Contacts of the helix formed by residues 240 - 250 (chain B) in PDB entry 1XFV
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 ALA 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B LYS* 3.3 44.7 - - + +
214B PHE* 3.5 24.7 - - + -
236B GLU 3.6 4.4 + - - +
237B PHE* 4.3 6.1 - - + +
238B GLN 2.6 6.1 + - - -
239B HIS* 1.3 75.0 - - - +
241B PHE* 1.3 59.0 + - - +
242B SER 3.3 1.3 - - - -
243B LEU* 3.6 1.6 + - - +
244B ALA* 3.1 26.0 + - - +
264B MET* 4.2 4.0 - - + -
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Residues in contact with PHE 241 (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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176B GLY* 4.9 4.0 - - - -
179B LEU* 4.6 9.2 - - + -
180B ASP* 3.8 26.9 - - + -
183B SER* 3.5 27.4 - - - -
184B LYS* 5.8 0.7 - - + -
185B ASP* 4.6 11.2 - - + +
194B ASN* 4.9 7.0 - - - +
237B PHE 3.7 12.8 + - - +
238B GLN* 2.7 11.9 + - - +
240B ALA* 1.3 74.0 - - - +
242B SER* 1.3 63.8 + - - +
244B ALA* 3.2 2.9 - - - +
245B PHE* 2.9 35.0 + + + +
264B MET* 3.7 12.3 - - + +
267B TYR* 4.0 18.8 - + - -
268B MET* 3.2 30.3 - - + -
271B LEU* 3.9 19.7 - - + -
276B PHE* 5.0 4.7 - + - -
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Residues in contact with SER 242 (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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173B ILE* 3.3 39.1 - - - +
176B GLY* 4.0 5.9 - - - -
177B ILE* 3.8 25.4 + - - +
180B ASP* 4.4 4.3 + - - +
238B GLN 2.8 20.3 + - - -
239B HIS* 4.5 3.5 - - - -
241B PHE* 1.3 79.7 - - - +
243B LEU* 1.3 59.8 + - - +
245B PHE* 3.3 6.8 + - - +
246B SER* 2.8 26.2 + - - -
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Residues in contact with LEU 243 (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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130B SER 5.4 0.4 - - - +
131B ARG* 4.0 34.8 - - + +
173B ILE* 3.1 34.1 - - + -
212B GLN* 3.3 28.7 - - + +
213B LYS* 3.9 12.6 - - + -
239B HIS* 2.8 26.2 - - - +
240B ALA 3.6 3.3 + - - +
242B SER* 1.3 72.3 - - - +
244B ALA* 1.3 60.1 + - - +
245B PHE 2.9 1.8 - - - -
246B SER* 2.6 24.0 + - - +
247B TYR* 2.6 31.7 + - + +
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Residues in contact with ALA 244 (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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213B LYS* 5.3 3.5 - - + +
240B ALA 3.1 18.3 + - - +
241B PHE 3.2 7.9 - - - +
243B LEU* 1.3 78.9 - - - +
245B PHE* 1.3 56.5 + - - +
247B TYR* 4.5 3.4 - - - -
248B TYR* 3.3 16.6 + - - +
257B LEU* 3.7 12.5 - - + +
264B MET* 3.4 23.8 - - + -
268B MET* 3.3 36.8 - - + +
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Residues in contact with PHE 245 (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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89B ILE* 4.1 13.5 - - + -
93B VAL* 3.5 34.5 - - + -
172B GLU* 3.4 36.6 - - + -
175B LYS* 4.2 11.7 - - + -
176B GLY* 4.6 8.5 - - - -
179B LEU* 4.3 9.2 - - + -
241B PHE* 2.9 23.8 + + + +
242B SER* 3.4 7.2 - - - +
243B LEU 2.9 0.4 - - - -
244B ALA* 1.3 76.0 - - - +
246B SER* 1.3 66.5 + - - +
247B TYR 3.2 1.6 - - - -
248B TYR* 3.1 1.9 + - - -
249B PHE* 3.1 55.8 + + - +
268B MET* 3.7 12.1 - - - -
276B PHE* 4.2 18.2 - + - -
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Residues in contact with SER 246 (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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131B ARG* 5.2 0.7 + - - -
169B VAL* 3.6 31.8 - - - +
172B GLU* 4.0 13.1 - - - +
173B ILE* 3.8 10.3 - - - -
242B SER 2.8 14.9 + - - -
243B LEU* 2.6 28.6 + - - +
245B PHE* 1.3 76.3 - - - +
247B TYR* 1.3 67.0 + - - +
250B ALA* 2.6 41.0 + - - +
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Residues in contact with TYR 247 (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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131B ARG* 2.7 44.5 + - - -
169B VAL* 4.5 0.7 - - + -
212B GLN* 3.9 14.8 + - - -
243B LEU* 2.6 23.8 + - + +
244B ALA 4.3 3.6 - - - +
246B SER* 1.3 85.6 + - - +
248B TYR* 1.3 63.7 + - - +
249B PHE 3.2 0.5 + - - -
250B ALA* 3.8 4.0 + - - -
253B HIS* 2.9 54.0 + + - +
254B ARG* 3.9 8.8 - - - +
256B VAL* 3.2 44.2 - - + +
257B LEU* 4.2 24.0 - - + -
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Residues in contact with TYR 248 (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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244B ALA 3.3 17.1 + - - +
245B PHE 3.1 6.7 + - - +
247B TYR* 1.3 78.7 - - - +
249B PHE* 1.3 82.4 + + + +
250B ALA 5.4 0.2 - - - -
254B ARG* 5.4 6.6 - - - +
257B LEU* 4.3 7.8 - - + +
265B PHE* 3.8 24.7 - + - -
268B MET* 3.2 24.2 - - + -
269B ASN* 3.4 48.8 + - + -
272B GLU* 2.9 34.7 + - + -
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Residues in contact with PHE 249 (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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88B LYS* 3.4 42.3 - - + +
89B ILE* 5.5 1.1 - - + -
90B PRO* 3.1 38.8 - - + -
172B GLU* 4.4 14.6 - - + -
245B PHE* 3.1 46.7 + + + +
248B TYR* 1.3 112.3 - + + +
250B ALA* 1.3 66.6 + - - +
251B PRO* 3.1 5.6 - - - +
268B MET* 5.5 3.6 - - + -
272B GLU* 4.7 14.8 - - + -
276B PHE* 4.1 12.1 - + - -
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 4.4 9.0 - - + +
172B GLU* 4.4 4.9 - - - +
246B SER 2.6 25.0 + - - +
247B TYR 3.8 3.9 + - - +
248B TYR 5.4 0.2 - - - -
249B PHE* 1.3 71.1 - - - +
251B PRO* 1.4 60.5 - - + +
252B ASP* 2.5 19.3 + - - +
253B HIS* 3.1 42.2 + - + +
254B ARG* 2.9 12.6 + - - -
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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