Contacts of the helix formed by residues 87 - 99 (chain C) in PDB entry 4XEK
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 87 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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925A ASP* 2.8 48.3 + - + +
928A LEU* 6.1 2.0 - - + -
86C LYS* 1.3 78.3 - - - +
88C SER* 1.3 65.5 + - - +
89C ALA* 3.6 5.1 + - - +
90C ALA* 3.2 14.7 + - - +
91C ALA* 3.0 22.3 + - - +
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Residues in contact with SER 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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944A LYS* 3.3 24.3 + - - -
87C THR* 1.3 74.4 - - - +
89C ALA* 1.3 57.6 + - - +
91C ALA* 3.3 6.6 + - - +
92C GLN* 2.9 31.7 + - - +
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Residues in contact with ALA 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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921A ILE* 4.1 11.2 - - + +
925A ASP* 5.1 0.2 - - - +
943A GLN* 4.0 33.4 - - + +
944A LYS* 3.9 17.5 - - + +
947A ASN* 2.9 30.5 + - - +
87C THR* 3.3 7.8 + - - +
88C SER* 1.3 78.8 + - - +
90C ALA* 1.3 62.2 + - - +
92C GLN* 4.3 0.2 - - - -
93C LEU* 3.1 13.0 + - - +
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Residues in contact with ALA 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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918A ARG* 6.3 1.1 - - - +
921A ILE* 3.9 11.6 - - + +
922A GLY* 6.1 1.1 - - - +
925A ASP* 3.8 11.2 - - - +
86C LYS* 4.2 16.2 - - + -
87C THR* 3.2 20.9 + - - +
89C ALA* 1.3 78.9 - - - +
91C ALA* 1.3 58.1 + - - +
93C LEU* 3.4 4.8 + - - +
94C ASP* 3.0 33.8 + - - +
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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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86C LYS* 4.1 23.9 - - + +
87C THR 3.0 16.8 + - - +
88C SER* 3.7 6.1 - - - +
90C ALA* 1.3 75.1 - - - +
92C GLN* 1.3 65.1 + - - +
94C ASP* 3.2 3.6 + - - +
95C GLU* 3.1 22.5 + - - +
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Residues in contact with GLN 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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944A LYS* 3.4 33.1 + - - +
947A ASN* 2.8 38.9 + - + +
948A LYS* 4.9 4.8 - - - +
88C SER* 2.9 16.6 + - - +
89C ALA 3.7 1.8 - - - +
91C ALA* 1.3 75.5 - - - +
93C LEU* 1.3 60.7 + - - +
95C GLU* 3.4 9.6 + - - +
96C LEU* 3.3 26.6 + - + +
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Residues in contact with LEU 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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914A GLY 4.9 0.7 - - - +
917A LEU* 3.8 6.1 - - + -
918A ARG* 3.5 39.5 - - + +
921A ILE* 3.7 22.2 - - + -
947A ASN* 3.4 21.5 - - - +
950A LEU* 3.4 33.4 - - + -
89C ALA 3.1 13.7 + - - +
90C ALA* 3.7 5.8 - - - +
91C ALA 3.2 0.2 - - - -
92C GLN* 1.3 72.5 - - - +
94C ASP* 1.3 62.6 + - - +
95C GLU 3.1 1.8 - - - -
96C LEU* 3.0 8.6 + - + +
97C MET* 2.9 37.3 + - + +
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Residues in contact with ASP 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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918A ARG* 3.2 44.5 + - - +
86C LYS* 2.9 36.5 + - - +
90C ALA* 3.0 17.3 + - - +
91C ALA 3.2 5.3 + - - +
93C LEU* 1.3 77.7 - - - +
95C GLU* 1.3 56.5 + - - +
97C MET* 3.5 7.2 + - - +
98C ALA* 3.1 28.1 + - - +
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Residues in contact with GLU 95 (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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91C ALA 3.1 12.4 + - - +
92C GLN* 3.4 12.8 - - - +
94C ASP* 1.3 78.4 - - - +
96C LEU* 1.3 63.1 + - + +
98C ALA* 3.6 15.7 + - - +
99C HIS* 3.6 8.7 + - - +
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Residues in contact with LEU 96 (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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947A ASN* 3.4 32.8 - - + +
950A LEU* 4.6 3.6 - - + -
951A ALA* 4.0 27.1 - - + +
954A ILE* 4.0 15.7 - - + +
92C GLN* 3.3 17.7 + - + +
93C LEU* 3.0 24.1 + - + +
95C GLU* 1.3 76.2 - - + +
97C MET* 1.3 61.7 + - - +
98C ALA 3.1 2.0 - - - -
99C HIS* 3.1 26.5 + - + +
100C LEU* 3.7 9.2 + - - +
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Residues in contact with MET 97 (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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911A LYS* 3.5 30.3 - - + +
914A GLY* 3.6 25.1 - - - +
915A LEU* 3.5 32.8 - - + -
918A ARG* 5.1 8.7 - - - -
950A LEU* 4.0 13.5 - - - -
93C LEU* 2.9 29.6 + - + +
94C ASP* 4.0 11.2 - - - +
96C LEU* 1.3 73.6 - - - +
98C ALA* 1.3 63.4 + - - +
99C HIS 3.3 0.2 - - - -
100C LEU* 3.3 18.0 + - + +
101C THR* 3.2 22.3 + - - -
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Residues in contact with ALA 98 (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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94C ASP 3.1 18.0 + - - +
95C GLU* 3.6 10.5 - - - +
96C LEU 3.1 0.2 - - - -
97C MET* 1.3 77.7 - - - +
99C HIS* 1.3 59.6 + - - +
100C LEU 3.1 3.1 + - - -
101C THR* 3.5 20.0 + - - +
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Residues in contact with HIS 99 (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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954A ILE* 5.5 7.6 - - + -
958A ARG* 3.2 24.3 + - - +
95C GLU 3.6 8.1 + - - +
96C LEU* 3.1 17.5 + - + +
98C ALA* 1.3 77.9 - - - +
100C LEU* 1.3 59.2 + - + +
101C THR 5.1 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
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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