Contacts of the helix formed by residues 106 - 123 (chain C) in PDB entry 2NS7
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 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C ASP* 5.6 0.7 - - - +
57C ILE* 4.0 26.3 - - + +
104C ARG* 4.0 10.5 - - + +
105C PRO* 1.3 74.2 - - - +
107C GLU* 1.3 60.7 + - - +
108C LYS* 4.0 16.3 + - + +
109C GLN* 2.9 29.5 + - - +
110C TYR* 3.0 32.5 + - - -
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Residues in contact with GLU 107 (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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106C THR* 1.3 73.7 - - - +
108C LYS* 1.3 70.6 + - + +
110C TYR* 3.9 11.7 - - + +
111C GLU* 3.1 30.2 + - - +
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Residues in contact with LYS 108 (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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57C ILE* 4.9 9.5 - - + +
61C ASP* 3.7 27.6 + - - +
106C THR* 3.3 15.0 - - - +
107C GLU* 1.3 82.0 - - + +
109C GLN* 1.3 63.9 + - + +
111C GLU* 3.2 9.4 + - - +
112C THR* 3.0 27.3 + - - +
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Residues in contact with GLN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ILE* 4.7 14.1 - - - +
60C LEU* 3.2 32.6 - - + +
100C HIS* 5.7 0.8 + - - -
103C THR* 5.1 10.3 - - - +
104C ARG 3.6 4.5 - - - +
105C PRO* 3.2 16.3 - - + +
106C THR* 2.9 42.3 + - - +
107C GLU 3.3 0.2 - - - -
108C LYS* 1.3 83.9 - - + +
110C TYR* 1.3 61.9 + - - +
112C THR* 3.4 9.9 + - - -
113C LEU* 3.2 28.9 + - + +
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Residues in contact with TYR 110 (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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105C PRO* 3.4 48.2 + - + +
106C THR 3.0 22.7 + - - +
107C GLU* 3.9 10.8 - - + +
108C LYS 3.3 0.4 - - - -
109C GLN* 1.3 74.4 - - - +
111C GLU* 1.3 65.3 + - - +
113C LEU* 3.1 26.8 + - + +
114C GLU* 3.3 15.6 + - - +
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Residues in contact with GLU 111 (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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107C GLU* 3.1 22.6 + - - +
108C LYS* 3.5 7.0 - - - +
110C TYR* 1.3 74.5 - - - +
112C THR* 1.3 56.9 + - - +
114C GLU* 3.7 4.7 + - - +
115C ASN* 3.1 30.8 + - - +
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Residues in contact with THR 112 (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 PHE* 3.3 51.9 - - + +
68C SER* 5.5 0.4 - - - -
108C LYS 3.0 15.4 + - - -
109C GLN* 3.5 12.3 - - - -
110C TYR 3.1 0.2 - - - -
111C GLU* 1.3 78.4 - - - +
113C LEU* 1.3 57.6 + - + +
115C ASN* 3.4 7.8 - - + +
116C GLN* 2.8 37.8 + - - +
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Residues in contact with LEU 113 (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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105C PRO* 6.1 2.5 - - + -
109C GLN* 3.2 21.0 + - + +
110C TYR* 3.1 23.5 + - + +
112C THR* 1.3 74.4 - - - +
114C GLU* 1.3 60.7 + - - +
115C ASN 3.2 0.2 - - - -
116C GLN* 3.6 17.9 - - - +
117C LEU* 2.8 42.9 + - + +
131C LEU* 5.3 10.5 - - + -
134C LEU* 4.6 17.3 - - + -
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Residues in contact with GLU 114 (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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110C TYR 3.3 11.2 + - - +
111C GLU* 4.2 6.5 - - - +
113C LEU* 1.3 76.6 - - - +
115C ASN* 1.3 53.0 + - - +
117C LEU* 3.3 21.1 + - + +
118C ALA* 2.8 36.0 + - - +
127C LEU* 5.8 2.8 - - - +
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Residues in contact with ASN 115 (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 SER* 4.2 22.7 - - - -
69C PRO* 4.6 7.5 - - - +
111C GLU* 3.1 22.2 + - - +
112C THR* 3.4 10.8 - - + +
