Contacts of the helix formed by residues 257 - 267 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B HIS 3.7 17.3 + - - -
109B LEU* 4.2 12.3 - - + -
112B PHE* 3.1 49.8 - + + +
113B TYR* 3.4 20.1 + + + -
252B PHE* 3.0 10.5 + - - +
253B ILE* 3.7 33.4 - - + +
256B VAL* 1.3 72.2 - - - +
258B ILE* 1.3 61.3 + - + +
260B ASP* 3.8 1.0 - - - +
261B LEU* 2.9 35.9 + - + +
411B THR 4.8 1.9 + - - -
414B ARG* 3.8 16.3 - - - +
415B GLY* 3.7 26.0 + - - -
418B CYS* 4.0 22.2 - - + -
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Residues in contact with ILE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B ILE* 2.8 39.8 + - + +
254B GLU* 4.1 11.2 - - - +
256B VAL 3.4 0.2 - - - -
257B TYR* 1.3 82.7 - - + +
259B THR* 1.3 60.4 + - + +
261B LEU* 3.2 12.6 + - + +
262B LEU* 3.0 43.9 + - + +
392B LEU* 4.8 13.7 - - + -
393B VAL* 5.5 5.2 - - + -
415B GLY* 3.2 40.6 - - - +
416B ILE* 5.4 0.2 - - - -
419B LEU* 4.6 15.5 - - + -
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Residues in contact with THR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B LEU* 3.9 35.0 - - - +
142B SER* 3.9 8.0 + - - -
143B PRO* 5.3 1.3 - - + -
195B HIS* 5.5 0.5 - - - -
254B GLU 3.6 15.3 - - - +
255B GLN* 2.9 29.5 + - - +
256B VAL* 3.1 7.3 + - - -
258B ILE* 1.3 77.4 - - + +
260B ASP* 1.3 67.8 + - - +
262B LEU* 3.4 7.7 + - - +
263B ALA* 3.1 24.3 + - - +
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Residues in contact with ASP 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 4.2 10.3 - - + -
113B TYR* 2.9 19.4 + - + +
141B LEU* 5.4 4.7 - - - +
191B ILE* 3.9 13.4 - - - +
192B ALA* 4.6 6.4 - - + -
195B HIS* 2.2 48.6 + - - +
256B VAL 3.0 17.3 + - - +
257B TYR 3.9 1.1 - - - +
259B THR* 1.3 78.5 + - - +
261B LEU* 1.3 68.3 + - - +
263B ALA* 4.3 5.1 - - - +
264B VAL* 3.0 32.0 + - + +
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Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 3.9 24.0 - - + -
257B TYR* 2.9 26.2 + - + +
258B ILE* 3.4 17.3 - - + +
260B ASP* 1.3 80.5 - - - +
262B LEU* 1.3 68.5 + - + +
264B VAL* 4.0 1.4 - - - +
265B ALA* 3.0 29.2 + - + +
393B VAL* 6.4 1.3 - - + -
411B THR* 3.6 34.1 - - + +
412B ALA* 4.2 18.4 - - + +
415B GLY* 3.6 31.2 - - - -
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ILE* 3.0 33.3 + - + +
259B THR* 3.4 5.1 + - - +
260B ASP 3.3 0.4 - - - -
261B LEU* 1.3 83.0 - - + +
263B ALA* 1.3 54.0 - - - +
265B ALA* 4.4 1.1 - - + -
266B GLY* 2.9 28.6 + - - -
392B LEU* 4.7 8.1 - - + -
393B VAL* 3.7 45.1 - - + +
396B THR* 3.5 37.6 - - + +
397B LEU* 3.4 25.0 - - + +
412B ALA* 5.4 2.7 - - + -
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Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B LEU* 3.7 29.2 - - + -
188B VAL* 5.4 6.1 - - + -
259B THR 3.1 17.6 + - - +
260B ASP* 3.8 6.7 - - - +
261B LEU 3.2 0.2 - - - -
262B LEU* 1.3 74.2 - - - +
264B VAL* 1.3 68.6 + - + +
266B GLY* 3.2 9.3 + - - -
267B PHE* 3.0 26.8 - - + -
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Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 5.3 12.1 - - + -
120B TRP* 3.9 32.5 - - + -
121B VAL* 4.8 8.7 - - + -
184B LEU* 4.1 19.1 - - + -
188B VAL* 4.3 10.5 - - + -
192B ALA* 5.2 6.5 - - + -
260B ASP* 3.0 19.5 + - + +
261B LEU* 4.2 2.5 - - - +
263B ALA* 1.3 76.4 - - + +
265B ALA* 1.3 64.9 + - - +
267B PHE* 2.8 19.8 + - - +
268B TYR* 3.4 21.5 - - + -
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Residues in contact with ALA 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B LEU* 3.0 24.1 + - + +
262B LEU* 3.8 5.6 - - + +
264B VAL* 1.3 77.5 - - - +
266B GLY* 1.3 62.2 + - - +
268B TYR* 2.9 17.0 + - - +
269B LYS* 3.4 13.2 + - - +
397B LEU* 3.9 18.4 - - + -
408B LEU* 4.0 31.8 - - + +
411B THR* 6.4 0.7 - - + -
412B ALA* 6.1 3.4 - - + -
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Residues in contact with GLY 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LEU 2.9 15.9 + - - -
263B ALA* 3.2 7.8 + - - -
264B VAL 3.0 0.8 - - - -
265B ALA* 1.3 77.3 - - - +
267B PHE* 1.3 61.1 + - - +
268B TYR 3.3 0.6 + - - -
269B LYS* 3.8 23.1 + - - +
397B LEU* 3.9 9.8 - - - +
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Residues in contact with PHE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B VAL* 3.5 21.1 - - + +
184B LEU* 3.2 33.9 - - + -
185B PRO* 3.7 30.5 - - + -
188B VAL* 3.9 24.5 - - + -
263B ALA* 3.0 34.1 - - + -
264B VAL 2.8 9.1 + - - +
266B GLY* 1.3 72.6 - - - -
268B TYR* 1.3 63.0 + - + +
269B LYS 3.7 1.6 - - - -
270B 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