Contacts of the helix formed by residues 102 - 116 (chain C) in PDB entry 1DT0
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 SER 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C ILE* 4.5 2.7 - - - -
97C ASN* 3.5 17.4 + - - +
100C PHE* 3.3 5.7 + - - +
101C GLY* 1.3 78.4 - - - +
103C PHE* 1.3 64.6 + - - +
104C ASP* 3.8 7.3 + - - +
105C LYS* 3.2 28.9 + - - +
106C PHE* 3.0 20.6 + - - +
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Residues in contact with PHE 103 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C GLY 3.3 23.3 - - - -
87C GLN* 3.5 35.9 - - + +
88C PRO* 3.1 31.6 - - + -
96C ILE* 4.2 13.2 - - + -
97C ASN* 3.9 14.8 + - - +
102C SER* 1.3 71.1 - - - +
104C ASP* 1.3 69.7 + - - +
106C PHE* 3.2 16.0 + + - +
107C LYS* 3.0 53.0 + - + +
178C TRP* 5.3 0.4 - + - -
183C TRP* 3.3 34.3 - + - -
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Residues in contact with ASP 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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87C GLN* 4.9 4.5 - - - +
102C SER* 3.3 7.7 + - - +
103C PHE* 1.3 83.7 - - - +
105C LYS* 1.3 59.5 - - + +
107C LYS* 3.4 26.7 + - - +
108C GLU* 3.1 32.6 + - - +
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Residues in contact with LYS 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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100C PHE* 3.5 24.2 - - - +
101C GLY* 5.3 1.1 - - - -
102C SER* 3.2 19.4 + - - +
103C PHE 3.2 0.6 - - - -
104C ASP* 1.3 76.7 - - + +
106C PHE* 1.3 62.9 + - - +
108C GLU* 3.5 33.3 - - - +
109C GLU* 3.2 30.5 + - - +
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Residues in contact with PHE 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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96C ILE* 3.7 17.5 - - + -
100C PHE* 3.6 37.2 - + + +
102C SER 3.0 13.4 + - - +
103C PHE* 3.4 20.6 - + - +
105C LYS* 1.3 76.5 - - - +
107C LYS* 1.3 61.1 + - + +
109C GLU* 3.2 2.4 + - - +
110C PHE* 2.8 49.5 + + + +
125C LEU* 3.5 42.2 - - + -
135C LEU* 4.1 11.4 - - + +
153C LEU* 4.4 1.8 - - + -
178C TRP* 3.6 23.6 - + - -
183C TRP* 3.9 20.6 - + - -
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Residues in contact with LYS 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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87C GLN* 5.9 0.4 + - - -
103C PHE* 3.0 37.3 + - + +
104C ASP* 3.6 30.8 + - - +
106C PHE* 1.3 88.2 - - + +
108C GLU* 1.3 53.1 + - - +
110C PHE* 3.8 0.2 - - - +
111C THR* 2.8 39.9 + - - -
178C TRP* 3.7 54.2 - - + +
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Residues in contact with GLU 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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104C ASP* 3.1 19.6 + - - +
105C LYS* 3.5 38.8 - - - +
107C LYS* 1.3 77.1 - - - +
109C GLU* 1.3 59.7 + - + +
111C THR* 3.4 5.3 + - - -
112C LYS* 2.9 34.4 + - + +
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Residues in contact with GLU 109 (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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100C PHE* 3.6 32.1 - - + +
105C LYS* 3.2 16.6 + - - +
106C PHE 3.9 2.0 - - - +
108C GLU* 1.3 81.1 - - + +
110C PHE* 1.3 61.3 + - - +
112C LYS* 3.8 7.9 - - + +
113C THR* 3.0 31.0 + - - -
135C LEU* 3.3 14.1 - - + +
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Residues in contact with PHE 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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106C PHE* 2.8 32.7 + + + +
107C LYS 3.8 3.1 - - - +
109C GLU* 1.3 70.2 - - - +
111C THR* 1.3 62.7 + - - +
113C THR* 3.3 5.0 + - - -
114C SER* 2.9 45.9 + - - -
123C GLY 3.7 18.6 - - - -
124C TRP* 3.6 24.9 - - - -
125C LEU* 3.7 8.3 - - + -
135C LEU* 3.6 28.4 - - + +
153C LEU* 4.1 17.9 - - + -
155C CYS* 3.8 12.1 - - + -
174C VAL* 4.9 1.8 - - + -
177C PHE* 3.7 20.4 - + - -
178C TRP* 3.4 23.3 - + + -
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Residues in contact with THR 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 LYS 2.8 22.2 + - - -
108C GLU* 3.6 6.1 - - - -
110C PHE* 1.3 77.0 - - - +
112C LYS* 1.3 74.5 + - - +
114C SER* 3.2 0.5 + - - -
115C VAL* 2.8 42.4 + - + +
171C PRO* 5.5 6.1 - - + +
174C VAL* 3.5 21.2 - - + +
175C GLU* 5.4 0.8 + - - +
178C TRP* 3.2 22.2 + - - -
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Residues in contact with LYS 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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108C GLU* 2.9 21.7 + - + +
109C GLU* 3.8 8.7 - - + +
110C PHE 3.3 0.2 - - - -
111C THR* 1.3 96.3 + - - +
113C THR* 1.3 57.4 + - - +
115C VAL* 4.6 14.0 - - - +
116C GLY* 2.9 27.9 + - - +
171C PRO* 6.1 1.8 - - - +
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Residues in contact with THR 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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109C GLU 3.0 20.5 + - - -
110C PHE* 3.6 8.1 - - + +
111C THR 3.2 0.2 - - - -
112C LYS* 1.3 76.5 - - - +
114C SER* 1.3 61.3 + - - +
116C GLY* 4.1 1.6 - - - -
117C THR* 3.1 21.5 + - - -
123C GLY* 4.5 4.7 - - - -
124C TRP 4.7 2.0 - - - +
135C LEU* 3.8 14.8 - - + +
136C ALA* 3.6 32.5 - - - +
137C SER* 3.7 17.0 - - - -
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Residues in contact with SER 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 PHE* 2.9 37.9 + - - -
111C THR* 3.6 5.4 - - - -
113C THR* 1.3 74.5 - - - +
115C VAL* 1.3 66.3 + - - +
117C THR* 3.0 25.3 + - - -
123C GLY* 3.5 18.7 - - - -
155C CYS* 4.0 5.1 - - - +
157C VAL* 3.8 21.9 - - - +
170C ARG* 3.7 5.4 + - - -
174C VAL* 4.4 13.0 - - - -
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Residues in contact with VAL 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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111C THR* 2.8 30.4 + - + +
112C LYS* 4.4 14.6 - - - +
114C SER* 1.3 74.0 - - - +
116C GLY* 1.3 58.6 + - - +
117C THR 3.3 0.7 + - - +
170C ARG* 3.2 30.1 + - + +
171C PRO* 4.0 42.8 - - + -
174C VAL* 4.0 14.6 - - + -
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Residues in contact with GLY 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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112C LYS 2.9 20.3 + - - -
113C THR 3.8 3.3 + - - -
114C SER 3.1 0.4 - - - -
115C VAL* 1.3 77.8 - - - +
117C THR* 1.3 60.6 + - - +
118C PHE* 3.3 5.9 + - - +
137C SER* 5.3 0.2 - - - -
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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