Contacts of the helix formed by residues 257 - 267 (chain F) in PDB entry 2FRV
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 TYR 257 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108F HIS 3.7 17.0 + - - -
109F LEU* 4.2 12.6 - - + -
112F PHE* 3.1 48.5 - + + +
113F TYR* 3.4 18.7 + + + -
252F PHE* 3.0 10.6 + - - +
253F ILE* 3.7 33.4 - - + +
256F VAL* 1.3 72.4 - - - +
258F ILE* 1.3 60.0 + - + +
260F ASP* 3.8 1.0 - - - +
261F LEU* 2.9 35.6 + - + +
411F THR 4.8 1.7 + - - -
414F ARG* 3.8 16.3 - - - +
415F GLY* 3.7 27.2 + - - -
418F CYS* 4.0 22.2 - - + -
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Residues in contact with ILE 258 (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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253F ILE* 2.8 40.9 + - + +
254F GLU* 4.1 11.7 - - - +
256F VAL 3.4 0.4 - - - +
257F TYR* 1.3 81.6 - - + +
259F THR* 1.3 57.7 + - + +
261F LEU* 3.2 11.4 + - + +
262F LEU* 3.0 45.6 + - + +
392F LEU* 4.8 13.2 - - + -
393F VAL* 5.5 4.5 - - + -
415F GLY* 3.2 41.7 - - - +
416F ILE* 6.3 0.2 - - + -
419F LEU* 4.6 15.9 - - + -
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Residues in contact with THR 259 (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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141F LEU* 3.9 34.5 - - - +
142F SER* 3.9 8.4 + - - -
143F PRO* 5.3 1.3 - - + -
195F HIS* 5.5 0.9 - - - -
254F GLU 3.6 16.2 - - - +
255F GLN* 2.9 28.3 + - - +
256F VAL* 3.1 7.1 + - - -
258F ILE* 1.3 75.7 - - + +
260F ASP* 1.3 68.1 + - - +
262F LEU* 3.4 7.0 + - - +
263F ALA* 3.1 24.7 + - - +
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Residues in contact with ASP 260 (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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112F PHE* 4.2 10.5 - - + -
113F TYR* 2.9 19.3 + - + +
141F LEU* 5.4 4.3 - - - +
191F ILE* 3.9 14.4 - - - +
192F ALA* 4.6 5.7 - - + -
195F HIS* 2.2 47.6 + - - +
256F VAL 3.0 16.9 + - - +
257F TYR 3.9 1.1 - - - +
259F THR* 1.3 78.3 + - - +
261F LEU* 1.3 68.1 + - - +
263F ALA* 3.8 5.3 - - - +
264F VAL* 3.0 32.1 + - + +
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Residues in contact with LEU 261 (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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112F PHE* 3.9 25.1 - - + -
257F TYR* 2.9 25.9 + - + +
258F ILE* 3.4 17.7 - - + +
259F THR 3.2 0.2 - - - -
260F ASP* 1.3 80.7 - - - +
262F LEU* 1.3 68.5 + - + +
264F VAL* 4.0 1.4 - - - +
265F ALA* 3.0 29.4 + - + +
393F VAL* 6.4 1.6 - - + -
411F THR* 3.6 34.8 - - + +
412F ALA* 4.2 17.3 - - + +
415F GLY* 3.6 31.4 - - - +
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Residues in contact with LEU 262 (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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258F ILE* 3.0 33.4 + - + +
259F THR* 4.2 5.6 - - - +
261F LEU* 1.3 83.4 - - + +
263F ALA* 1.3 53.4 - - - +
265F ALA* 3.5 2.0 + - + -
266F GLY* 2.9 29.3 + - - -
392F LEU* 4.7 7.9 - - + -
393F VAL* 3.7 44.9 - - + +
396F THR* 3.5 38.4 - - + +
397F LEU* 3.4 24.7 - - + +
412F ALA* 5.4 2.5 - - + -
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Residues in contact with ALA 263 (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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141F LEU* 3.7 30.1 - - + -
188F VAL* 5.5 6.3 - - + -
259F THR 3.1 18.8 + - - +
260F ASP* 3.8 6.3 - - - +
261F LEU 3.2 0.2 - - - -
262F LEU* 1.3 73.4 - - - +
264F VAL* 1.3 68.1 + - + +
266F GLY* 3.2 8.8 + - - -
267F PHE* 3.0 29.8 - - + -
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Residues in contact with VAL 264 (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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112F PHE* 5.3 12.6 - - + -
120F TRP* 3.9 31.6 - - + -
121F VAL* 4.8 8.5 - - + -
184F LEU* 4.1 18.6 - - + -
188F VAL* 4.3 10.8 - - + -
192F ALA* 5.2 7.0 - - + -
260F ASP* 3.0 19.5 + - + +
261F LEU* 4.2 2.2 - - - +
263F ALA* 1.3 76.0 - - + +
265F ALA* 1.3 65.6 + - - +
267F PHE* 2.9 19.4 + - - +
268F TYR* 3.4 21.8 - - + -
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Residues in contact with ALA 265 (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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261F LEU* 3.0 24.3 + - + +
262F LEU* 3.8 5.6 - - + +
264F VAL* 1.3 76.8 - - - +
266F GLY* 1.3 63.1 + - - +
268F TYR* 2.9 17.5 + - - +
269F LYS* 3.4 12.5 + - - +
397F LEU* 3.9 17.7 - - + -
408F LEU* 4.0 31.5 - - + +
411F THR* 6.4 0.4 - - + -
412F ALA* 6.1 4.0 - - + -
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Residues in contact with GLY 266 (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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262F LEU 2.9 15.5 + - - -
263F ALA* 3.6 7.0 - - - -
264F VAL 3.0 1.0 - - - -
265F ALA* 1.3 79.0 - - - +
267F PHE* 1.3 59.8 + - - +
268F TYR 3.3 1.0 + - - -
269F LYS* 3.8 22.0 - - - +
397F LEU* 3.9 10.1 - - - +
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Residues in contact with PHE 267 (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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183F VAL* 3.5 21.0 - - + +
184F LEU* 3.2 34.1 - - + -
185F PRO* 3.7 29.8 - - + -
188F VAL* 3.9 24.9 - - + -
263F ALA* 3.0 33.2 - - + -
264F VAL 2.9 8.9 + - - +
266F GLY* 1.3 73.0 - - - -
268F TYR* 1.3 65.6 + - + +
269F LYS 3.7 1.1 - - - -
270F ASN* 5.4 0.9 + - - -
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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