Contacts of the strand formed by residues 246 - 253 (chain F) in PDB entry 4OZH
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 246 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F PRO* 3.8 26.1 - - - +
226F GLN* 3.5 3.8 - - - +
227F PHE* 2.9 39.7 + - + +
242F LYS 3.8 18.2 + - - -
243F PRO* 4.2 0.4 - - - +
244F VAL* 2.9 26.6 + - + +
245F THR* 1.3 73.7 - - - +
247F ILE* 1.3 66.4 + - - +
248F VAL* 3.6 23.2 - - + +
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Residues in contact with ILE 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F ARG* 5.1 0.4 - - - +
224F GLN* 3.6 39.7 - - + +
225F VAL 3.7 3.1 - - - +
226F GLN* 3.4 39.5 - - + +
246F GLN* 1.3 73.9 - - - +
248F VAL* 1.3 62.8 + - - +
249F SER* 4.0 8.9 + - - +
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Residues in contact with VAL 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F PRO* 4.9 0.7 - - + -
136F PRO* 3.4 44.6 - - + +
137F GLU* 5.0 0.7 - - - -
138F VAL* 3.7 30.9 - - + +
225F VAL 3.0 31.1 + - - +
246F GLN* 3.6 27.8 - - + +
247F ILE* 1.3 73.2 - - - +
249F SER* 1.3 68.4 + - - +
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Residues in contact with SER 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F VAL* 4.2 9.9 - - - +
222F ARG* 3.1 36.8 + - - -
223F CYS 3.3 9.4 - - - -
224F GLN* 3.9 7.3 - - - +
247F ILE* 4.0 7.4 + - - +
248F VAL* 1.3 80.6 + - - +
250F ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F VAL* 3.5 31.0 - - + +
139F ALA* 3.9 1.3 - - - -
140F VAL* 3.7 30.8 - - + +
222F ARG* 3.6 2.3 - - - -
223F CYS* 2.9 31.5 + - + +
249F SER* 1.3 74.5 - - - +
251F GLU* 1.3 60.2 + - - +
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Residues in contact with GLU 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E SER* 4.1 7.1 - - - -
140F VAL* 3.4 10.3 - - - +
220F HIS* 3.4 27.4 + - + +
221F PHE 3.3 5.4 - - - +
222F ARG* 4.5 9.6 - - + -
250F ALA* 1.3 75.0 - - - +
252F ALA* 1.3 61.0 + - - +
253F TRP* 3.3 26.2 + - + +
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Residues in contact with ALA 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E SER* 4.1 12.6 - - - -
140F VAL* 3.9 25.3 - - + +
142F GLU* 4.7 8.5 - - + -
156F LEU* 4.4 14.4 - - + -
214F TRP* 4.7 2.5 - - + -
220F HIS* 3.8 2.0 - - - -
221F PHE* 2.8 47.4 + - + +
251F GLU* 1.3 74.9 - - - +
253F TRP* 1.3 62.6 + - - +
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Residues in contact with TRP 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F GLU* 3.8 7.9 + - - +
214F TRP* 3.3 20.8 - - - -
217F PRO 3.4 20.2 - - - +
218F ARG* 3.7 17.0 - - - -
219F ASN 3.6 12.6 - - - -
220F HIS* 3.4 34.2 - + + -
221F PHE* 4.6 0.4 - - - -
251F GLU* 3.3 25.3 + - + -
252F ALA* 1.3 78.8 - - - +
254F GLY* 1.3 67.2 + - - +
255F ARG* 3.7 1.7 + - - +
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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