Contacts of the strand formed by residues 89 - 94 (chain C) in PDB entry 6KTR
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 THR 89 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ALA* 3.4 7.3 - - - +
85C VAL* 3.0 37.3 + - + -
86C ALA* 3.4 28.9 + - + +
87C LEU 3.5 1.0 - - - -
88C ARG* 1.3 84.4 + - - +
90C VAL* 1.3 64.2 + - - +
117C GLU* 6.3 0.2 - - + -
121C ALA* 3.7 9.2 - - + +
122C PHE 3.2 26.2 - - - +
123C GLU* 4.0 11.8 - - + +
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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
----------------------------------------------------------
43C ARG* 3.9 9.4 - - - +
82C ILE* 3.5 26.2 - - + -
83C LYS 3.6 5.2 - - - +
84C ALA* 4.9 4.7 - - + -
85C VAL* 4.3 4.7 - - - -
88C ARG 4.3 2.0 - - - +
89C THR* 1.3 81.5 - - - +
91C ALA* 1.3 67.6 + - - +
92C ILE* 3.8 18.8 - - + -
120C CYS 3.8 0.9 - - - +
121C ALA* 3.3 4.3 - - - -
122C PHE* 2.5 40.3 + - + +
124C GLU* 3.6 36.6 - - + +
134C TYR* 4.4 6.7 - - + -
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Residues in contact with ALA 91 (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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81C GLU 3.6 3.8 - - - +
82C ILE* 3.6 2.8 - - - -
83C LYS* 3.0 32.8 + - + +
85C VAL* 3.8 23.2 - - + +
90C VAL* 1.3 76.0 - - - +
92C ILE* 1.3 61.0 + - - +
100C TYR* 4.8 11.0 - - + -
115C TYR* 3.8 24.0 - - + -
120C CYS 3.8 5.4 - - - +
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Residues in contact with ILE 92 (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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47C LEU* 4.4 13.2 - - + -
62C ILE* 5.1 0.9 - - + -
80C LEU* 3.7 38.4 - - + -
81C GLU 3.5 4.5 - - - +
82C ILE* 4.3 9.2 - - + -
90C VAL* 3.8 13.7 - - + -
91C ALA* 1.3 77.6 - - - +
93C LYS* 1.3 58.9 + - - +
94C GLY 4.4 0.2 + - - -
100C TYR* 3.4 5.1 - - - +
101C LEU* 2.6 64.3 + - + +
120C CYS 4.4 4.6 + - - -
122C PHE* 4.4 12.3 - - + -
134C TYR* 4.1 31.2 - - + -
143C VAL* 5.7 0.4 - - + -
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Residues in contact with LYS 93 (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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62C ILE* 4.6 0.7 - - - -
80C LEU* 4.4 1.8 - - - -
81C GLU* 2.7 69.0 + - - +
91C ALA 4.2 0.2 - - - -
92C ILE* 1.3 74.3 - - - +
94C GLY* 1.3 72.6 + - - +
95C VAL* 3.4 5.4 + - - +
98C VAL* 4.3 24.4 - - + +
99C ARG 3.5 17.0 - - - +
100C TYR* 3.5 45.0 + - + -
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Residues in contact with GLY 94 (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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62C ILE* 3.6 22.0 - - - +
77C HIS* 5.2 3.1 - - - -
79C LEU 3.6 10.5 - - - -
80C LEU* 4.1 4.0 - - - -
93C LYS* 1.3 72.9 - - - +
95C VAL* 1.3 61.2 + - - -
96C HIS 3.4 2.2 - - - -
97C SER* 4.1 7.2 - - - -
98C VAL* 2.9 31.2 + - - -
99C ARG 3.1 12.3 + - - -
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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