Contacts of the helix formed by residues 257 - 267 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108J HIS 3.7 17.2 + - - -
109J LEU* 4.2 12.8 - - + -
112J PHE* 3.1 49.2 - + + +
113J TYR* 3.4 18.9 + + + -
252J PHE* 3.0 11.3 + - - +
253J ILE* 3.7 33.9 - - + +
256J VAL* 1.3 70.9 - - - +
258J ILE* 1.3 60.5 + - + +
260J ASP* 3.9 1.0 - - - +
261J LEU* 2.9 36.4 + - + +
411J THR 4.8 1.9 + - - -
414J ARG* 3.8 16.1 - - - +
415J GLY* 3.7 26.1 + - - -
418J CYS* 4.0 21.8 - - + -
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Residues in contact with ILE 258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253J ILE* 2.8 40.6 + - + +
254J GLU* 4.1 11.7 - - - +
256J VAL 3.4 0.2 - - - -
257J TYR* 1.3 81.6 - - + +
259J THR* 1.3 59.6 + - + +
261J LEU* 3.2 13.0 + - + +
262J LEU* 3.0 43.9 + - + +
392J LEU* 4.8 13.9 - - + -
393J VAL* 5.5 4.5 - - + -
415J GLY* 3.2 40.8 - - - +
419J LEU* 4.6 16.2 - - + -
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Residues in contact with THR 259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J LEU* 3.9 33.9 - - - +
142J SER* 3.9 8.4 + - - -
143J PRO* 5.3 1.1 - - + -
195J HIS* 5.5 0.5 - - - -
254J GLU 3.6 15.9 - - - +
255J GLN 2.9 28.5 + - - +
256J VAL* 3.1 7.3 + - - -
258J ILE* 1.3 78.3 - - + +
260J ASP* 1.3 67.1 + - - +
262J LEU* 3.4 7.0 + - - +
263J ALA* 3.1 24.5 + - - +
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Residues in contact with ASP 260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J PHE* 4.2 10.7 - - + -
113J TYR* 2.9 19.1 + - + +
141J LEU* 5.4 4.7 - - - +
191J ILE* 3.9 14.4 - - - +
192J ALA* 4.6 6.7 - - + -
195J HIS* 2.2 48.3 + - - +
256J VAL 3.0 17.7 + - - +
257J TYR 3.9 0.9 - - - +
259J THR* 1.3 77.8 + - - +
261J LEU* 1.3 69.4 + - - +
263J ALA* 3.8 5.3 - - - +
264J VAL* 3.0 32.7 + - + +
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Residues in contact with LEU 261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J PHE* 3.9 24.2 - - + -
257J TYR* 2.9 26.7 + - + +
258J ILE* 3.4 17.5 - - + +
259J THR 3.2 0.2 - - - -
260J ASP* 1.3 79.5 - - - +
262J LEU* 1.3 68.4 + - + +
264J VAL* 3.5 1.2 + - - +
265J ALA* 3.0 29.8 + - + +
411J THR* 3.6 35.0 - - + +
412J ALA* 4.2 15.9 - - + +
415J GLY* 3.6 32.1 - - - +
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Residues in contact with LEU 262 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258J ILE* 3.0 33.5 + - + +
259J THR* 3.4 5.4 + - - +
260J ASP 3.3 0.2 - - - -
261J LEU* 1.3 83.0 - - + +
263J ALA* 1.3 53.8 + - - +
265J ALA* 4.4 1.3 - - + -
266J GLY* 2.9 28.4 + - - -
392J LEU* 4.7 8.7 - - + -
393J VAL* 3.7 45.1 - - + +
396J THR* 3.5 37.8 - - + +
397J LEU* 3.4 24.5 - - + +
412J ALA* 5.4 2.7 - - + -
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Residues in contact with ALA 263 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J LEU* 3.7 29.2 - - + -
188J VAL* 5.4 5.8 - - + -
259J THR 3.1 17.0 + - - +
260J ASP* 3.8 6.3 - - - +
261J LEU 3.2 0.2 - - - -
262J LEU* 1.3 75.0 - - - +
264J VAL* 1.3 67.9 + - + +
266J GLY* 3.2 8.8 + - - -
267J PHE* 3.0 28.1 - - + -
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Residues in contact with VAL 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J PHE* 5.3 11.7 - - + -
120J TRP* 3.9 31.4 - - + -
121J VAL* 4.8 8.7 - - + -
184J LEU* 4.1 18.8 - - + -
188J VAL* 4.3 10.5 - - + -
192J ALA* 5.2 7.0 - - + -
260J ASP* 3.0 20.0 + - + +
261J LEU* 4.2 2.2 - - - +
263J ALA* 1.3 76.2 - - + +
265J ALA* 1.3 65.5 + - - +
267J PHE* 2.8 19.6 + - - +
268J TYR* 3.4 22.1 - - + -
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Residues in contact with ALA 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261J LEU* 3.0 24.1 + - + +
262J LEU* 3.8 6.1 - - + +
264J VAL* 1.3 77.0 - - - +
266J GLY* 1.3 62.0 + - - +
268J TYR* 2.9 16.6 + - - +
269J LYS* 3.4 12.8 + - - +
397J LEU* 3.9 17.7 - - + -
408J LEU* 4.0 31.8 - - + +
411J THR* 6.4 0.9 - - + -
412J ALA* 6.1 3.6 - - + -
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Residues in contact with GLY 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262J LEU 2.9 15.7 + - - -
263J ALA 3.6 6.5 - - - -
264J VAL 3.0 1.2 - - - -
265J ALA* 1.3 77.6 - - - +
267J PHE* 1.3 60.3 + - - +
268J TYR 3.3 0.8 + - - -
269J LYS* 3.8 23.7 - - - +
397J LEU* 3.9 10.5 - - - +
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Residues in contact with PHE 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183J VAL* 3.5 20.5 - - + +
184J LEU* 3.2 33.9 - - + -
185J PRO* 3.7 30.3 - - + -
188J VAL* 3.9 24.9 - - + -
263J ALA* 3.0 33.9 - - + -
264J VAL 2.8 9.9 + - - +
266J GLY* 1.3 72.4 - - - -
268J TYR* 1.3 64.2 - - + +
269J LYS 3.7 1.3 - - - -
270J ASN* 5.4 0.7 + - - -
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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