Contacts of the helix formed by residues 257 - 267 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108L HIS 3.7 17.4 + - - -
109L LEU* 4.2 12.6 - - + -
112L PHE* 3.1 49.6 - + + +
113L TYR* 3.4 19.4 + + + -
252L PHE* 3.0 10.9 + - - +
253L ILE* 3.7 33.0 - - + +
256L VAL* 1.3 72.4 - - - +
258L ILE* 1.3 60.9 + - + +
260L ASP* 3.8 1.2 - - - +
261L LEU* 2.9 36.2 + - + +
411L THR 4.8 1.6 + - - -
414L ARG* 3.8 16.5 - - - +
415L GLY* 3.7 27.1 + - - -
418L CYS* 4.0 22.4 - - + -
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Residues in contact with ILE 258 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253L ILE* 2.8 40.7 + - + +
254L GLU* 4.1 12.3 - - - +
256L VAL 3.4 0.6 - - - +
257L TYR* 1.3 82.6 - - + +
259L THR* 1.3 59.8 + - + +
261L LEU* 3.2 12.0 + - + +
262L LEU* 3.0 44.0 + - + +
392L LEU* 4.8 13.7 - - + -
393L VAL* 5.5 5.2 - - + -
415L GLY* 3.2 40.6 - - - +
419L LEU* 4.6 15.7 - - + -
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Residues in contact with THR 259 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L LEU* 3.9 34.2 - - - +
142L SER* 3.9 8.1 + - - -
143L PRO* 5.3 1.1 - - + -
195L HIS* 5.5 0.9 - - - -
254L GLU 3.6 15.7 - - - +
255L GLN* 2.9 29.2 + - - +
256L VAL* 3.1 6.8 + - - -
258L ILE* 1.3 77.0 - - + +
260L ASP* 1.3 69.1 + - - +
262L LEU* 3.4 7.6 + - - +
263L ALA* 3.1 24.4 + - - +
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Residues in contact with ASP 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L PHE* 4.2 10.3 - - + -
113L TYR* 2.9 18.8 + - - +
141L LEU* 5.4 5.2 - - - +
191L ILE* 3.9 13.9 - - - +
192L ALA* 4.6 6.0 - - + -
195L HIS* 2.2 47.9 + - - +
256L VAL 3.0 17.7 + - - +
257L TYR 3.9 0.7 - - - +
259L THR* 1.3 77.5 + - - +
261L LEU* 1.3 68.4 + - - +
263L ALA* 4.3 6.1 - - - -
264L VAL* 3.0 32.0 + - + +
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Residues in contact with LEU 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L PHE* 3.9 24.2 - - + -
257L TYR* 2.9 26.9 + - + +
258L ILE* 3.4 17.7 - - + +
259L THR 3.2 0.2 - - - -
260L ASP* 1.3 80.4 - - - +
262L LEU* 1.3 68.0 + - + +
264L VAL* 4.0 1.0 - - - +
265L ALA* 3.0 29.5 + - + +
411L THR* 3.6 35.0 - - + +
412L ALA* 4.2 17.3 - - + +
415L GLY* 3.6 31.9 - - - +
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Residues in contact with LEU 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258L ILE* 3.0 32.8 + - + +
259L THR* 4.2 5.6 - - - +
261L LEU* 1.3 84.1 - - + +
263L ALA* 1.3 53.6 + - - +
265L ALA* 3.5 2.0 + - + -
266L GLY* 2.9 28.4 + - - -
392L LEU* 4.7 8.1 - - + -
393L VAL* 3.7 45.5 - - + +
396L THR* 3.5 38.7 - - + +
397L LEU* 3.4 24.6 - - + +
412L ALA* 5.4 2.5 - - + -
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Residues in contact with ALA 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L LEU* 3.7 29.2 - - + -
188L VAL* 5.4 6.5 - - + -
259L THR 3.1 18.2 + - - +
260L ASP* 3.8 7.2 - - - +
261L LEU 3.2 0.2 - - - -
262L LEU* 1.3 74.0 - - - +
264L VAL* 1.3 68.2 + - + +
266L GLY* 3.2 8.9 + - - -
267L PHE* 3.0 28.6 - - + -
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Residues in contact with VAL 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L PHE* 5.3 12.6 - - + -
120L TRP* 3.9 31.9 - - + -
121L VAL* 4.8 9.4 - - + -
184L LEU* 4.1 19.1 - - + -
188L VAL* 4.3 9.6 - - + -
192L ALA* 5.2 7.2 - - + -
260L ASP* 3.0 19.7 + - + +
261L LEU* 4.2 2.5 - - - +
263L ALA* 1.3 75.3 - - + +
265L ALA* 1.3 65.6 + - - +
267L PHE* 2.9 20.0 + - - +
268L TYR* 3.4 21.8 - - + -
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Residues in contact with ALA 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261L LEU* 3.0 23.9 + - + +
262L LEU* 3.8 6.1 - - + +
264L VAL* 1.3 78.3 - - - +
266L GLY* 1.3 63.2 + - - +
268L TYR* 2.9 15.7 + - - +
269L LYS* 3.4 13.3 + - - +
397L LEU* 3.9 17.7 - - + -
408L LEU* 4.0 32.0 - - + +
411L THR* 6.4 0.7 - - + -
412L ALA* 6.1 3.6 - - + -
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Residues in contact with GLY 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262L LEU 2.9 16.5 + - - -
263L ALA* 3.6 6.7 - - - -
264L VAL 3.0 1.2 - - - -
265L ALA* 1.3 77.7 - - - +
267L PHE* 1.3 60.1 + - - +
268L TYR 3.3 0.8 + - - -
269L LYS* 3.8 22.0 - - - +
397L LEU* 3.9 9.8 - - - +
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Residues in contact with PHE 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L LEU* 6.3 0.2 - - + -
183L VAL* 3.5 20.8 - - + +
184L LEU* 3.2 34.1 - - + -
185L PRO* 3.7 30.5 - - + -
188L VAL* 3.9 25.1 - - + -
263L ALA* 3.0 32.8 - - + -
264L VAL* 2.9 9.3 + - - +
266L GLY* 1.3 71.9 - - - -
268L TYR* 1.3 63.7 + - + +
269L LYS 3.7 1.6 - - - -
270L ASN* 5.4 1.0 + - - -
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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