Contacts of the strand formed by residues 241 - 246 (chain B) in PDB entry 3CFV
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 LEU 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B TRP* 3.5 6.8 - - - -
235B HIS* 2.9 39.5 + - + +
238B HIS* 3.2 35.8 + - + +
240B SER* 1.3 82.0 - - - +
242B PHE* 1.3 63.6 + - - +
253B ILE* 4.2 17.7 - - + -
254B TRP 3.4 15.5 - - - +
255B ASP* 4.1 21.3 - - + +
257B ARG* 5.0 4.5 - - - +
265B SER* 5.3 4.5 - - - +
280B PHE* 5.8 0.7 - - + -
302B LEU* 5.0 11.9 - - + -
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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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193B LEU* 3.4 33.0 - - + -
201B VAL* 4.1 17.5 - - + -
222B PHE* 3.7 38.8 - + - -
232B VAL* 3.8 10.5 - - + -
233B ALA 3.1 15.5 - - - +
234B TRP* 3.8 17.7 - + + +
235B HIS 4.2 1.6 - - - +
241B LEU* 1.3 75.8 - - - +
243B GLY* 1.3 59.3 + - - +
244B SER* 4.8 1.1 - - - -
253B ILE* 3.5 4.4 - - - +
254B TRP* 2.8 75.7 + + + -
256B THR* 4.1 13.2 - - + -
280B PHE* 4.5 4.5 - - - -
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Residues in contact with GLY 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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232B VAL* 3.4 7.6 - - - +
233B ALA 2.7 35.7 + - - -
242B PHE* 1.3 76.1 - - - +
244B SER* 1.3 58.9 + - - -
251B LEU* 5.0 0.9 - - - -
252B MSE 3.4 8.1 - - - -
253B ILE* 4.4 4.9 - - - -
278B LEU* 3.5 21.1 - - - +
280B PHE* 3.8 10.9 - - - -
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Residues in contact with SER 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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201B VAL* 4.4 17.7 - - - -
225B HIS* 2.9 25.0 - - - -
229B VAL* 4.6 0.4 - - - -
231B ASP 3.6 9.2 - - - -
232B VAL* 4.7 3.4 - - - -
242B PHE* 4.8 0.2 - - - -
243B GLY* 1.3 75.8 - - - -
245B VAL* 1.3 70.7 + - - +
251B LEU* 3.6 1.7 - - - +
252B MSE 2.7 32.8 + - - +
254B TRP* 2.6 32.3 + - - -
278B LEU* 4.0 0.8 - - - +
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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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225B HIS* 3.9 1.1 - - - -
229B VAL* 3.2 5.8 - - - +
230B GLU* 2.6 31.3 + - + -
231B ASP 3.1 13.6 + - - +
244B SER* 1.3 82.0 - - - +
246B ALA* 1.3 54.9 + - - +
250B LYS 3.8 3.6 - - - -
251B LEU* 4.0 21.8 - - + -
275B VAL* 2.8 54.3 - - + +
276B ASN 3.7 5.2 - - - +
277B CYS 3.8 9.6 - - - +
278B LEU* 4.1 21.3 - - + -
290B THR* 4.6 1.8 - - - +
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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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225B HIS* 3.2 33.9 - - + -
227B ALA 4.1 1.1 - - - +
228B VAL 3.4 8.7 - - - +
229B VAL* 3.4 18.4 - - - +
230B GLU 3.8 1.3 - - - +
245B VAL* 1.3 74.2 - - - +
247B ASP* 1.3 65.0 + - - +
248B ASP* 3.2 11.0 + - - +
249B GLN 3.5 5.9 + - - -
250B LYS 3.6 7.5 + - - -
275B VAL* 3.1 26.9 + - - +
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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