Contacts of the strand formed by residues 232 - 239 (chain E) in PDB entry 3VXR
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 232 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121E PRO* 3.6 33.9 - - + +
212E GLN* 3.4 6.8 - - - +
213E PHE* 2.9 35.6 + - + +
228E LYS 4.6 2.2 + - - -
229E PRO* 4.2 2.0 - - - +
230E VAL* 2.9 38.3 + - + +
231E THR* 1.3 76.2 - - - +
233E ILE* 1.3 62.3 + - - +
234E VAL* 4.2 17.3 - - + +
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Residues in contact with ILE 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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208E ARG* 4.8 2.2 - - - +
210E GLN* 3.5 46.7 - - + +
211E VAL 3.5 3.1 - - - +
212E GLN* 3.3 37.9 - - + +
232E GLN* 1.3 77.6 - - - +
234E VAL* 1.3 66.7 + - - +
235E SER* 4.0 10.3 - - - +
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Residues in contact with VAL 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E PRO* 4.8 1.1 - - + -
122E PRO* 3.7 38.1 - - + +
123E GLU* 5.1 0.7 - - - -
124E VAL* 3.7 29.3 - - + +
211E VAL* 2.7 43.8 + - - +
232E GLN* 4.2 21.1 - - + +
233E ILE* 1.3 78.8 - - - +
235E SER* 1.3 67.2 + - - +
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Residues in contact with SER 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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124E VAL* 4.0 10.8 - - - +
208E ARG* 3.2 36.4 + - - -
209E CYS 3.2 13.8 + - - -
210E GLN* 3.6 5.9 - - - +
233E ILE* 4.0 3.8 - - - +
234E VAL* 1.3 83.9 + - - +
236E ALA* 1.3 63.8 + - - +
237E GLU* 6.5 0.2 - - - -
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Residues in contact with ALA 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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127D SER* 5.6 0.9 - - - +
124E VAL* 3.8 10.2 - - + +
125E ALA* 3.7 13.9 - - - -
126E VAL* 3.5 33.8 - - + +
208E ARG* 3.6 2.6 - - - +
209E CYS 2.8 30.7 + - - +
235E SER* 1.3 76.3 - - - +
237E GLU* 1.3 63.5 + - - +
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Residues in contact with GLU 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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127D SER* 3.1 20.8 + - - -
128D LYS* 3.8 27.7 + - - +
126E VAL* 3.8 4.8 - - - +
206E HIS* 2.9 30.6 + - + -
207E PHE 3.1 13.2 - - - +
208E ARG* 4.2 12.5 - - + -
235E SER* 6.5 0.2 - - - -
236E ALA* 1.3 80.6 - - - +
238E ALA* 1.3 61.7 + - - +
239E TRP* 4.2 13.4 + - - +
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Residues in contact with ALA 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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127D SER* 3.8 14.6 - - - -
128D LYS* 5.3 0.4 - - - +
126E VAL* 3.7 20.2 - - + -
128E GLU* 4.0 14.1 - - + +
142E LEU* 4.4 11.4 - - + -
200E TRP* 4.6 2.0 - - + -
206E HIS* 3.8 2.3 + - - -
207E PHE* 2.8 35.8 + - - +
237E GLU* 1.3 77.9 - - - +
239E TRP* 1.3 72.3 + - - +
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Residues in contact with TRP 239 (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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128D LYS* 4.3 18.0 - - - +
128E GLU* 4.3 4.8 + - - +
200E TRP* 3.3 16.9 - - - -
203E PRO 4.6 10.3 - - - +
204E ARG* 4.8 7.4 - - - -
205E ASN 3.6 5.4 - - - +
206E HIS* 3.3 58.3 - + + -
237E GLU* 4.2 12.7 - - - +
238E ALA* 1.3 82.5 - - - +
240E GLY* 1.3 70.0 + - - +
241E ARG* 4.1 7.6 - - - +
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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