Contacts of the strand formed by residues 233 - 240 (chain E) in PDB entry 1OGA
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 233 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122E PRO* 3.8 24.9 - - - +
212E VAL 3.8 0.2 - - - +
213E GLN* 3.3 8.8 + - - +
214E PHE* 2.8 39.3 + - + +
229E LYS 4.4 2.1 - - - +
230E PRO* 4.2 2.9 - - - +
231E VAL* 2.9 31.4 + - + +
232E THR* 1.3 76.3 - - - +
234E ILE* 1.3 63.6 + - - +
235E VAL* 3.7 23.9 - - + +
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Residues in contact with ILE 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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209E ARG* 4.8 0.9 - - - +
211E GLN* 3.4 44.4 - - + +
212E VAL 3.4 4.0 - - - +
213E GLN* 3.2 34.1 - - + +
233E GLN* 1.3 78.1 + - - +
235E VAL* 1.3 66.6 + - - +
236E SER* 3.7 11.7 - - - +
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Residues in contact with VAL 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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122E PRO* 4.9 0.7 - - + -
123E PRO* 3.6 33.9 - - + +
124E GLU* 4.7 0.9 - - - -
125E VAL* 3.5 36.6 - - + +
212E VAL 2.9 32.0 + - - +
233E GLN* 3.7 28.3 - - + +
234E ILE* 1.3 76.9 - - - +
236E SER* 1.3 67.5 + - - +
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Residues in contact with SER 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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125E VAL* 4.2 7.6 - - - +
209E ARG* 3.0 38.7 + - - -
210E CYS 3.1 12.6 - - - -
211E GLN* 3.7 2.3 - - - -
234E ILE* 3.7 11.8 - - - +
235E VAL* 1.3 83.3 + - - +
237E ALA* 1.3 61.8 + - - +
238E GLU* 5.8 1.1 - - - -
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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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126D SER* 5.5 1.6 - - - +
127D LYS* 6.5 0.2 - - + -
125E VAL* 3.5 29.6 - - + +
126E ALA* 3.8 0.9 - - - -
127E VAL* 3.6 31.2 - - + +
209E ARG* 3.4 3.3 - - - +
210E CYS 2.9 29.4 + - - +
236E SER* 1.3 74.0 - - - +
238E GLU* 1.3 65.0 + - - +
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Residues in contact with GLU 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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126D SER* 3.0 22.7 + - - -
127D LYS* 6.3 1.1 - - - +
127E VAL* 4.4 4.7 - - - +
207E HIS* 2.6 36.3 + - + +
208E PHE 3.2 14.4 - - - +
209E ARG* 4.2 12.4 - - + +
236E SER* 5.8 0.9 - - - -
237E ALA* 1.3 78.4 - - - +
239E ALA* 1.3 61.5 + - - +
240E TRP* 3.6 28.4 - - + -
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Residues in contact with ALA 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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126D SER* 4.3 11.9 - - - -
127E VAL* 4.1 18.8 - - + -
129E GLU* 4.4 5.2 - - + -
143E LEU* 4.5 6.3 - - + -
201E TRP* 4.3 20.4 - - + -
207E HIS* 3.6 5.5 - - - -
208E PHE* 2.8 33.3 + - - +
238E GLU* 1.3 76.6 - - - +
240E TRP* 1.3 69.6 + - - +
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Residues in contact with TRP 240 (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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201E TRP* 3.3 9.5 - - - -
204E PRO 4.6 11.2 - - - +
205E ARG 5.2 1.6 - - - -
206E ASN 3.4 8.5 - - - -
207E HIS* 3.5 37.9 - + + +
238E GLU* 3.6 38.8 - - + -
239E ALA* 1.3 82.7 - - - +
241E GLY* 1.3 65.5 + - - +
242E ARG* 2.7 30.6 + - - +
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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