Contacts of the strand formed by residues 85 - 90 (chain C) in PDB entry 1AUT
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 85 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 4.7 0.9 - - + -
59C MET* 6.2 1.1 - - - -
64C LEU* 3.4 41.0 + - + +
66C VAL* 3.7 30.3 - - + +
83C LEU 4.0 0.2 + - - -
84C ASP* 1.3 78.7 + - - +
86C LYS* 1.3 65.1 + - - +
87C GLU 3.7 20.6 - - - +
88C VAL* 3.8 21.3 - - + -
106C LEU* 4.0 28.7 - - + -
107C HIS 4.2 3.8 - - - +
108C LEU* 4.6 4.3 - - + +
109C ALA* 4.5 1.1 - - - +
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ASP* 3.2 4.4 + - - -
85C ILE* 1.3 75.1 - - - +
87C GLU* 1.3 84.6 + - + +
107C HIS* 2.9 36.0 + - - +
108C LEU 3.9 1.3 + - - +
109C ALA* 3.7 33.6 + - + +
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Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ILE* 3.7 3.8 - - - +
86C LYS* 1.3 108.3 - - + +
88C VAL* 1.3 65.3 + - - +
89C PHE* 3.2 34.3 - - + -
105C LEU 4.1 0.3 - - - +
107C HIS* 2.8 46.2 + - + +
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C MET* 3.7 15.7 - - + -
85C ILE* 3.8 24.5 - - + -
86C LYS 6.0 0.2 - - - -
87C GLU* 1.3 74.8 - - - +
89C PHE* 1.3 74.7 + - - +
90C VAL* 3.7 26.2 + - + +
104C ALA* 4.8 0.2 - - + -
105C LEU 3.9 2.2 - - - -
106C LEU* 3.7 21.1 - - + -
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TRP* 3.2 38.1 - + - -
87C GLU* 3.2 32.1 - - + -
88C VAL* 1.3 83.3 - - - +
90C VAL* 1.3 64.1 + - - +
105C LEU* 2.8 53.2 + - + +
107C HIS* 4.0 9.2 - - + -
237C TRP* 3.2 17.0 - - + -
241C HIS* 3.8 33.4 - + - +
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Residues in contact with VAL 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA* 4.3 8.1 - - + +
59C MET* 3.4 34.1 - - + -
88C VAL* 3.7 9.6 + - + -
89C PHE* 1.3 73.7 - - - +
91C HIS* 1.3 73.3 + - - +
92C PRO* 3.1 7.2 - - + +
94C TYR* 4.6 16.6 - - + -
104C ALA* 3.8 11.9 - - + +
237C TRP* 4.1 0.7 - - - -
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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