Contacts of the strand formed by residues 236 - 240 (chain B) in PDB entry 3K72
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 236 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ILE* 4.7 3.1 - - + -
106B ASP 3.0 8.0 + - - +
107B LEU* 3.2 27.7 - - + +
108B TYR 3.0 22.3 + - - -
234B THR* 3.1 35.2 - - + -
235B ARG* 1.3 77.0 - - - +
237B LEU* 1.3 66.2 + - - +
295B GLN* 3.9 10.5 - - + +
297B ILE* 4.2 11.4 - - + -
334B ILE* 5.7 1.6 - - + -
337B ALA* 5.4 1.8 - - + -
338B TYR* 4.6 25.1 - - + +
341B LEU* 3.6 32.5 - - + -
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 5.6 0.7 - - - -
108B TYR* 3.5 19.3 - - + +
110B LEU* 3.6 26.7 - - + -
218B MET* 4.4 11.2 - - + +
221B VAL* 4.1 21.1 - - + -
222B ALA* 5.9 0.4 - - + -
230B TRP* 3.3 34.8 - - + -
235B ARG 4.2 0.2 + - - -
236B LEU* 1.3 78.3 - - - +
238B VAL* 1.3 63.2 + - - +
289B LEU* 5.2 2.0 - - + -
294B ILE* 3.5 22.9 - - + -
295B GLN 3.3 8.8 + - - +
296B PRO* 3.2 20.9 - - + +
297B ILE* 2.8 26.0 + - - +
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 5.6 6.5 - - + -
108B TYR 3.2 18.6 + - - +
109B TYR* 3.8 32.5 - - + -
110B LEU* 3.2 24.0 + - - +
237B LEU* 1.3 79.7 - - - +
239B PHE* 1.3 68.0 + - - +
240B ALA* 4.6 3.4 - - + +
297B ILE* 3.4 28.0 - - + +
299B ALA* 4.5 10.1 - - + -
330B VAL* 5.8 0.4 - - + -
333B LEU* 4.7 9.9 - - + -
334B ILE* 6.4 5.4 - - + -
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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
----------------------------------------------------------
110B LEU* 3.9 6.7 - - + +
149B PHE* 3.6 33.2 - + - -
212B GLU* 5.9 0.9 - - + -
214B GLY* 4.0 18.6 - - - -
215B LEU* 5.0 4.0 - - + -
218B MET* 3.7 33.9 - - + -
238B VAL* 1.3 72.6 - - - +
240B ALA* 1.3 59.2 + - - +
241B THR* 3.2 31.9 - - + -
244B GLY 5.0 2.7 - - - -
245B PHE* 5.2 7.4 - - + -
296B PRO* 4.8 7.9 - - + +
297B ILE 3.4 10.4 + - - +
298B PHE* 4.5 19.7 - + + -
299B ALA* 3.2 28.6 + - - +
300B VAL* 4.7 2.5 - - + -
308B TYR* 3.4 24.2 - + - -
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 4.5 20.2 - - + +
110B LEU 3.1 15.3 + - - +
111B MET* 4.3 12.3 - - + -
112B ASP* 3.0 24.4 + - - +
117B MET* 4.5 5.3 - - + +
149B PHE* 3.8 1.7 - - - -
238B VAL* 4.6 5.2 - - + +
239B PHE* 1.3 78.6 - - - +
241B THR* 1.3 64.4 + - - +
299B ALA* 3.5 11.2 - - + +
300B VAL* 4.5 0.2 - - - -
327B SER* 6.1 0.9 - - - +
330B VAL* 6.3 0.4 - - + -
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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
------------------------------------------------------------
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