114C GLU* 1.3 76.2 - - - +
116C GLN* 1.3 63.2 + - - +
118C ALA* 3.0 17.3 + - - +
119C PHE* 3.1 14.9 + - - +
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Residues in contact with GLN 116 (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 HIS* 5.0 1.0 + - - -
67C PHE* 2.8 35.0 + - - +
68C SER* 5.1 1.6 - - - -
69C PRO* 5.8 1.1 - - - -
78C PHE* 3.7 17.8 - - + -
82C ASN* 3.8 17.2 + - - +
112C THR* 2.8 34.6 + - - +
113C LEU* 3.6 26.7 - - - +
115C ASN* 1.3 74.1 - - + +
117C LEU* 1.3 62.0 + - - +
119C PHE* 3.6 6.0 + - - +
120C LEU* 3.2 29.1 + - - +
134C LEU* 3.8 26.0 - - + +
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Residues in contact with LEU 117 (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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113C LEU* 2.8 38.3 + - + +
114C GLU* 3.4 26.0 - - + +
115C ASN 3.2 0.2 - - - -
116C GLN* 1.3 72.7 - - - +
118C ALA* 1.3 55.8 + - - +
120C LEU* 3.6 1.6 + - - +
121C THR* 2.5 35.3 + - - +
127C LEU* 3.9 22.4 - - + +
130C ALA* 3.8 14.9 - - + +
131C LEU* 3.8 46.4 - - + +
134C LEU* 4.3 6.9 - - + +
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Residues in contact with ALA 118 (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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114C GLU 2.8 19.6 + - - +
115C ASN* 3.0 8.9 + - - +
117C LEU* 1.3 74.4 - - - +
119C PHE* 1.3 61.4 + - - +
121C THR* 3.2 9.4 + - - -
122C GLN* 3.1 23.9 + - - +
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Residues in contact with PHE 119 (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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69C PRO* 3.5 44.4 - - + -
70C LEU 5.8 0.4 - - - -
73C GLU 3.5 25.1 - - - -
74C SER 4.2 1.3 - - - -
75C TRP* 3.8 22.2 - - + -
78C PHE* 3.7 32.3 - + + -
115C ASN* 3.1 15.3 + - - +
116C GLN* 4.0 2.9 - - - +
118C ALA* 1.3 75.4 - - - +
120C LEU* 1.3 68.1 + - + +
122C GLN* 3.2 23.8 - - - +
123C GLN* 2.9 48.7 + - - +
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Residues in contact with LEU 120 (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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75C TRP* 3.8 27.6 - - + -
78C PHE* 5.1 1.3 - - + -
79C LEU* 3.8 21.1 - - + -
116C GLN 3.2 15.9 + - - +
119C PHE* 1.3 85.9 - - + +
121C THR* 1.3 60.3 - - - +
123C GLN* 3.3 6.4 + - - -
125C PHE* 3.1 49.2 + - + +
130C ALA* 3.6 40.2 - - + +
133C ALA* 5.0 6.1 - - + -
134C LEU* 3.8 24.2 - - + -
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Residues in contact with THR 121 (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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117C LEU* 2.5 23.5 + - - +
118C ALA* 3.2 11.1 + - - -
120C LEU* 1.3 73.8 - - - +
122C GLN* 1.3 64.8 + - - +
123C GLN 3.1 1.8 - - - -
124C GLY* 3.0 13.2 + - - -
125C PHE* 3.8 19.9 + - - +
127C LEU* 5.3 13.0 - - - +
130C ALA* 4.8 5.2 - - - +
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Residues in contact with GLN 122 (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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118C ALA 3.1 14.3 + - - +
119C PHE* 3.2 29.9 + - - +
121C THR* 1.3 75.9 - - - +
123C GLN* 1.3 77.5 + - - +
124C GLY* 3.3 3.8 + - - -
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Residues in contact with GLN 123 (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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73C GLU 5.7 0.9 - - - -
74C SER* 6.0 0.7 - - - -
75C TRP* 3.5 45.9 + - + +
119C PHE* 2.9 48.6 + - + +
120C LEU* 3.8 7.2 - - - +
121C THR 3.1 1.2 - - - -
122C GLN* 1.3 94.9 - - - +
124C GLY* 1.3 59.2 + - - +
125C PHE* 3.5 3.5 + - + -
201C LEU* 4.6 10.4 - - - +
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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