Contacts of the strand formed by residues 241 - 245 (chain B) in PDB entry 2FV7
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 CYS 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ILE* 3.9 17.0 - - + -
234B ILE 3.3 14.8 - - - +
235B THR* 4.0 8.3 - - + -
236B LEU* 4.2 4.5 - - - -
239B GLU 3.6 2.4 + - - -
240B GLY* 1.3 75.5 - - - +
242B VAL* 1.3 57.5 + - - +
253B HIS* 3.4 7.4 - - - -
254B ILE* 2.8 47.0 + - - +
271B PHE* 4.1 17.3 - - + -
291B LEU* 4.3 15.0 - - - -
295B ASN* 3.9 18.2 - - - +
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA 4.5 4.9 - - - +
217B ALA* 3.5 35.4 - - + +
218B GLY* 4.3 7.6 - - - +
221B ALA* 5.0 1.8 - - + -
232B VAL 3.8 0.7 - - - +
233B ILE* 3.4 5.4 - - - +
234B ILE* 3.0 42.6 + - + +
236B LEU* 4.3 7.4 - - + +
241B CYS* 1.3 75.2 - - - +
243B VAL* 1.3 63.7 + - - +
244B LEU* 4.2 5.7 - - + +
251B PRO* 3.8 26.2 - - + -
252B LYS 3.4 14.6 - - - +
253B HIS* 4.5 6.7 - - + +
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B VAL* 3.9 15.7 - - + -
232B VAL 3.3 10.5 - - - +
233B ILE* 4.0 3.1 - - + -
242B VAL* 1.3 75.1 - - - +
244B LEU* 1.3 76.9 + - - +
245B SER* 5.7 0.2 - - - -
248B GLU 5.0 0.2 - - - +
250B GLU 3.9 2.1 - - - +
251B PRO* 3.6 1.4 - - - +
252B LYS* 3.0 53.5 + - + +
254B ILE* 3.6 22.0 - - + -
287B LEU* 4.0 9.9 - - + -
288B GLU* 5.4 2.7 - - + -
291B LEU* 3.6 23.1 - - + -
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Residues in contact with LEU 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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218B GLY 4.0 1.1 - - - +
221B ALA* 3.1 27.6 - - + +
222B LEU* 3.6 38.6 - - + +
225B LEU* 4.3 11.2 - - + -
231B VAL* 3.4 4.9 - - - +
232B VAL* 2.8 32.6 + - + +
242B VAL* 4.2 6.7 - - + -
243B VAL* 1.3 84.6 - - - +
245B SER* 1.3 63.7 + - - +
248B GLU 4.0 6.1 - - - -
249B PRO 3.4 25.6 - - - +
250B GLU 4.7 0.2 - - - -
251B PRO* 3.7 30.1 - - + -
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Residues in contact with SER 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 LEU* 3.6 8.5 - - - +
230B GLN 3.2 13.0 - - - -
231B VAL* 3.9 15.9 - - - -
243B VAL* 5.7 0.4 - - - -
244B LEU* 1.3 76.3 - - - +
246B GLN* 1.3 59.8 - - - +
247B THR* 3.3 10.7 + - - -
248B GLU* 3.0 28.8 + - - +
249B PRO* 3.0 29.6 - - - +
287B LEU* 5.3 4.5 - - - -
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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