Contacts of the helix formed by residues 108 - 125 (chain C) in PDB entry 5DQZ
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 ASP 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C LYS* 3.4 7.2 + - + +
105C LEU 3.4 0.9 - - - +
106C ALA 4.6 0.2 - - - -
107C LEU* 1.3 78.6 - - - +
109C GLU* 1.3 58.6 + - - +
110C ASP* 3.5 21.7 + - - +
111C LEU* 3.3 36.1 + - + +
112C ARG* 2.7 36.0 + - - +
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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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106C ALA 5.4 0.9 - - - +
107C LEU 3.6 8.5 + - - +
108C ASP* 1.3 76.1 + - - +
110C ASP* 1.3 64.8 + - - +
112C ARG* 3.3 36.6 + - - +
113C LEU* 2.9 29.1 + - - +
134C VAL* 5.1 4.2 - - - +
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Residues in contact with ASP 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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108C ASP* 3.3 14.6 - - - +
109C GLU* 1.3 80.1 - - - +
111C LEU* 1.3 62.1 + - + +
113C LEU* 3.3 9.6 + - - +
114C LYS* 3.0 42.4 + - - +
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Residues in contact with LEU 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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104C LYS* 3.9 26.7 - - + +
105C LEU* 3.8 22.4 - - + +
108C ASP* 3.3 35.1 + - + +
110C ASP* 1.3 76.9 - - + +
112C ARG* 1.3 65.0 - - - +
114C LYS* 3.0 17.2 + - + +
115C VAL* 3.0 27.0 + - - +
275C GLY* 3.4 25.7 - - - +
277C ILE* 4.3 18.4 - - + -
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Residues in contact with ARG 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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105C LEU 3.2 12.4 + - - +
106C ALA 4.0 13.9 - - - +
108C ASP 2.7 22.1 + - - +
109C GLU* 3.3 36.2 + - - +
111C LEU* 1.3 72.2 - - - +
113C LEU* 1.3 57.0 + - - +
115C VAL* 3.2 3.8 + - - +
116C VAL* 2.9 36.4 + - + +
134C VAL* 3.9 28.7 - - + +
138C ARG* 4.4 9.7 - - - +
205C GLY 5.2 0.4 + - - -
206C PHE* 3.1 48.7 + - + +
209C THR* 4.1 17.7 + - - +
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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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109C GLU 2.9 18.8 + - - +
110C ASP* 3.4 9.2 - - - +
111C LEU 3.2 0.2 - - - -
112C ARG* 1.3 73.8 - - - +
114C LYS* 1.3 59.5 + - + +
116C VAL* 4.4 2.5 - - + -
117C ARG* 2.9 47.0 + - + +
132C ARG 3.5 26.7 - - - +
133C SER* 5.0 2.5 - - - -
134C VAL* 3.9 26.7 - - + +
137C LEU* 4.1 17.3 - - + -
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Residues in contact with LYS 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 ASP* 3.0 28.7 + - - +
111C LEU* 3.0 17.4 + - + +
113C LEU* 1.3 75.4 - - + +
115C VAL* 1.3 63.6 + - - +
117C ARG* 3.3 11.5 + - - +
118C LYS* 3.0 23.0 + - - +
274C ALA* 3.6 19.4 - - - +
275C GLY* 3.8 21.1 - - - +
276C GLU* 3.8 21.8 + - - +
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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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105C LEU* 4.2 21.1 - - + -
111C LEU 3.0 17.0 + - - +
112C ARG 3.5 7.0 - - - +
114C LYS* 1.3 75.5 - - - +
116C VAL* 1.3 58.3 + - - +
118C LYS* 3.1 5.6 + - - +
119C MET* 2.9 51.6 + - + +
206C PHE* 3.9 29.8 - - + -
271C VAL* 3.7 28.4 - - + +
272C LEU* 4.3 7.9 - - + +
274C ALA* 4.6 0.9 - - - -
275C GLY 4.3 3.8 - - - +
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Residues in contact with VAL 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 ARG* 2.9 24.1 + - + +
113C LEU* 3.8 6.1 - - - +
115C VAL* 1.3 74.2 - - - +
117C ARG* 1.3 58.8 + - - +
119C MET* 3.1 10.6 + - - +
120C PHE* 2.9 27.1 + - + +
134C VAL* 4.2 21.1 - - + -
137C LEU* 3.8 25.6 - - + -
206C PHE* 3.9 32.8 - - + +
207C VAL* 3.9 20.9 - - + -
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Residues in contact with ARG 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* 2.9 39.4 + - + +
