Contacts of the helix formed by residues 89 - 100 (chain C) in PDB entry 3THT
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
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Residue Dist Surf HB Arom Phob DC
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43C GLN* 3.9 6.5 - - - +
87C TYR* 3.7 8.8 - - - +
88C ARG* 1.3 92.7 - - + +
90C THR* 1.3 63.1 + - - +
91C GLU* 3.1 9.2 + - - +
92C GLU* 3.0 42.1 + - - +
93C SER* 3.4 9.2 + - - -
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Residues in contact with THR 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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41C ALA* 3.6 33.1 + - - +
42C THR* 4.1 0.9 - - - -
43C GLN* 3.9 31.2 - - + +
89C THR* 1.3 72.7 - - - +
91C GLU* 1.3 67.5 + - + +
93C SER* 3.6 3.3 - - - -
94C LYS* 3.3 20.4 + - - +
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Residues in contact with GLU 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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89C THR* 3.1 9.1 - - - +
90C THR* 1.3 84.2 - - + +
92C GLU* 1.3 66.2 + - + +
94C LYS* 3.1 48.8 + - - +
95C ARG* 3.1 23.3 + - - +
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Residues in contact with GLU 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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68C CYS* 3.9 19.2 - - - +
69C GLY* 3.5 4.7 - - - -
70C LEU* 3.2 26.4 + - - +
87C TYR* 4.0 12.1 - - + -
88C ARG* 3.5 17.4 + - - +
89C THR* 3.0 41.7 + - - +
91C GLU* 1.3 76.6 - - + +
93C SER* 1.3 62.8 + - - +
95C ARG* 3.0 31.9 + - - +
96C ALA* 3.1 8.3 + - - +
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Residues in contact with SER 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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42C THR 2.8 28.8 + - - -
43C GLN 3.5 16.9 + - - -
45C LEU* 3.5 21.1 - - - +
87C TYR* 3.7 14.0 - - - -
89C THR 3.4 8.0 + - - -
90C THR 3.6 5.8 - - - -
91C GLU 3.1 0.4 - - - -
92C GLU* 1.3 80.2 - - - +
94C LYS* 1.3 57.5 + - - +
96C ALA* 3.0 5.9 + - - +
97C TYR* 2.9 26.7 + - - +
119C PHE* 3.6 3.6 - - - -
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Residues in contact with LYS 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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41C ALA* 4.2 14.8 - - + -
90C THR 3.3 9.8 + - - +
91C GLU* 3.1 41.3 + - - +
93C SER* 1.3 79.9 - - - +
95C ARG* 1.3 60.9 + - - +
97C TYR* 3.4 1.4 + - + +
98C VAL* 3.1 37.2 + - + +
119C PHE* 3.7 24.7 - - + -
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Residues in contact with ARG 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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67C LYS 5.3 0.9 - - - -
68C CYS* 3.3 33.0 + - + +
91C GLU* 3.1 18.6 + - - +
92C GLU* 3.0 27.3 + - - +
94C LYS* 1.3 79.2 - - - +
96C ALA* 1.3 53.0 + - - +
98C VAL* 3.1 10.0 - - + +
99C THR* 2.6 50.5 + - + +
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Residues in contact with ALA 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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45C LEU* 4.4 1.3 - - + -
68C CYS* 3.6 14.8 - - - -
87C TYR* 3.7 31.0 - - + +
92C GLU 3.1 5.7 + - - +
93C SER 3.0 9.1 + - - +
95C ARG* 1.3 78.0 - - - +
97C TYR* 1.3 62.5 + - - +
100C LEU* 2.8 45.3 + - + +
101C ASN 3.7 0.9 + - - -
117C LEU* 4.1 10.3 - - + +
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Residues in contact with TYR 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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45C LEU* 4.3 7.5 - - + +
93C SER 2.9 8.6 + - - +
94C LYS* 3.5 5.2 - - + +
95C ARG 3.3 0.2 - - - -
96C ALA* 1.3 77.0 - - - +
98C VAL* 1.3 72.6 + - + +
101C ASN* 3.0 41.8 - - - +
117C LEU* 3.3 34.5 - - + -
118C ASN* 4.2 18.7 + - - -
119C PHE* 3.5 48.0 - + + -
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Residues in contact with VAL 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 LYS* 3.1 27.3 + - + +
95C ARG* 3.1 15.3 - - + +
97C TYR* 1.3 94.0 - - + +
99C THR* 1.3 67.2 + - + +
101C ASN* 4.7 3.6 - - - +
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Residues in contact with THR 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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67C LYS* 5.4 5.8 - - - -
68C CYS* 3.2 22.3 - - - -
95C ARG* 2.6 34.5 + - + +
98C VAL* 1.3 90.7 - - + +
100C LEU* 1.3 69.7 + - - +
101C ASN 3.4 5.0 - - - +
103C LYS* 4.9 4.0 + - - +
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Residues in contact with LEU 100 (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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64C VAL* 3.7 44.0 - - + +
65C LEU* 4.1 23.1 - - + -
67C LYS* 4.4 7.9 - - - +
68C CYS* 3.7 22.9 - - - -
96C ALA* 2.8 29.4 + - + +
99C THR* 1.3 76.0 - - - +
101C ASN* 1.3 65.9 + - - +
102C GLY 2.9 0.9 + - - -
103C LYS* 2.8 38.1 + - + +
115C LEU* 4.0 7.5 - - + +
117C LEU* 3.9 17.8 - - + +
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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