Contacts of the strand formed by residues 240 - 246 (chain B) in PDB entry 4A0L
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 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B THR* 3.1 20.6 + - - +
211B SER* 4.6 3.1 - - - -
212B SER 3.9 17.1 + - - +
213B ILE 4.9 0.2 + - - -
216B ALA* 3.8 20.2 - - + -
217B THR* 3.6 18.4 - - - +
231B ALA* 3.5 23.1 - - + +
232B LYS 4.1 8.6 + - - -
233B THR* 4.0 15.5 - - - -
238B TYR* 4.1 18.8 + + - -
239B TRP* 1.3 79.2 - - - +
241B CYS* 1.3 59.8 + - - +
242B CYS 3.8 0.2 - - - -
254B THR* 3.4 24.0 - - + -
255B GLY 3.4 8.3 - - - -
256B ASP* 3.9 18.9 + - + -
260B ARG 5.8 0.2 - - - -
262B LEU* 3.3 34.4 - - + +
273B LYS* 5.6 3.8 + - - +
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Residues in contact with CYS 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B THR* 3.3 30.6 - - + +
239B TRP* 3.7 33.0 - - - -
240B TYR* 1.3 75.7 - - - +
242B CYS* 1.3 62.2 + - - +
255B GLY 2.7 10.1 + - - +
257B SER 3.8 6.1 - - - -
280B LYS* 3.6 33.0 - - + -
281B VAL 3.4 19.3 - - - +
282B THR* 3.6 9.4 - - - +
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Residues in contact with CYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B THR 4.1 6.1 - - - +
197B GLY* 4.7 0.2 - - - -
211B SER* 3.6 11.7 + - - -
241B CYS* 1.3 78.3 - - - +
243B VAL* 1.3 62.5 + - - +
254B THR* 2.8 31.8 - - - +
255B GLY* 3.5 21.8 - - - -
281B VAL* 3.7 16.4 - - - -
282B THR 3.5 11.0 - - - +
283B HIS* 3.7 30.1 - - - +
284B ALA* 3.7 15.0 - - - +
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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
----------------------------------------------------------
197B GLY* 3.6 33.3 - - - +
198B MET* 3.8 6.7 + - - +
199B LYS* 4.9 7.4 - - + +
209B PHE* 4.1 16.8 - - + +
210B VAL 4.7 1.8 - - - +
211B SER* 3.6 16.4 - - - +
217B THR* 3.4 33.2 - - + -
242B CYS* 1.3 82.3 - - - +
244B ASP* 1.3 64.5 + - - +
245B VAL* 6.1 0.2 - - + -
252B LEU* 4.7 7.0 - - + -
253B ALA 3.3 6.1 - - - +
254B THR* 3.9 6.7 - - + +
283B HIS* 5.5 5.0 - - - -
284B ALA 4.6 4.4 - - - +
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Residues in contact with ASP 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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199B LYS* 2.7 38.8 + - - +
243B VAL* 1.3 76.4 - - - +
245B VAL* 1.3 69.2 + - - +
252B LEU* 3.4 3.6 - - - +
253B ALA* 2.9 33.2 + - + +
283B HIS* 6.1 1.3 - - + -
284B ALA 3.3 18.4 - - - +
285B GLU* 3.2 14.0 - - - +
286B PHE* 2.8 45.0 + - + +
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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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199B LYS* 3.7 30.7 + - + +
200B PHE 4.9 2.5 - - - +
201B ASN* 6.0 0.2 - - - -
209B PHE* 3.8 47.8 - - + -
243B VAL* 6.1 0.2 - - + -
244B ASP* 1.3 92.5 + - - +
246B SER* 1.3 62.6 + - - +
247B VAL* 4.2 10.3 + - + -
251B MET 3.5 5.6 - - - +
252B LEU* 3.9 21.1 - - + -
266B LEU* 4.4 7.0 - - + -
286B PHE* 3.8 7.4 - - - +
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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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245B VAL* 1.3 74.8 - - - +
247B VAL* 1.3 59.2 + - - +
248B SER* 3.2 19.8 + - - -
249B ARG* 3.4 15.6 + - - +
250B GLN* 3.0 4.9 + - - -
251B MET 2.8 36.3 + - - +
266B LEU* 4.3 2.0 - - - +
286B PHE* 3.6 37.2 - - - +
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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