Contacts of the strand formed by residues 241 - 250 (chain B) in PDB entry 5F2R
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 VAL 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B THR* 3.7 1.2 + - - +
237B ILE* 3.6 4.7 - - - +
238B ASP* 2.9 32.7 + - - +
239B ASN* 3.6 13.7 - - + +
240B GLY* 1.3 79.5 - - - +
242B PHE* 1.3 71.6 + - - +
243B GLU* 4.0 1.9 + - + +
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Residues in contact with PHE 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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203B THR* 3.5 28.9 - - + +
206B ALA* 3.8 26.5 - - + -
207B ILE* 3.7 21.3 - - + -
212B ASP* 3.6 42.4 - - + -
220B ILE* 4.0 8.7 - - + -
235B LEU* 4.2 15.7 - - + -
236B THR 3.3 8.7 - - - -
237B ILE* 3.8 26.2 - - + -
240B GLY 4.3 6.5 - - - -
241B VAL* 1.3 84.7 - - - +
243B GLU* 1.3 60.8 + - - +
244B VAL* 6.0 0.9 - - + -
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Residues in contact with GLU 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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235B LEU* 3.2 8.2 - - - -
236B THR* 2.9 44.7 + - - +
241B VAL* 4.0 1.8 + - + +
242B PHE* 1.3 75.0 - - - +
244B VAL* 1.3 71.3 + - - +
245B VAL* 3.5 17.5 + - - +
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Residues in contact with VAL 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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174B ALA* 4.2 15.9 - - + +
200B ASN* 3.6 27.6 - - - +
203B THR* 4.7 3.6 - - - +
233B SER* 5.1 0.4 - - - -
234B LEU 3.8 2.7 - - - -
235B LEU* 3.7 21.3 - - + -
242B PHE* 5.9 0.7 - - + +
243B GLU* 1.3 78.0 - - - +
245B VAL* 1.3 63.2 + - - +
246B ALA 4.1 7.9 - - - +
247B THR* 3.6 31.4 - - + -
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Residues in contact with VAL 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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234B LEU* 2.8 30.9 + - + +
236B THR* 3.8 28.7 - - + +
243B GLU* 4.0 22.2 - - - +
244B VAL* 1.3 77.3 - - - +
246B ALA* 1.3 59.1 + - + +
349B SER* 3.8 24.9 - - - +
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Residues in contact with ALA 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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233B SER* 3.5 2.3 - - - -
234B LEU* 2.8 29.2 + - + +
244B VAL* 3.6 2.1 - - - +
245B VAL* 1.3 81.5 - - + +
247B THR* 1.3 68.6 + - - +
345B VAL* 4.3 15.5 - - + +
348B ASP* 4.7 14.1 - - + +
349B SER* 3.3 22.9 - - - +
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Residues in contact with THR 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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174B ALA* 3.8 20.0 - - + -
175B TYR* 4.0 27.9 - - + +
232B VAL 3.2 9.0 - - - -
233B SER* 4.3 6.5 - - - +
244B VAL* 3.6 22.4 - - + -
246B ALA* 1.3 81.2 - - - +
248B ASN* 1.3 71.5 + - - +
345B VAL* 4.2 2.8 - - - +
348B ASP* 5.6 1.2 - - - +
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Residues in contact with ASN 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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175B TYR* 5.9 1.2 - - - -
230B PHE 4.0 0.3 - - - +
231B ASP* 3.5 10.2 - - - +
232B VAL* 2.8 27.2 + - - +
247B THR* 1.3 77.2 + - - +
249B GLY* 1.3 78.8 + - - +
341B PRO* 3.8 15.9 - - - +
344B LYS* 3.6 29.5 - - - +
345B VAL* 3.5 20.7 - - + +
348B ASP* 4.6 7.3 + - - -
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Residues in contact with GLY 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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230B PHE* 3.2 17.5 - - - -
232B VAL 4.3 1.8 - - - -
248B ASN* 1.3 94.5 + - - +
250B ASP* 1.3 62.3 + - - +
341B PRO* 3.6 24.9 - - - +
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Residues in contact with ASP 250 (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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230B PHE* 2.8 43.7 + - + +
249B GLY* 1.3 73.9 - - - +
251B THR* 1.3 62.6 + - - +
252B HIS* 2.9 24.9 + - - +
253B LEU* 3.7 32.2 + - + +
341B PRO* 5.3 2.5 - - + -
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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