114C LYS* 3.5 8.5 - - - +
116C VAL* 1.3 75.5 - - - +
118C LYS* 1.3 58.7 + - - +
120C PHE* 3.2 8.9 + - - +
121C GLU* 3.0 27.4 + - - +
127C PRO* 5.0 5.1 - - - +
128C ALA* 2.9 39.1 + - + +
129C PRO 3.1 23.4 + - - -
130C ALA* 4.5 7.9 - - - +
131C ARG 4.6 5.0 - - - +
132C ARG* 4.7 10.1 + - - +
137C LEU* 4.2 14.9 - - + +
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Residues in contact with LYS 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 LYS 3.0 7.0 + - - +
115C VAL 3.4 7.0 - - - +
117C ARG* 1.3 73.9 - - - +
119C MET* 1.3 65.6 + - - +
121C GLU* 2.9 32.6 + - - +
122C LEU* 2.9 44.1 + - + +
270C ASP* 3.6 33.0 + - - +
271C VAL* 4.2 11.4 - - - +
274C ALA* 3.3 33.2 - - + -
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Residues in contact with MET 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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115C VAL* 2.9 37.8 + - + +
116C VAL* 3.3 10.5 - - - +
118C LYS* 1.3 75.5 - - - +
120C PHE* 1.3 57.5 + - - +
122C LEU* 3.4 4.6 + - - +
123C ARG* 2.9 31.9 + - - +
206C PHE* 3.7 22.0 - - + -
207C VAL* 3.9 26.5 - - + -
215C PHE* 4.2 5.2 - - + -
218C ASP* 3.7 26.9 - - + +
219C ILE* 5.0 1.8 - - + -
222C ILE* 3.9 25.6 - - + +
271C VAL* 3.7 21.3 - - + -
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Residues in contact with PHE 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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116C VAL* 2.9 13.2 + - + +
117C ARG* 3.4 10.1 - - - +
118C LYS 3.2 0.4 - - - -
119C MET* 1.3 77.4 - - - +
121C GLU* 1.3 57.1 + - - +
123C ARG* 3.3 1.7 + - - +
124C PHE* 2.9 67.5 + + + +
126C GLU* 3.7 9.6 - - + -
127C PRO 4.2 2.2 - - - -
128C ALA* 3.4 45.5 - - + -
129C PRO* 4.7 3.8 - - + -
137C LEU* 4.5 22.0 - - + -
140C ILE* 3.9 34.5 - - + -
141C GLU* 4.8 1.6 - - + -
144C ARG* 4.2 16.2 - - - -
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Residues in contact with GLU 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 ARG 3.0 13.1 + - - +
118C LYS* 2.9 42.5 + - - +
120C PHE* 1.3 78.6 - - - +
122C LEU* 1.3 59.9 + - + +
125C GLY* 3.0 29.3 + - - -
126C GLU* 3.4 25.8 - - - +
127C PRO* 4.4 19.9 - - + +
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Residues in contact with LEU 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 LYS* 2.9 43.7 + - + +
119C MET* 3.8 3.8 - - - +
121C GLU* 1.3 79.4 - - + +
123C ARG* 1.3 64.0 + - - +
125C GLY* 4.4 2.4 + - - -
222C ILE* 4.1 15.9 - - + +
226C ASP* 5.0 4.0 - - - +
267C LEU* 4.3 19.1 - - + +
270C ASP* 4.1 16.8 - - - +
271C VAL* 3.7 31.0 - - + +
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Residues in contact with ARG 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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119C MET 2.9 19.3 + - - +
120C PHE* 3.8 3.6 - - - +
121C GLU 3.3 0.2 - - - -
122C LEU* 1.3 80.5 - - - +
124C PHE* 1.3 87.5 + - + +
141C GLU* 2.5 37.3 + - - -
145C VAL* 3.2 28.6 - - - +
221C ASP* 3.1 41.3 + - - +
222C ILE* 3.8 27.0 - - + +
224C LYS* 5.2 0.2 - - - +
225C PHE* 3.4 23.4 - - - -
226C ASP* 4.7 10.6 - - - +
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Residues in contact with PHE 124 (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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120C PHE* 2.9 65.4 + + + +
123C ARG* 1.3 113.2 - - + +
125C GLY* 1.3 60.9 + - - +
126C GLU* 3.5 4.7 - - + +
141C GLU* 4.0 28.7 - - + -
144C ARG* 3.5 55.5 + - + +
145C VAL* 5.2 1.3 - - + -
148C THR* 5.7 2.5 - - - -
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Residues in contact with GLY 125 (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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121C GLU* 3.0 13.8 + - - -
122C LEU 4.4 1.7 + - - -
123C ARG 3.7 1.2 - - - -
124C PHE* 1.3 78.4 - - - +
126C GLU* 1.3 65.1 + - - +
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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