Contacts of the strand formed by residues 267 - 273 (chain F) in PDB entry 3FZ7
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 VAL 267 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240F MET* 3.6 13.2 - - - +
242F ILE* 3.8 28.5 - - + -
260F TRP 4.0 2.9 - - - +
261F ASP 3.4 19.3 - - - +
262F PHE* 3.5 9.8 - - + -
264F LEU* 3.0 25.5 + - + +
266F ARG* 1.3 72.4 - - - +
268F LYS* 1.3 60.4 + - - +
269F SER 3.7 6.7 - - - +
270F ILE* 3.6 37.2 - - + -
290F ARG* 3.3 23.4 + - - -
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Residues in contact with LYS 268 (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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140F ARG* 3.5 35.7 - - - +
144F ARG* 5.8 0.8 - - - +
239F ASP* 2.7 34.7 + - + +
240F MET 2.9 9.5 + - - +
262F PHE* 3.9 0.4 - - - -
265F PRO 3.6 16.8 - - - +
266F ARG* 3.1 21.0 + - - +
267F VAL* 1.3 76.4 - - - +
269F SER* 1.3 65.5 + - - +
289F TRP* 3.4 2.8 - - - -
290F ARG* 2.8 37.6 + - + +
294F ALA* 3.5 18.8 - - + +
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Residues in contact with SER 269 (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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133F GLY* 4.3 6.6 + - - -
137F MET* 5.3 0.2 - - - +
140F ARG* 4.7 5.9 + - - -
240F MET 3.7 1.9 + - - -
241F HIS* 2.7 36.6 + - - +
242F ILE 3.1 21.5 + - - -
262F PHE* 3.9 2.2 - - - -
267F VAL* 3.5 3.4 - - - +
268F LYS* 1.3 83.9 - - - +
270F ILE* 1.3 67.8 + - - +
287F VAL* 4.6 0.9 - - - -
288F ILE 3.1 15.0 - - - -
289F TRP* 3.4 25.6 + - - -
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Residues in contact with ILE 270 (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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108F TRP* 3.5 34.0 - - + -
241F HIS* 3.8 2.9 - - - -
242F ILE* 3.6 16.6 - - + +
244F ALA* 4.0 0.7 - - + -
260F TRP* 3.6 22.0 - - + -
261F ASP* 3.7 31.9 - - + -
262F PHE* 3.4 34.5 - - + +
267F VAL* 3.6 12.1 - - + -
269F SER* 1.3 81.0 - - - +
271F SER* 1.3 67.5 + - - +
287F VAL* 3.3 3.6 - - - +
288F ILE 2.9 30.8 + - - -
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Residues in contact with SER 271 (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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108F TRP* 4.1 2.5 - - - -
126F SER* 4.7 2.3 + - - -
129F ALA* 3.7 21.5 - - - -
130F CYS* 3.7 16.3 - - - -
241F HIS* 2.9 27.5 + - - -
242F ILE 3.2 6.2 + - - -
243F ASP* 4.0 5.7 + - - -
244F ALA* 2.8 32.6 + - - +
245F ALA 4.4 0.7 - - - -
270F ILE* 1.3 74.7 - - - +
272F ALA* 1.3 61.4 + - - +
286F TRP 3.1 11.7 - - - -
287F VAL* 4.2 1.8 - - - -
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Residues in contact with ALA 272 (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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108F TRP* 3.4 28.5 - - + -
126F SER* 3.3 11.4 + - - -
244F ALA 3.5 17.5 - - - +
245F ALA* 3.7 4.0 - - - +
248F GLY* 4.3 1.3 - - - -
249F PHE* 3.8 17.3 - - + -
271F SER* 1.3 77.7 - - - +
273F SER* 1.3 60.2 + - - +
274F GLY 4.1 0.2 - - - -
285F GLY* 3.6 1.4 - - - -
286F TRP* 2.8 31.3 + - + +
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Residues in contact with SER 273 (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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126F SER* 2.6 24.2 + - - -
245F ALA* 3.0 20.9 + - - +
249F PHE* 3.8 6.4 - - - -
272F ALA* 1.3 71.2 - - - +
274F GLY* 1.3 65.3 + - - +
275F HIS* 3.3 13.1 + - - -
276F LYS* 2.9 44.1 + - - +
278F GLY 3.6 9.7 + - - -
284F CYS 3.8 4.0 - - - -
285F GLY* 4.2 1.1 - - - -
467F PO4 3.4 2.3 + - - -
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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