Contacts of the strand formed by residues 231 - 238 (chain E) in PDB entry 2BNQ
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 GLN 231 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120E PRO* 3.7 24.7 - - + +
211E GLN* 3.1 9.8 + - - +
212E PHE* 2.7 42.6 + - + +
227E LYS 4.4 1.9 - - - +
228E PRO* 4.1 2.4 - - - +
229E VAL* 2.8 34.2 + - + +
230E THR* 1.3 77.7 - - - +
232E ILE* 1.3 62.2 + - - +
233E VAL* 3.8 23.2 - - + +
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Residues in contact with ILE 232 (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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209E GLN* 3.3 47.3 - - + +
210E VAL 3.4 4.5 - - - +
211E GLN* 3.2 33.4 - - - +
231E GLN* 1.3 80.2 + - - +
233E VAL* 1.3 65.0 + - - +
234E SER* 3.7 12.0 + - - +
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Residues in contact with VAL 233 (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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120E PRO* 5.0 0.7 - - + -
121E PRO* 3.4 41.1 - - + +
122E GLU* 4.6 1.1 - - - -
123E VAL* 3.6 31.1 - - + +
209E GLN* 3.9 0.2 - - - -
210E VAL 2.8 31.1 + - - +
231E GLN* 3.8 24.5 - - + +
232E ILE* 1.3 77.3 - - - +
234E SER* 1.3 68.2 + - - +
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Residues in contact with SER 234 (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* 4.3 7.0 - - - +
207E ARG* 4.0 22.2 + - - -
208E CYS 3.2 10.8 - - - -
209E GLN* 3.7 15.8 + - - +
232E ILE* 3.7 13.1 + - - +
233E VAL* 1.3 85.2 + - - +
235E ALA* 1.3 64.0 + - - +
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Residues in contact with ALA 235 (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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129D SER* 6.0 0.2 - - - +
123E VAL* 3.5 28.9 - - + +
124E ALA* 3.6 11.7 - - - -
125E VAL* 3.4 22.5 - - + +
207E ARG* 3.5 3.8 - - - +
208E CYS 2.9 28.9 + - - +
234E SER* 1.3 75.3 - - - +
236E GLU* 1.3 61.1 + - - +
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Residues in contact with GLU 236 (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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129D SER* 2.8 22.2 + - - -
125E VAL* 4.3 4.4 - - - +
205E HIS* 2.5 38.0 + - + +
206E PHE 3.2 11.9 - - - +
207E ARG* 4.4 7.2 - - + -
235E ALA* 1.3 76.9 - - - +
237E ALA* 1.3 62.7 + - - +
238E TRP* 4.2 9.5 + - + +
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Residues in contact with ALA 237 (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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129D SER* 3.8 20.0 - - - -
125E VAL* 3.9 17.2 - - + +
127E GLU* 4.3 7.9 - - + +
141E LEU* 4.7 4.5 - - + -
199E TRP* 4.5 14.1 - - + -
205E HIS* 3.7 1.9 - - - -
206E PHE* 2.8 34.8 + - - +
236E GLU* 1.3 77.6 - - - +
238E TRP* 1.3 67.4 + - - +
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Residues in contact with TRP 238 (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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127E GLU* 4.4 5.9 + - - +
199E TRP* 3.2 18.7 - - - -
202E PRO 3.5 20.4 - - - +
203E ARG* 3.7 18.8 - - - -
204E ASN 3.4 15.9 - - - -
205E HIS* 3.4 35.5 - + + -
236E GLU* 4.2 10.5 + - + -
237E ALA* 1.3 80.2 - - - +
239E GLY* 1.3 72.4 + - - +
240E ARG* 4.4 2.8 - - - +
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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