Contacts of the helix formed by residues 120 - 134 (chain C) in PDB entry 2Y4T
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 LYS 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C LEU* 4.2 16.0 - - - +
115C LEU* 2.8 33.9 + - + +
118C GLN* 2.9 32.3 + - + +
119C GLY* 1.3 75.4 - - - +
121C LEU* 1.3 58.8 + - - +
123C GLU* 3.1 26.7 + - + +
124C ALA* 2.8 26.7 + - - +
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Residues in contact with LEU 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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116C LEU* 3.5 29.4 - - + -
119C GLY* 3.2 12.7 + - - +
120C LYS* 1.3 67.8 - - - +
122C ASP* 1.3 61.4 + - - +
124C ALA* 3.1 6.3 + - - +
125C GLU* 2.8 36.3 + - - +
151C SER* 4.0 6.3 - - - +
154C MET* 3.6 22.0 - - + +
155C GLN* 3.5 50.7 - - - +
158C ARG* 4.1 21.5 - - - +
180C ILE* 5.8 1.3 - - + -
184C CYS* 3.9 13.9 - - - -
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Residues in contact with ASP 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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120C LYS 3.5 0.6 - - - -
121C LEU* 1.3 78.3 - - - +
123C GLU* 1.3 71.1 + - - +
125C GLU* 3.7 10.9 + - - +
126C ASP* 3.2 29.1 + - - +
155C GLN* 2.9 28.7 + - - +
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Residues in contact with GLU 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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115C LEU* 3.7 30.3 - - + +
120C LYS* 3.1 34.8 + - + +
122C ASP* 1.3 81.6 + - - +
124C ALA* 1.3 64.2 - - - +
126C ASP* 3.6 10.0 + - - +
127C ASP* 3.6 17.0 + - - +
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Residues in contact with ALA 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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112C GLY* 3.7 11.4 - - - +
115C LEU* 3.7 10.0 - - + +
116C LEU* 3.6 36.1 - - + +
120C LYS 2.8 15.9 + - - +
121C LEU* 3.6 6.5 - - - +
123C GLU* 1.3 74.4 - - - +
125C GLU* 1.3 64.0 + - - +
127C ASP* 3.2 4.9 + - - +
128C PHE* 3.0 32.7 + - + -
151C SER* 5.1 1.6 - - - +
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Residues in contact with GLU 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 LEU 2.8 17.0 + - - +
122C ASP* 3.8 12.5 - - - +
124C ALA* 1.3 73.8 - - - +
126C ASP* 1.3 58.8 + - - +
128C PHE* 3.4 7.4 + - - +
129C LYS* 2.9 54.9 + - - +
148C LEU* 3.9 15.9 - - + -
151C SER* 3.2 25.9 + - - +
152C ASP* 3.6 18.6 - - - +
155C GLN* 2.8 27.7 - - - +
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Residues in contact with ASP 126 (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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122C ASP 3.2 18.1 + - - +
123C GLU* 3.7 9.8 - - - +
124C ALA 3.3 0.6 - - - -
125C GLU* 1.3 76.0 - - - +
127C ASP* 1.3 62.7 + - - +
129C LYS* 4.0 7.1 + - - +
130C LYS* 2.9 50.4 + - - +
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Residues in contact with ASP 127 (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 ARG* 3.5 37.1 + - + +
111C ARG* 2.7 49.5 + - - +
112C GLY* 4.1 6.3 - - - -
115C LEU* 3.3 16.6 - - - +
123C GLU 3.6 5.5 + - - +
124C ALA 3.2 9.0 + - - +
126C ASP* 1.3 80.6 - - - +
128C PHE* 1.3 57.8 + - - +
130C LYS* 3.4 5.7 + - - +
131C VAL* 2.9 34.9 + - - +
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Residues in contact with PHE 128 (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 LEU* 3.7 27.1 - - + -
112C GLY* 3.1 41.7 - - - -
113C HIS* 3.4 4.9 - - - -
116C LEU* 4.1 10.5 - - + -
124C ALA* 3.0 32.7 + - + +
125C GLU* 3.8 6.3 - - - +
127C ASP* 1.3 76.3 - - - +
129C LYS* 1.3 57.6 + - - +
131C VAL* 3.3 8.4 - - - +
132C LEU* 3.2 29.8 + - - +
144C ALA* 4.0 20.1 - - - +
147C GLN* 3.6 38.1 - - + -
148C LEU* 3.9 24.9 - - + -
151C SER* 5.5 3.4 - - - -
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Residues in contact with LYS 129 (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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125C GLU* 2.9 40.2 + - - +
126C ASP* 4.0 7.2 + - - +
128C PHE* 1.3 75.6 - - - +
130C LYS* 1.3 59.3 + - - +
132C LEU* 3.1 8.9 + - + +
133C LYS* 3.0 44.1 + - - +
148C LEU* 3.8 33.4 - - + +
152C ASP* 5.7 1.4 + - - -
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Residues in contact with LYS 130 (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 ARG* 4.2 33.1 - - - +
126C ASP* 2.9 34.5 + - - +
127C ASP* 3.9 5.5 + - - +
129C LYS* 1.3 71.5 - - - +
131C VAL* 1.3 65.3 + - - +
133C LYS* 3.9 27.1 - - + +
134C SER* 3.2 24.9 + - - -
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Residues in contact with VAL 131 (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 THR* 4.0 17.5 - - - +
108C ARG* 3.9 13.0 - - + +
109C LEU* 3.7 36.1 - - + +
127C ASP 2.9 18.9 + - - +
128C PHE* 3.3 11.0 - - - +
129C LYS 3.2 0.2 - - - -
130C LYS* 1.3 77.7 - - - +
132C LEU* 1.3 57.8 + - + +
134C SER* 2.9 24.0 - - - +
136C PRO* 3.6 15.5 - - + +
140C GLU* 4.4 13.2 - - + +
144C ALA* 3.9 24.2 - - + -
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Residues in contact with LEU 132 (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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128C PHE 3.2 10.0 + - - +
129C LYS* 3.1 11.9 + - + +
131C VAL* 1.3 75.6 - - + +
133C LYS* 1.3 60.7 + - - +
134C SER 3.0 9.9 - - - +
136C PRO* 4.2 13.8 - - + +
141C GLU* 4.2 11.2 - - + -
144C ALA* 4.1 15.0 - - + -
145C GLN* 3.8 41.1 - - + +
148C LEU* 3.8 27.6 - - + -
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Residues in contact with LYS 133 (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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129C LYS* 3.0 35.7 + - - +
130C LYS* 3.9 24.8 - - + +
131C VAL 3.5 0.2 - - - -
132C LEU* 1.3 73.3 - - + +
134C SER* 1.3 63.9 + - - +
135C ASN* 3.9 2.8 + - - +
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Residues in contact with SER 134 (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 THR* 3.4 28.4 - - - +
130C LYS 3.2 14.7 + - - -
131C VAL 2.9 19.7 - - - +
132C LEU 3.0 6.6 - - - +
133C LYS* 1.3 78.6 - - - +
135C ASN* 1.3 65.0 + - - +
136C PRO* 2.9 9.7 - - - +
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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