Contacts of the strand formed by residues 107 - 112 (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 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ILE* 3.7 25.6 - - + -
106B ASP* 1.3 77.7 - - - +
108B TYR* 1.3 63.6 + - - +
131B LEU* 5.8 10.8 - - + -
135B LEU* 6.4 2.9 - - + -
143B ARG 3.3 13.0 + - - +
144B ILE* 5.1 11.4 - - + -
145B GLY 3.2 21.0 + - - +
188B LEU* 3.7 8.0 - - - +
236B LEU* 3.2 34.3 - - + +
237B LEU* 5.5 2.5 - - - +
238B VAL* 5.6 6.7 - - + -
297B ILE* 5.4 4.9 - - + -
334B ILE* 3.8 31.6 - - + -
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Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 1.3 76.6 - - - +
109B TYR* 1.3 59.3 + - - +
110B LEU* 3.4 29.1 + - + -
145B GLY* 3.3 17.0 - - - -
146B PHE 2.8 29.4 + - - -
147B GLY* 3.0 26.6 - - - -
182B PHE* 4.0 8.3 - - - -
184B HIS* 2.9 32.5 + + - -
186B LEU 4.3 0.7 - - - -
188B LEU* 4.2 7.2 - - + -
221B VAL* 4.2 13.7 - - + -
228B ILE* 5.0 3.8 - - + +
230B TRP* 4.0 17.5 - + + -
236B LEU 3.0 4.9 + - - -
237B LEU* 3.5 25.0 - - + +
238B VAL* 3.2 28.3 + - - +
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Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B TYR* 1.3 71.0 - - - +
110B LEU* 1.3 62.4 + - - +
111B MET* 3.2 54.3 + - + +
124B VAL* 4.0 20.7 - - + +
131B LEU* 6.1 4.7 - - + -
145B GLY 3.1 12.8 + - - +
146B PHE* 3.4 25.7 - + + -
147B GLY 2.9 24.1 + - - +
195B PHE* 5.5 2.9 - - + -
238B VAL* 3.8 21.1 - - + -
240B ALA* 4.5 12.4 - - + +
327B SER* 4.9 2.6 + - - -
330B VAL* 3.6 32.0 - - + +
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Residues in contact with LEU 110 (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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108B TYR* 3.4 33.8 + - + -
109B TYR* 1.3 70.1 - - - +
111B MET* 1.3 56.4 + - - +
147B GLY 3.4 9.4 - - - +
149B PHE* 3.4 22.9 - - + -
182B PHE* 4.8 3.6 - - + -
217B ALA* 5.4 2.0 - - + -
218B MET* 3.1 44.4 - - + -
221B VAL* 3.9 14.8 - - + -
237B LEU* 3.6 21.3 - - + -
238B VAL 3.2 18.1 + - - +
239B PHE* 4.3 5.2 - - + -
240B ALA* 3.1 25.1 + - - +
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Residues in contact with MET 111 (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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109B TYR* 3.2 51.5 + - + +
110B LEU* 1.3 72.7 - - - +
112B ASP* 1.3 73.4 + - - +
113B LEU* 3.5 20.6 + - + +
117B MET* 3.8 22.9 - - + +
120B ASP* 4.3 18.2 - - + +
121B LEU* 4.9 14.8 - - - -
124B VAL* 4.5 8.1 - - + -
146B PHE* 4.0 13.5 - - + -
147B GLY 3.3 3.8 + - - -
148B SER* 3.7 6.2 + - - -
149B PHE* 3.4 23.4 + - - -
240B ALA* 3.8 6.7 - - + -
327B SER* 4.7 4.0 - - - +
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Residues in contact with ASP 112 (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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111B MET* 1.3 77.1 - - - +
113B LEU* 1.3 59.2 + - - +
114B SER* 3.0 21.7 + - - -
117B MET* 2.9 29.2 - - + +
149B PHE* 3.1 27.8 - - + +
150B VAL* 3.6 4.2 - - - -
212B GLU* 3.1 30.7 - - - +
240B ALA 3.0 15.5 + - - +
241B THR* 2.9 30.6 + - - +
242B ASP* 4.2 3.1 - - - +
243B ASP* 3.4 5.5 - - - +
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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
------------------------------------------------------------
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