Contacts of the strand formed by residues 40 - 44 (chain B) in PDB entry 5KYT
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 ILE 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLY 3.3 14.1 + - - +
39B THR* 1.3 74.9 - - - +
41B ALA* 1.3 61.2 + - - +
42B PHE 3.5 22.2 - - - +
43B THR* 3.7 12.3 - - - +
50B ASN* 4.0 21.3 - - + +
51B ILE 3.6 7.2 - - - +
52B THR* 4.0 6.3 - - + +
53B TYR* 3.3 11.5 - - - -
259B GLY 4.8 0.5 - - - +
260B PHE 4.0 0.2 - - - -
261B ARG* 3.3 61.3 + - + +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 1.3 74.3 - - - +
42B PHE* 1.3 67.1 + - + +
51B ILE 2.9 14.7 + - - +
52B THR 4.2 2.0 - - - +
53B TYR* 3.3 44.4 - - + +
56B TYR* 4.3 8.3 - - + -
256B LEU* 4.2 6.1 - - + +
260B PHE 3.6 2.9 - - - +
262B VAL* 2.7 36.3 + - - +
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Residues in contact with PHE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 3.5 3.5 - - - +
41B ALA* 1.3 80.8 - - + +
43B THR* 1.3 65.4 + - - +
50B ASN* 3.5 0.3 - - - -
51B ILE* 2.9 31.4 + - + +
56B TYR* 3.3 46.7 - + + -
85B SER 5.2 1.8 - - - -
86B LEU* 3.6 20.6 - - + +
89B PHE* 3.8 25.4 - + - -
243B PHE* 4.4 7.2 - + - -
252B THR* 3.9 12.1 - - + -
256B LEU* 3.7 29.8 - - + -
262B VAL* 3.3 37.2 - - + -
264B LEU* 3.9 14.8 - - + -
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Residues in contact with THR 43 (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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40B ILE* 3.7 1.2 - - - +
42B PHE* 1.3 74.4 + - - +
44B ASP* 1.3 66.6 + - - +
45B ALA 3.4 0.7 + - - +
48B GLU* 5.2 0.4 - - - -
49B VAL 3.3 9.9 - - - +
50B ASN* 2.6 28.0 + - - +
86B LEU* 3.9 3.1 - - - -
261B ARG* 2.9 21.6 + - - +
262B VAL 3.0 7.1 + - - -
263B VAL* 3.4 11.5 - - + -
264B LEU* 2.8 30.7 + - - +
280B TYR* 3.5 36.3 - - + +
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Residues in contact with ASP 44 (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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43B THR* 1.3 71.0 - - - +
45B ALA* 1.3 58.9 + - - +
46B HIS* 2.9 26.8 + - - +
47B ILE* 3.3 31.0 + - + +
48B GLU* 2.8 30.1 + - - -
49B VAL 2.9 9.3 + - - +
84B ASN 5.5 0.5 - - - +
85B SER* 5.0 2.8 - - - -
86B LEU* 3.5 26.8 + - + +
264B LEU* 3.9 23.8 - - + +
265B MET* 4.8 1.4 - - - -
266B TYR* 5.3 4.2 + - - +
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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