Contacts of the strand formed by residues 237 - 241 (chain B) in PDB entry 3A3K
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 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B TRP* 3.8 19.7 - - + -
208B ARG 3.1 4.8 + - - +
209B VAL* 4.0 16.6 - - + -
210B ILE* 2.9 29.1 + - - +
236B TYR* 1.3 75.0 - - - +
238B PHE* 1.3 64.9 + - - +
239B PHE* 3.8 37.2 - - + -
276B ALA 3.6 9.6 - - - +
278B LYS* 4.2 13.9 - - + -
411B TRP* 4.0 24.7 - - + -
417B PRO* 4.2 6.0 - - + +
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Residues in contact with PHE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 4.1 16.4 - - + -
210B ILE* 3.5 38.4 - - + -
212B ILE* 4.4 4.7 - - + -
219B PHE* 4.0 4.6 - - + -
223B MET* 3.5 42.6 - - + -
226B ALA* 3.8 28.7 - - + -
231B LEU* 4.6 7.2 - - + -
236B TYR* 3.8 31.6 - + + -
237B VAL* 1.3 72.5 - - - +
239B PHE* 1.3 61.4 + - - +
240B HIS 3.8 0.9 + - - -
276B ALA* 2.9 28.9 + - + +
277B ALA* 3.3 3.5 - - - +
278B LYS 3.0 26.3 + - - +
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Residues in contact with PHE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 4.1 15.0 - - + -
144B LEU* 5.1 1.8 - - + -
146B TRP* 3.6 41.3 - + - -
209B VAL* 4.1 2.7 - - + -
210B ILE 2.7 15.2 + - - -
211B TYR* 3.4 39.6 - + + +
212B ILE* 2.9 27.3 + - - +
219B PHE* 4.2 2.2 - - - -
237B VAL* 3.8 22.9 - - + -
238B PHE* 1.3 70.1 - - - +
240B HIS* 1.3 62.8 + - - +
241B LEU 3.3 1.2 + - - -
278B LYS* 3.4 27.4 - - + -
280B ILE* 3.9 20.4 - - + -
378B LEU* 3.8 22.2 - - + -
409B LEU* 6.6 0.2 - - + -
411B TRP* 5.2 0.9 - + - -
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Residues in contact with HIS 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE 3.3 15.9 - - - -
214B SER* 3.0 28.3 + - - -
215B SER 4.1 1.2 + - - -
216B PRO* 3.9 24.5 - - + -
219B PHE* 3.4 45.9 - + + +
239B PHE* 1.3 70.9 - - - +
241B LEU* 1.3 66.2 + - - +
242B ASP* 3.2 31.1 + - + +
247B SER* 3.9 12.6 + - - -
278B LYS 2.8 14.0 + - - +
279B ILE* 3.6 10.7 - - + +
280B ILE* 2.8 29.4 + - - -
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Residues in contact with LEU 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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133B LEU* 4.3 16.6 - - + -
137B VAL* 5.4 0.2 - - + -
152B VAL* 4.8 7.2 - - + -
167B ILE* 3.9 22.2 - - + +
168B VAL* 4.9 1.6 - - + -
171B LEU* 3.8 28.9 - - + -
211B TYR* 4.1 23.3 - - + -
212B ILE 2.8 16.4 + - - +
213B CYS* 4.1 32.9 - - + +
214B SER 4.5 2.1 + - - +
239B PHE 3.3 5.1 + - - +
240B HIS* 1.3 76.1 + - - +
242B ASP* 1.3 60.4 + - - +
243B VAL* 3.7 7.3 + - + -
280B ILE* 4.0 28.0 - - + -
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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
------------------------------------------------------------
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