Contacts of the helix formed by residues 96 - 106 (chain C) in PDB entry 1TAD
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 ARG 96 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C TYR* 3.5 19.7 - - + -
93C ASP* 2.9 33.8 + - + +
95C ALA* 1.3 95.0 - - - +
97C GLN* 1.3 56.6 + - - +
99C ASP* 2.8 34.1 + - - +
100C ALA* 2.8 30.7 + - - +
125C ARG* 3.5 49.8 - - - +
126C LEU* 3.6 10.6 - - + +
129C ASP* 3.2 30.3 - - - +
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Residues in contact with GLN 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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91C TYR* 3.8 30.2 - - + -
94C SER* 3.0 19.2 + - - +
96C ARG* 1.3 79.1 - - - +
98C ASP* 1.3 61.5 + - - +
100C ALA* 3.4 3.0 + - + +
101C ARG* 3.1 22.9 + - + +
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Residues in contact with ASP 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 SER 4.1 0.8 + - - +
95C ALA* 3.2 13.1 + - - +
96C ARG 3.2 0.2 - - - -
97C GLN* 1.3 75.5 - - - +
99C ASP* 1.3 66.2 + - - +
101C ARG* 3.2 9.8 + - - +
102C LYS* 3.0 50.8 + - - +
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Residues in contact with ASP 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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95C ALA 3.9 6.0 - - - +
96C ARG* 2.8 46.1 + - - +
98C ASP* 1.3 78.8 - - - +
100C ALA* 1.3 57.6 + - - +
102C LYS* 3.0 26.3 + - - +
103C LEU* 2.8 30.5 + - - +
122C ILE* 3.5 17.5 - - + +
125C ARG* 2.8 35.1 + - - +
126C LEU* 4.3 6.3 - - + -
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Residues in contact with ALA 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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81C VAL* 3.9 14.3 - - + +
91C TYR* 3.1 30.1 - - + +
96C ARG 2.8 17.7 + - - +
97C GLN* 3.5 6.7 - - + +
99C ASP* 1.3 72.6 - - - +
101C ARG* 1.3 62.6 + - - +
103C LEU* 3.2 4.5 + - - +
104C MET* 3.0 28.0 + - - +
126C LEU* 4.1 16.7 - - + +
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Residues in contact with ARG 101 (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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97C GLN* 3.1 11.5 + - + +
98C ASP* 3.2 12.1 + - - +
100C ALA* 1.3 80.2 - - - +
102C LYS* 1.3 61.8 + - - +
104C MET* 3.2 12.0 + - + +
105C HIS* 3.1 19.9 + - - +
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Residues in contact with LYS 102 (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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98C ASP* 3.0 39.6 + - - +
99C ASP* 3.0 43.3 + - - +
101C ARG* 1.3 72.8 - - - +
103C LEU* 1.3 62.3 + - - +
105C HIS* 3.4 7.4 + - - +
106C MET* 3.0 34.2 + - + +
118C GLU* 6.0 2.9 - - - +
122C ILE* 3.5 20.6 - - + -
125C ARG* 4.3 5.0 - - - +
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Residues in contact with LEU 103 (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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74C LEU* 4.6 2.5 - - + -
77C ILE* 4.0 25.1 - - + -
78C LEU* 4.1 15.5 - - + -
81C VAL* 4.5 7.0 - - + -
99C ASP 2.8 13.2 + - - +
100C ALA* 3.3 9.4 - - - +
101C ARG 3.2 0.2 - - - -
102C LYS* 1.3 76.4 - - - +
104C MET* 1.3 58.2 + - + +
106C MET* 3.3 6.1 + - - +
107C ALA* 2.9 29.0 + - - +
119C MET* 3.7 35.4 - - + +
122C ILE* 3.8 15.0 - - + -
123C ILE* 3.8 14.8 - - + -
126C LEU* 3.7 24.2 - - + -
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Residues in contact with MET 104 (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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78C LEU* 3.9 22.4 - - - +
81C VAL* 4.4 20.4 - - + -
82C ARG* 3.6 40.6 - - + +
100C ALA 3.0 22.6 + - - +
101C ARG* 3.2 12.8 + - + +
103C LEU* 1.3 77.8 - - - +
105C HIS* 1.3 59.9 + - - +
107C ALA* 3.3 15.8 - - - +
108C ASP* 3.1 15.7 - - - +
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Residues in contact with HIS 105 (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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101C ARG 3.1 11.7 + - - +
102C LYS* 3.9 8.7 - - - +
103C LEU 3.3 0.4 - - - -
104C MET* 1.3 73.2 - - - +
106C MET* 1.3 67.9 + - + +
108C ASP* 3.0 27.5 + - - +
109C THR* 2.8 36.2 + - + -
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Residues in contact with MET 106 (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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102C LYS* 3.0 28.7 + - + +
103C LEU* 3.3 6.5 + - - +
105C HIS* 1.3 77.9 - - + +
107C ALA* 1.3 54.0 + - - +
109C THR* 2.7 28.8 + - - -
110C ILE* 2.7 23.2 + - + +
116C PRO* 4.1 13.2 - - + -
118C GLU* 3.8 37.7 - - + +
119C MET* 3.7 47.6 - - + +
122C ILE* 4.2 13.0 - - - -
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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