E CYS* 4.4 1.1 - - - -
209E GLN* 1.3 80.3 - - - +
211E GLN* 1.3 61.5 + - - +
212E PHE* 3.5 1.6 + - - +
231E GLN 3.7 0.3 - - - +
232E ILE* 3.4 3.1 - - - -
233E VAL* 2.8 39.2 + - - +
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Residues in contact with GLN 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E VAL* 3.1 7.4 - - - +
154E GLU* 2.8 48.3 + - + +
209E GLN* 4.1 8.9 + - - +
210E VAL* 1.3 72.2 - - - +
212E PHE* 1.3 71.0 + - - +
213E TYR* 3.6 32.7 - - + +
230E THR* 3.6 15.5 - - - +
231E GLN* 3.1 28.7 + - - +
232E ILE* 3.3 25.9 - - + +
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Residues in contact with PHE 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E VAL* 4.0 7.6 - - + -
119E PHE 3.3 23.8 - - - -
120E PRO* 3.7 21.1 - - + -
121E PRO* 3.6 29.2 - - + -
148E PHE* 4.4 1.3 - - + -
149E TYR 3.6 11.7 - - - -
150E PRO* 3.9 20.6 - - + -
152E HIS 3.5 9.4 - - - -
153E VAL* 3.9 7.6 - - + -
210E VAL 3.5 1.0 + - - +
211E GLN* 1.3 81.0 + - - +
213E TYR* 1.3 77.5 + - - +
214E GLY* 3.7 15.3 - - - -
228E PRO 3.9 11.9 - - - -
229E VAL 3.8 15.0 - - - -
230E THR* 3.2 2.8 - - - +
231E GLN* 2.7 42.9 + - + +
233E VAL* 5.6 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